Contacts of the helix formed by residues 124 - 154 (chain A) in PDB entry 2PFV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 124 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLU* 3.2 27.2 + - + +
123A GLU* 1.3 76.1 - - - +
125A SER* 1.3 65.2 + - - +
126A GLU* 3.2 22.4 + - - +
127A PHE* 2.9 33.6 + - - +
128A HIS* 3.0 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ASN* 1.3 73.7 - - - +
126A GLU* 1.3 57.3 + - - +
128A HIS* 3.9 10.1 + - - +
129A GLY* 2.7 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 3.3 45.3 + - + +
75A LYS* 4.7 10.7 + - - +
124A ASN* 3.1 20.4 + - + +
125A SER* 1.3 84.1 + - - +
127A PHE* 1.3 60.9 + - - +
129A GLY* 3.9 1.0 - - - -
130A ILE 3.3 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 4.3 11.0 - - + -
114A ILE* 3.3 33.4 - - + -
115A GLN* 4.7 4.9 - - - -
121A ARG* 3.7 33.4 - - + -
122A GLU 3.4 28.5 - - - +
123A GLU* 4.2 18.6 - - - -
124A ASN* 2.9 12.4 + - - +
126A GLU* 1.3 74.0 - - - +
128A HIS* 1.3 79.0 + + - +
130A ILE* 3.1 15.5 - - + +
131A LEU* 3.0 57.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLU* 2.7 48.4 + - + -
124A ASN 3.0 24.2 + - - +
125A SER* 3.9 7.3 + - - +
127A PHE* 1.3 87.1 - + - +
129A GLY* 1.3 63.0 + - - +
131A LEU* 3.3 13.4 + - + +
132A THR* 3.1 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A SER 2.7 21.8 + - - -
126A GLU* 3.9 1.8 - - - -
128A HIS* 1.3 75.1 - - - +
130A ILE* 1.3 55.8 + - - +
132A THR* 3.4 4.8 + - - -
133A HIS* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 4.1 14.6 - - + +
77A LEU* 3.4 38.4 - - + +
78A ALA* 3.4 24.2 - - + +
81A ALA* 5.1 0.7 - - + -
110A MET* 4.6 1.3 - - - -
114A ILE* 3.9 19.1 - - + -
126A GLU 3.3 11.4 + - - +
127A PHE* 3.1 24.0 - - + +
129A GLY* 1.3 71.9 - - - +
131A LEU* 1.3 63.4 + - - +
133A HIS* 4.2 7.0 - - + +
134A LEU* 2.9 53.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 3.7 13.6 - - + +
114A ILE* 3.9 15.5 - - + -
115A GLN* 3.6 34.1 - - + +
123A GLU* 5.6 0.4 - - - +
127A PHE* 3.0 52.8 + - + +
128A HIS* 3.6 15.9 - - + +
129A GLY 3.3 0.2 - - - -
130A ILE* 1.3 78.4 - - - +
132A THR* 1.3 58.2 + - - +
134A LEU* 3.5 1.6 + - - +
135A GLU* 3.0 45.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A HIS* 3.1 16.8 + - - +
129A GLY* 3.9 4.3 - - - -
131A LEU* 1.3 74.6 - - - +
133A HIS* 1.3 61.7 + - - +
135A GLU* 3.7 12.8 + - - +
136A GLN* 2.8 53.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ALA* 5.3 3.2 + - - +
81A ALA* 4.3 23.9 - - + +
82A SER* 4.2 17.7 - - - -
85A GLU* 3.3 37.0 + - - -
129A GLY 3.0 17.6 + - - +
130A ILE* 3.7 10.0 - - - +
131A LEU 3.3 0.2 - - - -
132A THR* 1.3 78.8 - - - +
134A LEU* 1.3 64.8 + - + +
136A GLN* 3.9 2.4 - - + +
137A LEU* 2.9 31.1 + - + +
140A ARG* 4.7 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ALA* 3.6 31.9 - - + -
107A LEU* 4.1 24.0 - - + +
110A MET* 4.0 17.9 - - + -
111A LEU* 4.0 26.0 - - + -
114A ILE* 3.9 26.0 - - + -
130A ILE* 2.9 29.0 + - + +
131A LEU 3.9 2.7 - - - +
133A HIS* 1.3 80.5 - - + +
135A GLU* 1.3 64.2 + - - +
137A LEU* 3.8 4.7 - - + +
138A ILE* 3.0 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 3.7 23.1 - - + +
115A GLN* 3.7 20.3 + - - +
131A LEU* 3.0 37.6 + - - +
132A THR* 3.7 14.5 + - - +
134A LEU* 1.3 77.3 - - - +
136A GLN* 1.3 64.4 + - + +
138A ILE* 3.7 4.7 - - - +
139A LYS* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A THR* 2.8 39.9 + - + +
133A HIS* 4.1 3.1 - - - +
135A GLU* 1.3 76.9 - - + +
137A LEU* 1.3 59.9 + - - +
139A LYS* 3.1 28.2 + - - +
140A ARG* 2.8 57.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ALA* 4.2 8.3 - - + +
85A GLU* 3.7 40.8 - - + +
88A LEU* 4.3 9.4 - - + -
89A GLN* 6.2 0.7 - - + -
107A LEU* 3.8 31.0 - - + -
133A HIS* 2.9 31.4 + - + +
134A LEU* 3.8 4.9 - - - +
136A GLN* 1.3 75.3 - - - +
138A ILE* 1.3 58.7 + - - +
140A ARG* 3.4 27.9 + - + +
141A SER* 2.7 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A VAL* 4.0 14.8 - - + +
107A LEU* 3.7 24.5 - - + +
108A ASP* 3.5 46.9 - - - +
111A LEU* 4.2 11.2 - - + -
134A LEU 3.0 25.6 + - - +
135A GLU* 3.7 4.5 - - - +
137A LEU* 1.3 75.4 - - - +
139A LYS* 1.3 60.0 + - - +
141A SER* 3.2 6.2 + - - -
142A GLU* 2.9 58.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLU 3.0 15.3 + - - +
136A GLN* 3.4 30.1 + - - +
138A ILE* 1.3 79.6 - - - +
140A ARG* 1.3 63.7 + - + +
142A GLU* 3.4 9.3 + - - +
143A ALA* 3.0 23.5 + - + +
146A ARG* 4.9 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLU* 3.3 24.9 + - - -
133A HIS* 4.7 6.5 - - - -
136A GLN* 2.8 51.6 + - - +
137A LEU* 3.8 28.0 - - + +
139A LYS* 1.3 73.3 - - + +
141A SER* 1.3 62.9 + - - +
143A ALA* 3.2 8.8 + - - +
144A GLN* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 3.5 21.9 - - - +
100A TYR* 3.6 20.5 + - - -
104A VAL* 3.8 24.5 - - - -
137A LEU* 2.7 26.0 + - - +
138A ILE* 3.6 5.1 - - - -
140A ARG* 1.3 74.1 - - - +
142A GLU* 1.3 65.9 + - - +
144A GLN* 3.1 5.9 + - - +
145A LEU* 3.1 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A VAL* 4.5 2.9 - - + -
108A ASP* 5.2 1.7 - - - +
138A ILE* 2.9 36.1 + - + +
139A LYS* 3.9 8.2 - - - +
141A SER* 1.3 73.8 - - - +
143A ALA* 1.3 65.4 + - - +
145A LEU* 3.1 19.5 + - + +
146A ARG* 3.2 26.1 + - - +
188A TYR* 2.7 41.2 + - + +
189A PHE* 3.5 14.2 - - + -
192A ASN* 4.0 11.7 + - - +
194A GLU* 4.0 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LYS* 3.0 15.2 + - + +
140A ARG* 3.5 11.2 - - - +
141A SER 3.2 0.2 - - - -
142A GLU* 1.3 78.7 - - - +
144A GLN* 1.3 62.4 + - - +
146A ARG* 3.2 20.7 + - - +
147A VAL* 3.1 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLY* 6.2 2.7 - - - -
92A ILE* 3.7 20.3 + - + +
100A TYR* 3.7 17.0 - - + +
140A ARG 3.0 12.6 + - - +
141A SER* 3.1 9.8 + - - +
143A ALA* 1.3 76.7 - - - +
145A LEU* 1.3 57.1 + - - +
147A VAL* 3.4 23.7 + - - +
148A TYR* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ILE* 3.7 21.3 - - + -
97A LEU* 4.0 11.4 - - + -
100A TYR* 4.0 17.7 - - + -
101A THR* 4.0 22.4 - - + -
104A VAL* 5.2 3.6 - - + -
141A SER 3.1 13.8 + - - +
142A GLU* 3.3 19.3 - - + +
143A ALA 3.1 0.4 - - - -
144A GLN* 1.3 75.7 - - - +
146A ARG* 1.3 60.4 + - - +
148A TYR* 3.5 2.8 + - - +
149A PHE* 2.9 27.0 + - - +
185A ILE* 3.9 13.9 - - + +
188A TYR* 3.8 38.8 - - + -
189A PHE* 3.9 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LYS* 4.9 2.4 + - - +
142A GLU* 3.2 16.4 + - - +
143A ALA* 3.2 33.7 + - - +
145A LEU* 1.3 73.7 - - - +
147A VAL* 1.3 56.9 + - + +
149A PHE* 3.2 7.3 - - - +
150A ILE* 2.7 46.1 + - + +
189A PHE* 3.8 23.0 - - + -
194A GLU* 2.7 37.6 + - - -
197A ILE* 4.4 11.0 - - - +
198A ILE* 4.8 2.4 - - + +
201A ILE* 3.8 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ALA* 3.1 14.7 + - + +
144A GLN* 3.5 28.9 - - - +
146A ARG* 1.3 78.6 - - + +
148A TYR* 1.3 58.1 + - - +
150A ILE* 3.3 9.3 + - + +
151A SER* 2.8 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ILE* 3.6 39.4 - - + +
93A ASN* 2.8 37.7 + - - -
97A LEU* 4.6 6.4 - - + +
144A GLN* 3.0 21.1 + - - +
145A LEU 3.6 5.8 - - - +
147A VAL* 1.3 77.6 - - - +
149A PHE* 1.3 62.8 + - - +
151A SER* 3.3 7.8 + - - -
152A ILE* 3.0 55.6 + - + +
181A ALA* 4.6 9.5 - - + +
185A ILE* 3.9 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU 2.9 15.4 + - - +
146A ARG* 3.2 11.0 - - - +
148A TYR* 1.3 76.3 - - - +
150A ILE* 1.3 61.6 + - - +
152A ILE* 3.3 5.9 + - - +
153A LEU* 3.2 45.6 + - + +
182A LEU* 3.5 44.7 - - + +
185A ILE* 3.7 30.0 - - + +
186A LEU* 4.2 12.8 - - + -
198A ILE* 3.6 31.4 - - + -
201A ILE* 3.8 19.7 - - + -
202A LEU* 4.0 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ARG* 2.7 31.3 + - + +
147A VAL* 3.7 7.6 - - + +
149A PHE* 1.3 73.8 - - - +
151A SER* 1.3 64.9 + - - +
153A LEU* 3.2 8.8 + - - +
154A ASN* 3.1 39.3 + - - +
201A ILE* 3.6 33.0 - - + -
205A GLU* 4.1 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A VAL* 2.8 21.1 + - - -
148A TYR* 3.4 11.0 - - - -
150A ILE* 1.3 79.2 - - - +
152A ILE* 1.3 63.5 + - - +
154A ASN* 3.2 14.1 + - - +
155A SER* 3.3 11.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A TYR* 3.0 50.0 + - + +
149A PHE* 3.8 7.0 - - - +
151A SER* 1.3 75.7 - - - +
153A LEU* 1.3 60.9 + - - +
155A SER* 2.7 29.6 + - - -
174A TYR* 3.3 5.3 - - + -
178A GLN* 3.9 35.4 - - + +
181A ALA* 3.7 22.9 - - + -
182A LEU* 3.8 29.6 - - + +
185A ILE* 5.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PHE* 3.2 41.3 + - + +
150A ILE* 3.2 7.8 + - - +
152A ILE* 1.3 79.3 - - - +
154A ASN* 1.3 62.0 + - - +
155A SER 3.3 0.9 + - - -
156A ILE 4.0 5.9 + - - +
174A TYR* 2.6 38.5 + - + +
182A LEU* 3.9 27.1 - - + -
202A LEU* 3.9 27.1 - - + -
205A GLU* 3.7 34.8 - - + -
206A ARG* 4.5 6.1 - - - -
209A LEU* 4.3 6.4 - - - +
256A LEU* 5.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE* 3.1 33.4 + - - +
151A SER* 3.2 6.5 + - - +
152A ILE 3.1 0.6 - - - -
153A LEU* 1.3 79.4 - - - +
155A SER* 1.3 63.5 + - - +
156A ILE 3.0 12.4 + - - +
157A LYS* 2.9 26.4 + - - +
205A GLU* 2.7 37.5 + - - +
208A LYS* 5.6 1.2 - - - +
209A LEU* 5.1 7.6 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il