Contacts of the helix formed by residues 124 - 145 (chain A) in PDB entry 4FJV
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 ASP 124 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LYS* 3.1 13.1 + - + +
121A VAL* 3.1 12.6 + - - +
123A ASN* 1.3 77.1 - - - +
125A GLN* 1.3 57.4 + - - +
126A SER* 3.3 8.7 + - - -
127A ALA* 3.1 31.0 + - + +
128A SER* 2.8 35.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASN* 4.6 7.8 + - - -
8A LEU* 3.8 34.0 - - + +
46A LYS* 5.5 1.8 - - - +
48A ASP* 5.2 1.8 + - - -
54A ARG* 4.6 2.0 - - - +
123A ASN 3.5 4.6 + - - +
124A ASP* 1.3 72.5 - - - +
126A SER* 1.3 57.8 + - - +
128A SER* 4.0 0.2 - - - -
129A ASP* 2.9 69.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ASP* 3.3 7.2 + - - -
125A GLN* 1.3 81.2 - - - +
127A ALA* 1.3 62.3 + - - +
129A ASP* 3.9 2.3 - - - +
130A HIS* 3.0 46.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ALA* 4.5 5.2 - - + +
121A VAL* 3.9 25.1 - - + +
124A ASP* 3.1 19.8 + - + +
126A SER* 1.3 77.6 - - - +
128A SER* 1.3 62.1 + - - +
130A HIS* 3.5 6.8 + - - +
131A ILE* 3.1 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.7 5.6 - - - -
54A ARG* 2.7 35.0 + - - +
121A VAL 3.8 2.9 + - - -
122A PHE* 2.8 35.5 + - - +
124A ASP 2.8 23.1 + - - -
125A GLN 4.0 0.2 - - - -
127A ALA* 1.3 74.5 - - - +
129A ASP* 1.3 62.0 + - - +
131A ILE* 3.2 12.0 + - - +
132A VAL* 3.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASP* 4.8 0.2 - - - +
50A ASN* 4.6 1.4 + - - -
54A ARG* 3.1 31.0 + - - +
125A GLN* 2.9 42.8 + - - +
126A SER* 4.0 3.8 - - - +
128A SER* 1.3 77.0 - - - +
130A HIS* 1.3 58.3 + - - +
132A VAL* 3.3 2.0 + - - +
133A GLN* 2.9 30.2 + - - +
171A MET* 3.8 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASN* 3.9 29.8 + - + +
98A PHE* 3.6 42.2 - + + +
101A ALA* 3.6 19.7 - - + -
126A SER* 3.0 41.3 + - - +
127A ALA* 3.7 4.3 - - - +
128A SER 3.2 0.2 - - - -
129A ASP* 1.3 75.5 - - - +
131A ILE* 1.3 60.7 - - - +
133A GLN* 3.5 0.6 + - - -
134A PHE* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLY* 5.4 0.2 - - - -
101A ALA* 4.1 22.2 - - - +
102A PHE* 3.7 29.8 - - + +
105A VAL* 4.0 16.6 - - + -
121A VAL* 3.8 25.1 - - + -
122A PHE* 4.0 31.0 - - + -
127A ALA* 3.1 20.7 + - + +
128A SER* 3.5 9.4 - - - +
130A HIS* 1.3 76.1 - - - +
132A VAL* 1.3 64.3 + - + +
134A PHE* 3.3 7.3 + - - +
135A LEU* 3.0 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASN* 3.7 13.7 - - + +
53A TYR* 4.0 11.9 - - + -
54A ARG* 3.8 50.5 - - + +
128A SER 3.0 16.7 + - - +
129A ASP 3.3 6.9 + - - +
131A ILE* 1.3 78.2 - - + +
133A GLN* 1.3 59.3 + - - +
135A LEU* 3.0 9.7 + - - +
136A ARG* 2.8 39.5 + - - +
171A MET* 3.5 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 3.6 44.6 - - + -
129A ASP 2.9 19.6 + - - +
131A ILE 3.4 0.2 - - - -
132A VAL* 1.3 73.5 - - - +
134A PHE* 1.3 61.8 + - - +
136A ARG* 3.4 8.0 + - - +
137A LEU* 3.0 35.5 + - + +
169A GLU 2.8 27.5 + - - +
170A PRO* 5.0 0.3 - - - +
171A MET* 3.5 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A VAL* 5.3 1.1 - - + -
81A THR* 3.7 26.5 - - + -
85A LEU* 4.0 20.6 - - + -
95A PHE 5.2 0.7 - - - -
98A PHE* 3.5 27.3 - - + +
99A PHE* 3.6 40.8 - + + -
102A PHE* 3.6 43.1 - + + -
130A HIS 3.0 10.2 + - - +
131A ILE 3.6 7.2 - - - +
132A VAL 3.2 0.2 - - - -
133A GLN* 1.3 75.3 - - - +
135A LEU* 1.3 66.2 - - + +
137A LEU* 3.2 7.2 + - + +
138A LEU* 3.0 45.7 + - + +
187A LEU* 5.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 3.6 34.1 - - + +
56A LEU* 5.8 0.9 - - + -
57A GLY* 4.2 14.1 - - - +
102A PHE* 4.1 17.0 - - + -
131A ILE* 3.0 34.4 + - + +
132A VAL* 3.0 8.1 + - - +
134A PHE* 1.3 82.9 - - + +
136A ARG* 1.3 56.9 + - - +
138A LEU* 3.4 4.6 + - + +
139A THR* 2.9 33.2 + - - -
183A LEU* 3.9 20.8 - - + +
187A LEU* 3.8 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY 3.1 13.7 + - - -
50A ASN* 2.8 29.1 + - - +
53A TYR* 3.2 36.6 + - + -
132A VAL* 2.8 22.7 + - + +
133A GLN* 3.5 14.4 - - - +
134A PHE 3.2 0.2 - - - -
135A LEU* 1.3 77.4 - - - +
137A LEU* 1.3 56.0 + - - +
139A THR* 3.3 6.6 + - - -
140A SER* 3.0 25.5 + - - -
167A GLU 4.8 0.2 + - - -
168A VAL* 3.2 31.0 + - - +
169A GLU* 3.6 8.7 - - - +
170A PRO 3.3 19.1 + - - -
171A MET* 3.7 12.0 - - - +
172A ALA 3.5 3.8 - - - +
173A THR* 2.9 43.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
85A LEU* 3.7 14.3 - - + +
90A PHE* 3.9 30.2 - - + -
94A LYS 5.0 0.9 - - - +
95A PHE* 3.9 29.2 - - + -
98A PHE* 3.9 26.9 - - + -
133A GLN* 3.0 32.6 + - - +
134A PHE* 3.7 7.6 - - + +
136A ARG* 1.3 71.7 - - - +
138A LEU* 1.3 60.8 + - - +
140A SER* 3.2 5.6 + - - -
141A ALA* 2.8 30.5 + - - +
169A GLU* 4.4 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A THR* 3.8 31.0 - - + -
84A ASP* 4.4 15.7 - - + +
85A LEU* 3.9 16.3 - - + +
134A PHE* 3.0 30.0 + - + +
135A LEU* 3.8 5.4 - - + +
137A LEU* 1.3 77.1 - - - +
139A THR* 1.3 62.9 + - - +
141A ALA* 3.4 1.5 + - + +
142A PHE* 3.0 24.2 + - + +
183A LEU* 4.4 3.1 - - + -
186A ALA* 4.0 17.7 - - + +
187A LEU* 3.5 43.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 3.9 5.1 - - - +
135A LEU 2.9 15.3 + - - -
136A ARG* 3.5 9.9 - - - -
137A LEU 3.2 0.2 - - - -
138A LEU* 1.3 76.6 - - - +
140A SER* 1.3 61.6 + - - +
142A PHE* 3.2 7.1 + - - +
143A ILE* 3.2 25.0 + - + +
168A VAL* 3.6 17.9 - - + -
179A GLN* 3.6 36.6 - - + +
182A ALA* 3.9 8.3 - - + -
183A LEU* 3.3 29.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 3.5 5.1 - - - -
136A ARG 3.0 14.4 + - - -
137A LEU 3.2 7.6 + - - -
139A THR* 1.3 75.7 - - - +
141A ALA* 1.3 57.2 + - - +
143A ILE* 3.2 3.0 + - - +
144A ARG* 2.9 42.8 + - - +
164A CYS* 3.2 13.3 - - - +
168A VAL* 3.7 10.2 - - - +
169A GLU* 2.8 39.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASP* 3.9 19.3 - - + +
85A LEU* 3.9 16.8 - - + -
88A ALA* 3.7 24.7 - - + -
90A PHE* 3.8 4.2 - - + -
137A LEU 2.8 20.1 + - - +
138A LEU* 3.8 4.9 - - + +
139A THR 3.3 0.2 - - - -
140A SER* 1.3 73.4 - - - +
142A PHE* 1.3 62.2 + - - +
144A ARG 3.8 0.2 - - - -
145A ASN* 2.9 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG* 6.0 0.4 - - - -
84A ASP* 6.2 1.3 - - - +
138A LEU 3.0 18.2 + - - +
139A THR* 3.2 6.5 + - - +
141A ALA* 1.3 76.3 - - - +
143A ILE* 1.3 61.9 + - - +
145A ASN* 5.0 0.7 - - - +
146A ARG* 3.0 77.0 + - - +
150A PHE* 4.1 15.3 - + - -
182A ALA* 3.8 23.1 - - + +
185A GLN* 3.6 39.3 - - + -
186A ALA* 3.7 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A THR* 3.2 24.5 + - + +
140A SER 3.7 5.4 - - - +
142A PHE* 1.3 74.9 - - - +
144A ARG* 1.3 66.3 + - - +
146A ARG 3.0 13.7 + - - -
147A ALA* 3.0 13.0 + - - -
150A PHE* 4.0 19.7 - - + -
160A ILE* 3.8 23.8 - - + -
163A PHE* 4.4 12.1 - - + -
164A CYS* 3.5 18.8 - - - -
168A VAL* 4.5 8.7 - - + -
178A ILE* 3.6 28.9 - - + +
179A GLN* 4.7 1.1 - - - -
182A ALA* 3.8 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ALA* 3.9 28.3 + - + +
90A PHE* 3.9 14.4 - - - -
140A SER* 2.9 34.2 + - - +
141A ALA 4.0 2.7 - - - +
143A ILE* 1.3 77.2 - - - +
145A ASN* 1.3 62.5 + - - +
146A ARG 3.2 1.0 + - - -
147A ALA* 3.4 19.6 + - - +
160A ILE* 4.8 7.6 - - + -
161A LYS* 3.5 39.5 + - + +
164A CYS* 3.7 13.9 - - - +
165A THR* 3.1 24.9 + - - +
169A GLU* 2.7 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASP* 3.2 34.2 + - - +
87A ALA* 3.4 16.4 - - - +
88A ALA* 3.3 24.7 + - - +
141A ALA 2.9 23.1 + - - +
142A PHE* 5.0 0.4 - - - +
143A ILE 3.2 0.2 - - - -
144A ARG* 1.3 75.7 - - - +
146A ARG* 1.3 78.6 + - - +
147A ALA 3.6 0.4 - - - -
----------------------------------------------------------
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