Contacts of the helix formed by residues 123 - 149 (chain A) in PDB entry 1N1Q
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 123 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.3 21.3 - - + +
63A ARG* 3.0 24.3 + - - -
67A ILE* 3.8 13.2 - - - +
118A ALA* 2.8 26.5 + - + +
119A ASP* 4.6 0.2 - - - +
121A ALA* 4.3 4.7 - - + +
122A ASP* 1.3 76.1 - - - +
124A GLU* 1.3 60.0 + - - +
125A ALA* 3.7 1.2 + - - +
126A THR* 2.6 28.8 + - - -
127A ALA* 3.2 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASP* 2.7 31.5 - - - +
122A ASP* 3.5 18.1 + - - +
123A ASP* 1.3 73.0 - - - +
125A ALA* 1.3 61.1 + - - +
127A ALA* 3.2 5.8 + - + +
128A ASP* 2.8 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ARG* 3.1 35.1 + - - +
123A ASP* 3.3 1.0 - - - +
124A GLU* 1.3 78.4 - - - +
126A THR* 1.3 60.5 + - - +
128A ASP* 3.4 6.6 + - - +
129A MET* 3.2 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.6 17.7 - - + +
13A LEU* 3.6 31.3 - - + +
63A ARG* 3.1 25.4 + - + +
67A ILE* 4.3 0.9 - - - +
118A ALA* 3.9 8.7 - - + -
123A ASP* 2.6 35.9 + - - -
125A ALA* 1.3 75.1 - - - +
127A ALA* 1.3 66.0 - - - +
129A MET* 3.2 4.9 + - - +
130A LEU* 3.0 27.3 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
115A ARG* 3.7 25.0 - - + +
118A ALA* 3.9 5.8 - - + +
119A ASP* 3.2 33.2 - - - +
123A ASP 3.2 7.8 + - - +
124A GLU* 3.2 8.5 + - + +
126A THR* 1.3 79.3 - - - +
128A ASP* 1.3 56.8 + - - +
130A LEU* 3.3 3.8 + - - +
131A ASP* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLU* 2.8 20.0 + - + +
125A ALA* 3.7 8.1 - - - +
126A THR 3.2 0.2 - - - -
127A ALA* 1.3 74.0 - - - +
129A MET* 1.3 63.1 + - - +
131A ASP* 3.2 12.8 + - - +
132A ALA* 3.0 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 4.9 2.7 - - - -
59A THR* 3.2 46.4 - - - +
60A LEU* 3.7 20.0 - - + +
63A ARG* 3.7 31.9 - - + -
125A ALA 3.2 10.5 + - - +
126A THR 3.6 9.2 - - - +
128A ASP* 1.3 80.8 + - - +
130A LEU* 1.3 73.2 + - + +
132A ALA* 3.2 11.4 + - - +
133A ILE* 2.8 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 5.9 0.4 - - + +
13A LEU* 3.7 24.2 - - + -
16A GLN* 4.8 6.5 - - + -
60A LEU* 3.9 18.2 - - + -
111A LEU* 3.8 25.5 - - + +
114A ALA* 3.7 30.7 - - + +
115A ARG* 3.6 24.5 - - + +
126A THR* 3.0 29.6 + - + +
127A ALA 3.6 5.6 - - - +
129A MET* 1.3 81.5 - - + +
131A ASP* 1.3 56.9 + - - +
133A ILE* 3.3 6.7 + - + +
134A GLU* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ARG* 3.9 31.5 + - - +
127A ALA 2.9 14.4 + - - +
128A ASP* 3.3 17.9 - - - +
130A LEU* 1.3 77.2 - - - +
132A ALA* 1.3 56.3 + - - +
134A GLU* 3.1 9.3 + - - +
135A ALA* 2.8 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ASP* 3.0 13.3 + - - +
129A MET* 3.2 12.1 + - - +
131A ASP* 1.3 77.2 - - - +
133A ILE* 1.3 65.0 + - + +
135A ALA* 3.6 6.7 + - - +
136A GLY* 3.3 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TRP* 4.2 21.8 - - + +
56A HIS* 3.5 38.2 - - + +
59A THR* 5.1 2.7 - - - +
60A LEU* 5.3 8.5 - - + -
111A LEU* 3.6 21.3 - - + -
129A MET* 2.8 42.6 - - + +
130A LEU* 3.3 8.9 + - - +
131A ASP 3.2 0.2 - - - -
132A ALA* 1.3 79.1 - - + +
134A GLU* 1.3 65.0 + - - +
136A GLY* 3.2 4.0 + - - -
137A LEU* 3.0 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A VAL* 4.1 13.2 - - + -
111A LEU* 3.6 18.8 - - + +
112A LYS* 3.7 27.7 + - - +
115A ARG* 2.8 40.3 + - - -
130A LEU 2.9 13.0 + - - +
131A ASP* 3.4 14.0 - - - +
133A ILE* 1.3 78.8 - - - +
135A ALA* 1.3 62.5 + - - +
137A LEU* 3.1 5.3 + - - +
138A GLU* 2.9 51.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ASP* 2.8 21.7 + - - +
132A ALA* 3.9 7.9 - - - +
133A ILE 3.3 0.2 - - - -
134A GLU* 1.3 73.7 - - - +
136A GLY* 1.3 62.8 + - - +
138A GLU* 3.4 13.4 + - - +
139A LYS* 3.2 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ALA 3.3 8.1 + - - -
133A ILE* 3.2 8.4 + - - -
135A ALA* 1.3 80.5 - - - +
137A LEU* 1.3 60.5 + - - +
139A LYS* 3.3 8.4 + - - +
140A HIS* 3.0 33.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
20A TRP* 3.9 13.5 - - + -
52A GLU* 6.0 0.4 - - - +
56A HIS* 5.4 2.9 - - - +
104A PHE* 3.7 45.9 - - + +
107A LEU* 3.7 37.0 - - + -
108A VAL* 4.0 10.8 - - + -
111A LEU* 3.9 19.3 - - + -
133A ILE* 3.0 22.8 + - + +
134A GLU 3.1 5.8 + - - +
136A GLY* 1.3 73.2 - - - +
138A GLU* 1.3 60.9 + - - +
140A HIS* 3.1 8.6 + - + +
141A VAL* 2.8 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A VAL* 3.8 23.7 - - + +
112A LYS* 4.4 4.9 + - - -
134A GLU* 2.9 46.9 + - - +
135A ALA* 3.7 10.2 - - - +
136A GLY 3.3 0.2 - - - -
137A LEU* 1.3 76.6 - - - +
139A LYS* 1.3 61.4 + - - +
141A VAL* 3.4 9.5 + - - +
142A TRP* 3.2 19.9 + - - +
----------------------------------------------------------
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 ALA 3.2 12.4 + - - +
136A GLY* 3.6 10.8 - - - +
137A LEU 3.1 0.6 - - - -
138A GLU* 1.3 74.9 - - - +
140A HIS* 1.3 65.5 + - - +
142A TRP* 3.2 35.2 + - + -
143A MET* 3.3 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LYS* 4.6 8.0 - - - -
48A GLU* 3.6 21.5 - - - -
49A LEU* 3.5 24.8 - - + +
52A GLU* 2.9 30.6 + - - -
104A PHE* 3.7 25.6 - + + -
136A GLY* 3.0 26.7 + - - -
137A LEU* 3.5 10.3 - - + +
139A LYS* 1.3 75.8 - - + +
141A VAL* 1.3 57.7 + - - +
143A MET* 3.2 20.0 + - + +
144A LEU* 2.9 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A VAL* 4.5 6.7 - - + +
104A PHE* 3.7 27.8 - - + +
105A VAL* 4.3 22.9 - - + +
108A VAL* 5.3 2.7 - - + -
137A LEU 2.8 25.9 + - - +
138A GLU* 3.6 9.4 - - - +
139A LYS 3.2 0.4 - - - -
140A HIS* 1.3 73.2 - - - +
142A TRP* 1.3 63.6 + - - +
144A LEU* 4.1 4.9 - - - +
145A GLU* 3.0 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLU 3.2 10.2 + - - +
139A LYS* 3.2 40.6 + - + +
141A VAL* 1.3 79.7 - - - +
143A MET* 1.3 81.5 + - + +
145A GLU* 3.9 4.6 - - - +
146A ALA* 3.0 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LYS* 4.8 14.8 - - - +
139A LYS* 3.3 48.9 + - + +
140A HIS* 3.2 25.6 + - + +
142A TRP* 1.3 107.4 - - + +
144A LEU* 1.3 65.2 + - + +
146A ALA* 3.3 6.4 + - - +
147A PHE* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 5.8 3.4 - - + -
45A LYS* 4.6 24.7 - - + -
46A PHE* 5.8 3.4 - - + -
49A LEU* 4.8 6.5 - - + -
97A VAL* 3.6 21.9 - - + +
100A VAL* 3.6 34.3 - - + -
101A VAL* 3.5 23.8 - - + +
104A PHE* 4.5 8.1 - - + -
140A HIS* 2.9 33.0 + - + +
141A VAL 4.1 0.7 - - - +
143A MET* 1.3 75.4 - - + +
145A GLU* 1.3 62.5 + - - +
147A PHE* 3.3 10.0 - - + +
148A LEU* 3.2 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A VAL* 3.9 24.8 - - + +
105A VAL* 5.0 2.6 - - - +
141A VAL* 3.0 37.8 + - - +
142A TRP* 3.9 4.9 - - - +
144A LEU* 1.3 74.0 - - - +
146A ALA* 1.3 66.8 + - - +
148A LEU* 3.1 19.6 + - + +
149A GLU* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TRP* 3.0 32.5 + - + +
143A MET* 3.5 7.4 - - - +
144A LEU 3.3 0.2 - - - -
145A GLU* 1.3 76.6 - - - +
147A PHE* 1.3 62.3 + - - +
149A GLU* 3.1 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASN* 3.7 35.4 - - + -
41A THR* 5.1 8.3 - - + -
42A LEU* 4.1 26.0 - - + -
93A ALA* 5.8 0.7 - - + -
94A ALA* 5.3 5.4 - - + -
97A VAL* 3.8 24.5 - - + -
143A MET 3.0 13.2 + - - +
144A LEU* 3.3 13.7 - - + +
145A GLU 3.2 0.2 - - - -
146A ALA* 1.3 78.2 - - - +
148A LEU* 1.3 77.4 + - + +
149A GLU 3.5 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ALA* 3.8 33.0 - - + +
97A VAL* 3.7 16.2 - - + -
98A SER* 3.8 31.0 - - - +
101A VAL* 4.4 9.0 - - + -
144A LEU 3.4 13.5 - - - +
145A GLU* 3.1 13.2 + - + +
147A PHE* 1.3 83.5 - - + +
149A GLU* 1.3 67.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLU* 3.1 23.9 + - - +
146A ALA* 3.1 25.0 + - - +
147A PHE 4.6 2.5 - - - +
148A LEU* 1.3 85.6 - - - +
----------------------------------------------------------
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