Contacts of the helix formed by residues 6 - 21 (chain J) in PDB entry 2GTL
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 VAL 6 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I ALA* 4.6 17.5 - - + +
5J GLY* 1.3 71.1 - - - +
7J LEU* 1.3 75.2 + - + +
8J GLU* 3.4 2.8 + - - -
9J GLY* 3.2 2.8 + - - -
10J LEU* 2.9 38.2 + - + +
79J LEU 5.7 1.7 - - - +
80J ASP* 6.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 7 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I ALA 5.0 2.5 - - - +
34I ILE* 5.1 1.3 - - - -
37I ALA* 3.8 27.4 - - + -
122I VAL* 4.1 16.4 - - + -
125I GLN* 3.5 47.1 - - + +
126I VAL* 3.2 31.5 - - + -
6J VAL* 1.3 83.2 - - + +
8J GLU* 1.3 62.7 + - - +
9J GLY 2.7 15.3 + - - -
10J LEU* 2.7 23.2 + - + +
11J LYS* 2.9 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 8 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125I GLN* 4.1 23.2 + - - +
2J LYS* 3.5 31.3 - - + +
3J GLN 2.9 15.6 - - - +
4J CYS* 3.7 4.5 - - - -
5J GLY* 2.9 38.9 - - - +
6J VAL 3.4 5.5 + - - -
7J LEU* 1.3 80.7 + - - +
9J GLY* 1.3 59.4 + - - +
11J LYS* 3.8 4.7 - - - +
12J VAL* 3.1 29.8 + - - +
129J ALA* 4.3 13.9 - - + +
132J ALA* 5.8 0.2 - - + -
133J CYS* 3.8 3.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 9 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J CYS* 4.5 0.4 - - - -
5J GLY 3.6 11.7 + - - -
6J VAL 3.2 7.7 + - - -
7J LEU 2.7 3.2 + - - -
8J GLU* 1.3 77.4 - - - +
10J LEU* 1.3 55.3 + - - -
12J VAL* 2.9 4.5 + - - +
13J LYS* 2.7 36.8 + - - +
79J LEU* 4.2 18.6 - - - +
80J ASP* 6.5 0.2 - - - -
133J CYS* 4.1 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 10 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I ARG* 3.5 34.1 + - + +
33I ALA* 4.3 17.0 - - + -
34I ILE* 3.9 29.4 - - + +
126I VAL* 4.2 14.6 - - + -
6J VAL* 2.9 34.5 - - + +
7J LEU* 2.7 15.2 + - + +
9J GLY* 1.3 70.1 - - - +
11J LYS* 1.3 62.0 + - - +
13J LYS* 3.7 9.7 - - + +
14J SER* 3.0 25.3 + - - -
79J LEU 6.3 0.2 - - - -
80J ASP* 4.5 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 11 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I PRO 3.5 16.2 + - - -
125I GLN* 2.9 37.7 + - - +
126I VAL 3.5 16.1 + - - +
127I LEU* 3.5 19.6 + - - +
128I SER* 3.4 17.4 + - - +
2J LYS* 4.8 4.6 - - - +
7J LEU 2.9 6.2 + - - +
8J GLU* 3.8 8.5 - - - +
10J LEU* 1.3 74.2 - - - +
12J VAL* 1.3 67.3 + - + +
14J SER* 3.1 5.3 + - - -
15J GLU* 2.8 38.7 + - + +
126J ASP* 3.0 37.9 + - + +
129J ALA* 4.3 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 12 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J GLU 3.1 16.4 + - - +
9J GLY 2.9 5.6 + - - +
11J LYS* 1.3 75.0 - - - +
13J LYS* 1.3 57.3 + - - +
15J GLU* 3.9 0.2 - - - +
16J TRP* 2.7 37.2 + - - +
76J ILE* 4.2 17.7 - - + -
79J LEU* 4.6 2.0 - - + -
129J ALA* 3.6 34.5 - - + +
130J TRP* 3.7 43.3 - - + +
133J CYS* 3.8 18.2 - - + -
134J ILE* 5.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 13 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I ARG* 5.8 3.4 - - - +
9J GLY 2.7 20.6 + - - +
10J LEU* 3.7 12.1 - - + +
12J VAL* 1.3 73.6 - - - +
14J SER* 1.3 61.0 + - - +
16J TRP* 3.9 5.2 - - - +
17J GLY* 3.4 13.9 + - - -
76J ILE* 3.7 28.4 - - + +
77J SER* 3.4 29.6 + - - +
79J LEU* 5.2 2.7 - - + +
80J ASP* 2.9 35.6 + - + +
26K THR* 4.0 23.6 - - - +
27K GLU* 3.1 28.0 + - - +
29K SER* 3.5 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 14 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ASP* 4.5 17.3 + - - -
30I ARG* 4.1 22.5 + - - +
126I VAL 5.5 0.4 - - - -
10J LEU 3.0 19.1 + - - -
11J LYS* 3.5 4.9 - - - -
13J LYS* 1.3 75.0 - - - +
15J GLU* 1.3 63.2 + - - +
17J GLY* 2.8 22.7 + - - -
18J ARG* 3.4 14.0 + - - +
26K THR* 4.2 23.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 15 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127I LEU* 6.5 0.2 - - - -
128I SER* 2.8 36.8 + - - +
11J LYS* 2.8 32.5 + - + +
14J SER* 1.3 74.1 - - - +
16J TRP* 1.3 64.0 + - - +
18J ARG* 3.1 29.3 + - - +
19J ALA* 3.0 22.0 + - - +
121J LEU* 3.8 7.4 - - + +
124J CYS 3.7 2.9 - - - +
125J TYR* 3.4 17.0 - - - -
126J ASP 3.4 8.2 + - - -
130J TRP* 2.7 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 16 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J VAL 2.7 23.0 + - - +
13J LYS* 3.9 5.8 - - + +
15J GLU* 1.3 72.8 - - - +
17J GLY* 1.3 63.1 + - - +
19J ALA* 4.4 0.7 - - - +
20J TYR* 2.8 67.2 + + + +
29J PHE* 3.8 26.2 - + - -
69J LEU* 3.7 20.9 - - + -
72J LEU* 3.7 28.5 - - + -
73J ASP* 3.2 37.3 + - - +
76J ILE* 3.4 31.9 - - + -
77J SER* 5.5 1.6 - - - -
113J ILE* 5.1 2.0 - - + -
117J VAL* 5.0 1.3 - - + -
130J TRP* 3.4 36.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 17 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J LYS 3.4 8.1 + - - -
14J SER* 2.8 12.2 + - - -
16J TRP* 1.3 86.7 - - - +
18J ARG* 1.3 58.9 + - - -
20J TYR* 4.1 1.9 - - - +
21J GLY* 3.4 17.2 + - - -
26K THR* 6.4 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 18 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ASP* 4.5 19.5 + - - -
128I SER* 6.2 0.2 - - - -
14J SER* 3.4 16.4 + - - +
15J GLU* 3.1 20.9 + - - +
17J GLY* 1.3 80.2 - - - +
19J ALA* 1.3 62.4 + - - +
21J GLY* 3.7 8.7 + - - -
120J GLN* 4.8 2.6 - - - +
121J LEU* 3.7 22.4 + - + +
123J ARG* 3.8 14.5 - - - +
124J CYS* 3.4 45.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 19 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J GLU 3.0 14.6 + - - +
16J TRP* 3.9 5.2 - - + +
18J ARG* 1.3 73.5 - - - +
20J TYR* 1.3 68.9 + - - +
21J GLY* 4.4 0.2 - - - -
29J PHE* 3.5 26.4 - - + -
117J VAL* 4.0 24.9 - - + -
120J GLN* 3.3 25.2 - - + +
121J LEU* 3.6 17.0 - - + +
130J TRP* 4.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 20 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J TRP* 2.8 56.4 + + + +
17J GLY* 4.1 2.9 - - - +
19J ALA* 1.3 77.0 - - - +
21J GLY* 1.3 67.5 + - - +
22J SER 3.7 0.7 + - - -
25J ASP* 4.6 1.7 - - - +
26J ARG* 3.2 72.6 + - + -
29J PHE* 4.2 15.9 - + - +
66J ASP 4.3 3.8 + - - -
69J LEU* 3.9 22.1 - - + +
70J GLY* 3.8 21.5 + - - -
73J ASP* 3.6 26.9 - - + -
76K ASN* 5.6 0.9 + - - -
79K ASP* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 21 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J GLY 3.4 15.0 + - - -
18J ARG 3.7 7.6 + - - -
19J ALA 3.4 1.8 - - - -
20J TYR* 1.3 87.0 - - - +
22J SER* 1.3 62.3 + - - -
25J ASP* 5.1 4.7 - - - -
26J ARG* 3.1 20.1 + - - -
----------------------------------------------------------
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