Contacts of the helix formed by residues 21 - 33 (chain S) in PDB entry 1G3I
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 ALA 21 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19S GLY 3.5 1.7 + - - -
20S GLN* 1.3 84.8 - - - +
22S ASP* 1.3 65.8 + - - +
23S ALA 2.6 14.5 + - - +
24S LYS* 3.0 20.0 + - - +
25S ARG* 3.1 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 22 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21S ALA* 1.3 83.6 - - - +
23S ALA* 1.3 64.3 + - - +
25S ARG* 3.8 23.6 + - - +
26S ALA* 3.3 16.1 + - - +
331S VAL* 3.4 13.1 - - + +
332S GLU* 4.5 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20S GLN* 3.5 38.8 - - + +
21S ALA 2.6 4.2 + - - +
22S ASP* 1.3 76.8 - - - +
24S LYS* 1.3 70.1 + - - +
26S ALA* 3.1 2.8 + - - +
27S VAL* 3.0 23.9 + - + +
55S MET* 5.8 0.9 - - - -
66S ILE* 3.9 10.5 - - + -
331S VAL* 3.3 15.7 - - - +
332S GLU 4.9 1.8 + - - -
333S LEU* 3.7 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 24 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10S VAL* 4.7 18.2 - - + -
13S LEU* 4.3 24.5 - - + +
14S ASP* 2.8 31.2 + - - +
17S ILE* 2.6 37.9 + - - -
18S ILE* 4.1 1.8 - - - +
19S GLY 2.9 29.6 + - - +
20S GLN* 4.0 8.1 - - + -
21S ALA* 3.0 9.8 + - - +
23S ALA* 1.3 76.9 - - + +
25S ARG* 1.3 55.7 + - - +
27S VAL* 2.7 34.0 + - - +
28S ALA* 2.7 15.3 + - - +
66S ILE* 3.8 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 25 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10S VAL* 5.1 9.8 - - + +
21S ALA* 3.1 18.4 + - - +
22S ASP* 3.8 21.6 + - - +
24S LYS* 1.3 78.6 - - - +
26S ALA* 1.3 57.1 + - - +
28S ALA* 3.2 7.3 + - - +
29S ILE* 3.0 36.2 + - - +
405T ASP* 3.5 37.2 + - - -
406T LYS* 5.4 1.0 - - - +
409T PHE* 4.3 46.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22S ASP 3.3 14.3 + - - +
23S ALA 3.1 4.4 + - - +
25S ARG* 1.3 77.0 - - - +
27S VAL* 1.3 66.1 + - + +
29S ILE* 3.1 28.5 - - + +
30S ALA 3.4 2.4 + - - -
53S ILE* 3.1 19.1 - - + +
329S ILE* 4.1 22.7 - - + -
331S VAL* 4.4 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13S LEU* 5.1 4.3 - - + -
23S ALA* 3.0 19.7 + - + +
24S LYS* 2.7 13.3 + - - +
26S ALA* 1.3 72.3 - - + +
28S ALA* 1.3 60.2 + - - +
30S ALA* 3.2 15.6 - - - +
31S LEU 3.6 3.3 + - - -
53S ILE* 4.0 12.8 - - + -
55S MET* 5.3 12.3 - - + -
66S ILE* 3.3 37.7 - - + +
70S LEU* 3.3 42.9 - - + +
306S ILE* 5.0 6.5 - - + -
331S VAL* 5.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6S PRO* 3.8 32.8 - - + +
9S ILE* 4.4 23.1 - - + +
10S VAL* 4.8 5.6 - - + -
13S LEU* 6.2 1.1 - - + -
24S LYS 2.7 10.4 + - - +
25S ARG* 3.3 12.1 - - - +
27S VAL* 1.3 73.9 - - - +
29S ILE* 1.3 54.6 + - - +
30S ALA 2.5 17.8 + - - -
31S LEU* 2.6 17.5 + - - +
32S ARG* 3.1 8.7 + - - +
70S LEU* 5.5 0.2 - - - -
409T PHE* 5.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 29 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6S PRO* 5.0 2.9 - - + -
25S ARG* 3.4 11.7 - - + +
26S ALA* 3.1 34.5 - - + +
28S ALA* 1.3 71.9 - - + +
30S ALA* 1.3 59.1 + - - +
32S ARG* 4.0 11.4 - - - -
33S ASN* 2.7 39.8 + - - +
329S ILE* 5.0 5.8 - - + -
401T GLU* 4.0 20.4 - - - +
405T ASP* 4.3 21.1 - - - +
408T SER* 4.4 12.6 - - - +
409T PHE* 4.2 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26S ALA 3.5 10.5 - - - +
27S VAL 3.2 14.6 - - - +
28S ALA 2.5 5.9 + - - -
29S ILE* 1.3 77.7 - - - +
31S LEU* 1.3 60.7 + - - +
33S ASN* 3.7 9.4 + - - +
34S ARG* 3.7 12.6 + - - +
50S PRO* 6.0 1.6 - - - +
51S LYS* 4.8 5.6 - - - +
53S ILE* 3.7 17.7 - - + -
70S LEU* 5.7 2.5 - - + -
304S LEU* 4.7 28.2 - - + +
306S ILE* 6.2 0.4 - - + -
329S ILE* 5.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3S GLU* 4.9 20.1 - - + +
4S MET* 6.3 2.5 - - + -
9S ILE* 3.6 26.0 - - + -
27S VAL 3.6 6.0 + - - +
28S ALA 2.6 13.8 + - - +
30S ALA* 1.3 73.5 - - - +
32S ARG* 1.3 62.1 + - - +
34S ARG* 3.4 40.5 + - - +
35S TRP* 3.7 10.7 + - - +
70S LEU* 4.4 20.4 - - + +
73S LEU 4.5 3.8 - - - +
74S ALA* 3.5 33.9 - - + +
253S ILE* 5.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 32 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4S MET 2.6 32.3 + - - -
5S THR* 3.3 19.9 + - - +
6S PRO* 3.4 26.0 - - + +
9S ILE* 5.2 2.2 - - + +
28S ALA 3.1 11.4 + - - +
29S ILE* 4.2 10.1 - - - +
31S LEU* 1.3 79.9 - - - +
33S ASN* 1.3 58.2 + - - +
34S ARG 3.2 0.2 - - - -
35S TRP* 3.0 32.8 + - - +
36S ARG* 3.0 58.2 + - + +
363T GLU* 2.6 31.6 + - + -
408T SER* 5.1 10.1 - - - +
412T SER* 3.8 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 33 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29S ILE* 2.7 27.3 + - - +
30S ALA* 3.7 5.6 + - - +
31S LEU 3.3 0.8 - - - -
32S ARG* 1.3 79.2 - - - +
34S ARG* 1.3 56.0 + - - +
35S TRP 3.2 3.4 - - - -
36S ARG* 4.2 11.1 - - - +
37S ARG* 3.3 21.0 + - - +
50S PRO* 5.9 5.6 - - + +
51S LYS* 5.5 13.1 - - + +
356T TYR* 5.3 10.0 + - - -
359T LEU* 5.0 15.7 - - + +
360T MET* 4.3 14.4 - - - +
401T GLU* 5.2 9.7 + - - -
408T SER* 3.5 24.6 + - - -
----------------------------------------------------------
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