Contacts of the helix formed by residues 23 - 35 (chain B) in PDB entry 1GG3
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 GLY 23 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LYS* 1.3 84.2 - - - +
24B GLN* 1.3 51.7 + - - -
25B ASP 2.3 20.2 + - - -
26B LEU 2.5 13.3 + - - -
27B LEU 3.4 2.3 + - - -
56B LEU* 3.5 9.2 - - - -
57B ASP 3.4 11.9 - - - -
58B SER 3.4 3.1 + - - -
60B LYS 2.4 23.0 + - - -
62B ILE* 3.6 10.7 - - - +
65B GLN* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLY* 1.3 68.4 - - - -
25B ASP* 1.3 64.7 + - - +
26B LEU 2.7 0.6 + - - -
27B LEU* 3.9 5.6 - - - +
28B LYS* 2.3 65.9 + - + +
45B ALA* 3.8 7.9 - - - +
46B ILE* 3.1 39.7 + - + +
55B TRP* 5.1 1.0 - - - -
56B LEU* 2.9 34.9 + - + +
57B ASP* 4.6 0.2 - - - -
58B SER* 2.9 41.5 + - - +
78B LYS* 3.5 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LYS* 4.1 10.1 + - + +
23B GLY 2.3 13.1 + - - +
24B GLN* 1.3 68.2 - - - +
26B LEU* 1.3 78.4 + - + +
28B LYS* 4.4 2.2 - - - +
29B ARG* 3.0 22.5 + - - +
58B SER* 2.9 40.2 + - - +
59B ALA* 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 5.7 2.2 - - + -
18B GLU* 5.5 7.2 - - + +
21B ALA* 3.7 17.7 - - + -
22B LYS* 3.1 41.5 - - + +
23B GLY 2.5 10.1 + - - -
24B GLN 3.2 1.3 - - - -
25B ASP* 1.3 97.9 - - - +
27B LEU* 1.3 62.1 + - - +
29B ARG* 3.6 3.9 + - + +
30B VAL* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B CYS* 4.1 15.3 - - + -
5B VAL* 4.0 14.1 - - + -
15B CYS* 3.8 29.8 - - - -
17B VAL* 4.0 11.6 - - + +
22B LYS 4.2 0.6 + - - -
23B GLY 3.4 2.4 + - - -
24B GLN* 2.9 9.1 + - - -
26B LEU* 1.3 79.2 - - - +
28B LYS* 1.3 58.7 + - - +
30B VAL* 2.8 24.0 + - + +
31B CYS* 3.1 12.8 + - - -
46B ILE* 3.5 23.1 - - + -
56B LEU* 5.8 2.0 - - + -
62B ILE* 4.2 16.5 - - + +
73B PHE* 3.5 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLN* 2.3 61.7 + - + +
25B ASP* 3.9 1.4 - - - +
27B LEU* 1.3 69.6 - - - +
29B ARG* 1.3 64.1 + - - +
31B CYS* 3.0 3.7 + - - +
32B GLU* 2.9 48.3 + - + +
40B ASP* 5.4 4.5 - - - -
44B LEU 3.6 16.4 - - - +
45B ALA* 3.2 37.0 - - - +
46B ILE* 3.7 10.9 - - + +
58B SER* 3.6 6.1 + - - -
75B PHE* 4.8 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLN 3.0 5.3 + - - -
25B ASP 3.0 20.6 + - - +
26B LEU* 3.7 6.1 - - + +
27B LEU 3.2 0.2 - - - -
28B LYS* 1.3 76.3 - - - +
30B VAL* 1.3 64.4 + - + +
32B GLU* 3.3 6.0 + - - +
33B HIS* 3.1 64.3 + - + +
38B GLU* 5.4 5.7 + - - -
40B ASP* 2.7 36.7 + - - -
41B TYR* 6.0 3.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B TYR* 3.3 31.9 + - + +
15B CYS* 4.4 11.7 - - + -
17B VAL* 5.6 4.7 - - + -
26B LEU* 2.9 22.9 - - + +
27B LEU* 2.8 14.5 + - + +
29B ARG* 1.3 79.1 - - + +
31B CYS* 1.3 58.2 + - - +
33B HIS* 3.8 9.4 - - + +
34B LEU* 3.4 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 3.8 37.7 - - - -
7B LEU* 5.3 3.4 - - + -
13B TYR* 3.8 16.6 - - + -
27B LEU* 3.1 19.0 + - - -
28B LYS* 3.0 10.9 + - - +
30B VAL* 1.3 73.3 - - - +
32B GLU* 1.3 69.8 + - - +
33B HIS 3.0 2.0 - - - -
34B LEU* 3.2 6.8 + - - +
35B ASN* 2.9 30.8 + - - +
46B ILE* 4.8 4.5 - - - -
75B PHE* 4.2 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LYS* 2.9 38.9 + - + +
29B ARG* 3.6 6.5 - - - +
31B CYS* 1.3 74.1 - - - +
33B HIS* 1.3 60.8 + - - +
35B ASN* 3.2 5.2 + - - +
36B LEU 3.0 7.1 + - - -
37B LEU* 2.9 41.1 + - + +
40B ASP* 3.2 60.3 - - + +
44B LEU* 3.6 10.1 - - - +
75B PHE* 2.9 26.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ARG* 3.1 60.7 + - + +
30B VAL* 3.8 11.0 - - + +
32B GLU* 1.3 77.9 - - - +
34B LEU* 1.3 54.0 + - - +
35B ASN 2.8 5.4 + - - -
36B LEU* 2.7 28.0 + - - +
37B LEU 5.4 2.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 4.7 11.4 - - + -
13B TYR* 3.3 45.5 - - + +
30B VAL 3.4 15.2 + - - +
31B CYS* 3.2 6.3 + - - +
33B HIS* 1.3 76.5 - - - +
35B ASN* 1.3 65.5 + - - +
36B LEU* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 4.6 23.4 - - - +
31B CYS* 2.9 18.4 + - - +
32B GLU 3.5 4.9 - - - +
33B HIS 2.8 1.4 + - - -
34B LEU* 1.3 86.1 - - - +
36B LEU* 1.3 70.9 + - - +
37B LEU* 3.1 10.1 + - + +
75B PHE* 4.0 33.5 - - - -
91B ILE* 4.4 2.3 - - - +
95B TYR* 3.0 47.8 + - + +
----------------------------------------------------------
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