Contacts of the helix formed by residues 13 - 23 (chain B) in PDB entry 2GQ3
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 13 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ASP* 4.8 1.6 - - - +
4B ARG* 3.7 22.8 - - + +
12B ILE* 1.3 70.9 - - - +
14B ARG* 1.3 60.4 + - - +
15B VAL* 3.4 5.2 - - + +
16B LEU* 2.9 9.8 + - - +
17B TYR* 2.8 23.3 + - - -
281B ALA* 3.8 24.7 - - + -
348B ASP 4.6 1.6 - - - +
349B ALA* 3.1 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ASP* 3.3 45.2 + - + +
4B ARG* 4.7 0.4 - - - +
5B VAL* 3.6 28.8 - - - +
12B ILE 3.3 4.5 + - - -
13B ALA* 1.3 67.8 - - - +
15B VAL* 1.3 63.3 + - + +
17B TYR* 4.1 17.4 - - - -
18B ASP* 2.7 70.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA* 4.7 4.7 - - + +
14B ARG* 1.3 78.4 - - + +
16B LEU* 1.3 59.5 + - - +
18B ASP* 4.2 3.8 - - - +
19B PHE* 3.3 21.8 + - - +
281B ALA* 3.9 10.1 - - + +
282B ALA* 3.8 33.4 - - + +
285B VAL* 3.6 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 4.2 6.7 - - + -
13B ALA* 2.9 17.7 + - + +
15B VAL* 1.3 72.6 - - - +
17B TYR* 1.3 64.9 + - - +
18B ASP 3.2 1.8 - - - -
19B PHE* 3.3 2.3 + - + -
20B VAL* 3.0 48.4 + - + +
36B TRP* 4.7 0.7 - - + -
281B ALA* 4.8 5.4 - - + -
284B LYS* 6.1 0.4 - - + -
285B VAL* 3.6 20.2 - - + -
288B TYR* 4.0 25.1 - - + -
349B ALA* 3.8 21.3 - - + +
350B ILE* 3.8 30.7 - - + -
363B MET* 4.9 0.4 - - - -
367B PHE* 3.9 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 3.7 45.7 - - + +
7B VAL* 5.1 7.1 - - + +
12B ILE* 3.8 18.0 - - + +
13B ALA 2.8 16.0 + - - +
14B ARG* 3.1 14.1 + - - +
16B LEU* 1.3 71.0 - - - +
18B ASP* 1.3 66.9 + - - +
20B VAL* 3.5 0.3 + - - -
21B ASN* 2.9 57.8 + - + +
32B PRO* 5.8 1.2 - - - +
33B ASP* 4.9 7.8 + - - -
36B TRP* 3.4 47.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ARG* 2.7 58.3 + - - +
15B VAL* 4.2 2.9 - - - +
17B TYR* 1.3 79.2 - - - +
19B PHE* 1.3 60.5 + - - +
21B ASN* 5.0 1.6 - - - +
22B ASN* 2.8 45.6 + - - +
23B GLU* 4.2 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL 3.3 16.7 + - - +
16B LEU* 3.3 3.9 + - + +
18B ASP* 1.3 79.5 - - - +
20B VAL* 1.3 71.3 + - + +
23B GLU* 2.9 51.8 + - + +
24B ALA* 2.9 33.3 + - + -
285B VAL* 4.1 23.3 - - + -
288B TYR* 3.4 43.3 - + + -
289B ARG* 3.5 29.4 - - + +
292B LEU* 3.6 22.4 - - + -
367B PHE* 6.0 1.6 - - + -
371B ILE* 4.0 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.0 39.9 + - + +
19B PHE* 1.3 84.5 - - + +
21B ASN* 1.3 59.7 + - - +
24B ALA* 3.1 9.3 + - + -
25B LEU* 2.6 45.9 + - + +
35B PHE* 3.5 29.8 - - + -
36B TRP* 3.6 18.2 - - + -
367B PHE* 4.1 16.4 - - + -
370B LEU* 3.9 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B TYR* 2.9 51.0 + - + +
18B ASP* 5.0 1.1 - - - +
20B VAL* 1.3 77.4 - - - +
22B ASN* 1.3 66.9 + - - +
25B LEU* 3.4 20.0 - - - +
26B PRO* 3.3 20.6 - - - +
32B PRO* 4.9 9.8 - - + +
36B TRP* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ASP* 2.8 43.3 + - - +
21B ASN* 1.3 83.1 - - - +
23B GLU* 1.3 67.2 + - + +
26B PRO* 3.7 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ASP 4.2 2.8 - - - +
19B PHE* 2.9 42.4 + - + +
22B ASN* 1.3 89.2 - - + +
24B ALA* 1.3 62.5 + - - +
26B PRO* 3.6 7.2 - - - +
289B ARG* 2.9 42.8 + - - +
292B LEU* 3.7 20.5 - - + +
296B LYS* 4.0 17.2 + - - -
374B HIS* 4.6 0.3 + - - -
----------------------------------------------------------
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