Contacts of the helix formed by residues 21 - 33 (chain U) 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 U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19U GLY 3.5 1.3 + - - -
20U GLN* 1.3 86.9 - - - +
22U ASP* 1.3 64.7 + - - +
23U ALA 2.6 14.9 + - - +
24U LYS* 3.0 19.6 + - - +
25U ARG* 3.1 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 22 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21U ALA* 1.3 84.1 - - - +
23U ALA* 1.3 64.4 + - - +
25U ARG* 3.9 23.7 + - - +
26U ALA* 3.3 16.1 + - - +
331U VAL* 3.3 12.5 - - + +
332U GLU* 4.4 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20U GLN* 3.5 38.8 - - + +
21U ALA 2.6 1.2 + - - +
22U ASP* 1.3 81.8 - - - +
24U LYS* 1.3 69.5 + - - +
26U ALA* 3.1 2.6 + - - +
27U VAL* 3.0 24.6 + - + +
55U MET* 5.8 1.3 - - - -
66U ILE* 3.9 10.3 - - + -
331U VAL* 3.3 15.5 - - - +
332U GLU 4.9 1.6 + - - -
333U LEU* 3.7 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 24 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10U VAL* 4.7 17.0 - - + -
13U LEU* 4.3 24.2 - - + +
14U ASP* 2.8 32.0 + - - +
17U ILE* 2.7 38.2 + - - -
18U ILE* 4.1 2.0 - - - +
19U GLY 3.0 29.2 + - - +
20U GLN* 4.0 8.7 - - + -
21U ALA* 3.0 11.3 + - - +
23U ALA* 1.3 76.7 - - - +
25U ARG* 1.3 56.4 + - - +
27U VAL* 2.6 34.5 + - - +
28U ALA* 2.7 15.0 + - - +
66U ILE* 3.8 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 25 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10U VAL* 5.0 8.0 - - + +
21U ALA* 3.1 17.6 + - - +
22U ASP* 3.9 21.5 + - - +
24U LYS* 1.3 78.7 - - + +
26U ALA* 1.3 56.9 + - - +
28U ALA* 3.1 8.5 + - - +
29U ILE* 3.0 35.9 + - - +
405V ASP* 3.3 38.0 + - - -
406V LYS* 5.2 1.4 - - - +
409V PHE* 4.1 52.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22U ASP 3.3 14.3 + - - +
23U ALA 3.1 4.2 + - - +
25U ARG* 1.3 76.3 - - - +
27U VAL* 1.3 65.5 + - + +
29U ILE* 3.1 29.8 - - + +
30U ALA 3.4 2.8 + - - -
53U ILE* 3.1 19.0 - - + +
329U ILE* 4.1 23.6 - - + -
331U VAL* 4.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13U LEU* 5.0 3.1 - - + -
23U ALA* 3.0 20.0 - - + +
24U LYS* 2.6 16.6 + - - +
26U ALA* 1.3 74.2 - - + +
28U ALA* 1.3 58.4 + - - +
30U ALA* 3.2 15.2 - - - +
31U LEU 3.6 3.1 + - - -
53U ILE* 4.1 12.6 - - + -
55U MET* 5.2 13.2 - - + -
66U ILE* 3.3 38.6 - - + +
70U LEU* 3.3 41.7 - - + +
306U ILE* 5.0 6.5 - - + -
331U VAL* 5.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6U PRO* 3.8 32.3 - - + +
9U ILE* 4.4 23.6 - - + +
10U VAL* 4.8 5.6 - - + -
13U LEU* 6.0 1.1 - - + +
24U LYS 2.7 9.8 + - - +
25U ARG* 3.2 12.8 - - - +
27U VAL* 1.3 73.4 - - - +
29U ILE* 1.3 54.2 + - + +
30U ALA 2.5 17.1 + - - -
31U LEU* 2.6 17.8 + - - +
32U ARG* 3.1 9.5 + - - +
70U LEU* 5.5 0.4 - - - -
409V PHE* 5.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 29 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6U PRO* 4.6 3.3 - - + +
25U ARG* 3.4 11.2 - - + +
26U ALA* 3.1 35.4 - - + +
28U ALA* 1.3 76.6 - - - +
30U ALA* 1.3 58.3 + - - +
32U ARG* 4.0 11.7 - - - -
33U ASN* 2.7 35.3 + - - +
329U ILE* 5.0 4.9 - - + -
401V GLU* 4.0 20.9 - - - +
405V ASP* 4.4 20.4 - - - +
408V SER* 4.3 20.0 - - - +
409V PHE* 4.2 37.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26U ALA 3.5 10.5 - - - +
27U VAL* 3.2 14.6 - - - +
28U ALA 2.5 6.1 + - - -
29U ILE* 1.3 78.1 - - - +
31U LEU* 1.3 61.8 + - - +
32U ARG 3.3 0.2 - - - -
33U ASN* 3.7 10.2 + - - +
34U ARG* 3.7 13.2 + - - +
50U PRO* 5.9 1.7 - - - +
51U LYS* 4.8 6.3 - - - +
53U ILE* 3.7 18.4 - - + -
70U LEU* 5.7 2.2 - - + -
304U LEU* 4.7 25.9 - - + +
306U ILE* 6.2 0.4 - - + -
329U ILE* 5.1 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3U GLU* 4.9 19.9 - - + +
4U MET* 6.3 3.1 - - + -
9U ILE* 3.6 25.6 - - + -
27U VAL 3.6 5.1 + - - +
28U ALA 2.6 14.2 + - - +
30U ALA* 1.3 73.1 - - - +
32U ARG* 1.3 63.7 + - - +
34U ARG* 3.4 40.3 + - - +
35U TRP* 3.7 10.6 + - - +
70U LEU* 4.4 21.3 - - + +
73U LEU 4.5 3.6 - - - +
74U ALA* 3.5 34.3 - - + +
253U ILE* 5.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 32 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4U MET 2.7 32.8 + - - -
5U THR* 3.3 21.0 + - - +
6U PRO* 3.4 26.8 - - + +
9U ILE* 5.2 2.2 - - + +
28U ALA 3.1 11.5 + - - +
29U ILE* 4.3 9.6 - - - +
31U LEU* 1.3 79.9 - - - +
33U ASN* 1.3 58.6 + - - +
34U ARG 3.2 0.2 - - - -
35U TRP* 3.0 31.3 + - - +
36U ARG* 3.0 60.1 + - + +
360V MET* 6.4 0.9 - - + -
363V GLU* 2.7 31.5 + - + +
408V SER* 5.2 8.7 - - - +
412V SER* 3.9 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 33 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29U ILE* 2.7 28.4 + - - +
30U ALA* 3.7 5.6 + - - +
31U LEU 3.3 0.4 - - - -
32U ARG* 1.3 77.1 - - - +
34U ARG* 1.3 56.1 + - - +
35U TRP 3.2 4.9 - - - -
36U ARG* 4.2 10.9 - - - +
37U ARG* 3.3 21.5 + - - +
50U PRO* 5.9 5.7 - - + +
51U LYS* 5.5 13.9 - - + +
356V TYR* 5.3 10.2 + - - -
359V LEU* 4.8 17.4 - - + +
360V MET* 4.2 14.9 - - - +
401V GLU* 5.3 8.3 + - - -
408V SER* 3.5 23.9 + - - -
----------------------------------------------------------
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