Contacts of the helix formed by residues 1 - 13 (chain A) in PDB entry 3V9M
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 ASN 1 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 1.3 65.6 + - - +
3A ILE* 3.0 15.6 + - - +
4A GLN* 2.9 41.0 + - - +
5A PHE* 3.0 21.0 + - - +
62A PRO 4.1 5.4 + - - -
63A LYS 3.2 20.9 - - - +
64A LEU* 3.7 10.8 + - - +
65A THR 2.5 29.7 + - - +
66A LEU* 3.6 24.9 - - - +
67A TYR* 3.5 14.9 + - - -
92A ASP* 4.2 2.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 2 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ASN* 1.3 75.9 - - - +
3A ILE* 1.3 61.6 + - + +
5A PHE* 3.3 13.7 + - + +
6A GLY* 3.0 19.2 + - - -
52A TYR* 4.0 23.6 - - + +
63A LYS* 3.1 38.7 + - + +
201A EDO 4.6 16.8 - - - +
206A PEG 3.9 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 3 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ASN* 3.0 13.2 + - - +
2A LEU* 1.3 78.2 - - + +
4A GLN* 1.3 65.7 + - + +
6A GLY* 3.1 3.8 + - - -
7A ASN* 3.0 24.1 + - - +
203A SO4 5.8 0.9 - - - +
68B SER* 3.8 21.3 - - - +
69B TRP 3.3 26.2 - - - +
70B LYS* 3.1 41.2 - - + +
79B ASN* 3.9 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 4 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ASN* 2.9 46.7 + - - +
3A ILE* 1.3 74.3 - - + +
5A PHE* 1.3 52.1 + - - +
7A ASN* 3.0 5.5 + - - +
8A MET* 2.8 36.0 + - - +
65A THR 3.6 0.9 - - - +
66A LEU* 3.8 16.2 - - + +
67A TYR* 2.8 63.4 + - + +
69A TRP* 3.9 3.7 - - - +
203A SO4 3.0 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 5 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ASN 3.0 9.4 + - - +
2A LEU* 3.5 19.1 - - + +
3A ILE 3.3 0.2 - - - -
4A GLN* 1.3 75.5 - - - +
6A GLY* 1.3 62.7 + - - +
8A MET* 3.1 5.7 + - + +
9A ILE* 2.9 41.9 + - + +
48A HIS* 3.4 28.7 - + - -
52A TYR* 4.5 3.8 - - - +
67A TYR* 3.6 5.9 + - - -
92A ASP* 3.5 49.1 - - + +
95A ALA* 3.7 16.6 - - + -
96A ALA* 4.1 2.2 - - - -
99A PHE* 3.9 17.3 - + - -
201A EDO 3.3 26.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU 3.0 14.0 + - - -
3A ILE* 3.1 4.4 + - - -
5A PHE* 1.3 76.0 - - - +
7A ASN* 1.3 64.7 + - - +
9A ILE* 3.3 5.8 + - - -
10A GLN* 3.2 15.6 + - - +
19A SER* 2.9 35.5 + - - -
71B CYS 5.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 3.0 18.4 + - - +
4A GLN 3.0 8.6 + - - +
6A GLY* 1.3 78.5 - - - +
8A MET* 1.3 56.2 + - - +
10A GLN* 3.3 8.2 + - - +
11A CYS* 3.0 25.8 + - - +
69A TRP* 3.6 18.3 - - + -
203A SO4 2.9 20.6 + - - +
69B TRP* 3.2 41.0 + - + -
70B LYS* 3.4 5.4 - - - +
71B CYS* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN 2.8 17.8 + - - +
5A PHE* 3.4 8.1 - - + +
7A ASN* 1.3 72.3 - - - +
9A ILE* 1.3 68.2 + - - +
11A CYS* 3.1 3.9 + - - +
12A ALA* 3.0 20.6 + - - +
67A TYR* 3.4 34.8 - - + +
69A TRP* 3.8 35.7 - - + -
76A PRO* 3.9 7.1 - - + +
78A CYS* 4.6 0.2 - - - -
89A CYS* 3.6 26.9 - - - +
92A ASP* 3.5 11.2 - - - -
93A ALA* 3.4 32.8 - - + +
96A ALA* 3.6 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 2.9 41.6 + - + +
6A GLY* 3.6 13.7 - - - +
7A ASN 3.3 0.2 - - - -
8A MET* 1.3 77.7 - - - +
10A GLN* 1.3 69.4 + - - +
12A ALA* 3.4 1.7 + - - +
13A ASN* 3.0 42.8 + - + +
19A SER* 4.0 9.2 - - - +
22A TYR* 3.9 29.4 - - + -
96A ALA* 4.0 10.2 - - + +
99A PHE* 3.7 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLY 3.2 11.5 + - - +
7A ASN 3.7 6.7 - - - +
9A ILE* 1.3 75.9 - - - +
11A CYS* 1.3 66.4 + - - +
13A ASN* 3.5 2.7 - - - -
14A LYS* 3.2 4.3 + - - -
15A GLY* 3.0 48.4 + - - +
17A ARG 2.7 28.3 + - - +
18A PRO* 3.6 2.8 - - - +
19A SER* 3.0 26.1 + - - +
11B CYS* 5.9 2.3 - - - -
71B CYS* 3.4 47.0 - - + +
72B THR* 5.9 0.7 - - - -
73B GLY 5.5 1.7 + - - -
74B ASN* 4.3 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASN 3.0 13.2 + - - +
8A MET 3.1 9.8 + - - +
10A GLN* 1.3 80.8 - - - +
12A ALA* 1.3 61.7 + - - +
14A LYS* 3.5 7.3 + - - -
69A TRP* 3.8 8.5 - - + -
71A CYS* 2.0 60.4 - - + -
74A ASN* 3.6 21.0 - - - +
76A PRO 3.6 20.9 - - - -
10B GLN* 5.8 2.5 - - - -
11B CYS* 6.5 0.7 - - - +
15B GLY* 5.8 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A MET 3.0 14.2 + - - +
9A ILE 4.0 2.2 - - - +
11A CYS* 1.3 77.3 - - - +
13A ASN* 1.3 59.7 + - - +
14A LYS* 3.3 6.4 + - - +
74A ASN* 3.5 15.8 - - - +
76A PRO* 3.9 14.1 - - + -
96A ALA 3.4 31.2 - - - +
97A LYS* 4.1 4.0 - - - +
100A ALA* 3.4 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 3.0 29.7 + - + +
10A GLN* 3.3 6.1 - - - +
12A ALA* 1.3 75.7 - - - +
14A LYS* 1.3 68.5 + - - +
15A GLY* 2.7 19.6 + - - -
16A SER* 2.9 31.5 + - - +
17A ARG* 3.0 36.8 + - - +
22A TYR* 4.2 7.8 + - - +
99A PHE* 5.8 0.4 - - + -
100A ALA* 4.0 19.3 - - + +
----------------------------------------------------------
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