Contacts of the helix formed by residues 7 - 18 (chain B) in PDB entry 6BJV
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 7 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ARG 3.6 14.8 - - - -
4B ALA 3.2 8.7 + - - -
5B ILE 2.9 6.9 + - - -
6B GLN* 1.3 79.9 - - - +
8B ASN* 1.3 60.3 + - - -
9B ASP* 3.0 9.6 - - - -
10B THR* 2.5 30.0 + - - -
11B ARG* 3.3 5.5 + - - +
67B LYS* 4.7 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLN 3.8 1.6 + - - -
7B GLY* 1.3 72.1 - - - -
9B ASP* 1.3 74.9 + - - +
10B THR 3.1 1.0 + - - -
11B ARG* 3.9 17.9 - - + +
12B GLU* 3.0 37.0 + - + +
67B LYS* 4.7 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ALA 5.9 0.7 - - - +
7B GLY* 3.0 4.0 - - - -
8B ASN* 1.3 91.0 - - - +
10B THR* 1.3 61.9 + - + +
12B GLU* 4.5 5.1 - - - +
13B GLN* 3.7 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ALA 3.7 20.0 - - - +
5B ILE* 5.1 2.0 - - - -
6B GLN 3.8 8.7 + - - +
7B GLY 2.5 29.3 + - - +
9B ASP* 1.3 85.4 - - + +
11B ARG* 1.3 57.0 + - - -
12B GLU 3.3 1.6 - - - -
13B GLN* 3.2 13.8 + - - +
14B ALA* 2.9 26.4 + - - +
26B ILE* 4.3 3.2 - - - +
68B VAL* 3.9 11.2 - - - +
102B PHE* 4.9 16.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLY 3.3 3.0 + - - +
8B ASN* 3.7 24.5 - - - +
10B THR* 1.3 78.7 + - - +
12B GLU* 1.3 68.0 + - + +
14B ALA* 3.0 9.4 + - - +
15B ASN* 2.7 37.4 + - - +
67B LYS* 2.9 42.0 + - + +
68B VAL* 4.1 6.0 - - + +
69B VAL* 4.7 7.8 - - - +
9D G 3.6 35.6 + - - -
10D A 2.6 32.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASN* 3.0 26.4 + - + +
9B ASP* 4.6 5.4 - - - +
10B THR 3.3 0.6 - - - -
11B ARG* 1.3 85.1 - - + +
13B GLN* 1.3 58.4 + - + +
15B ASN* 3.4 9.7 + - - +
16B GLY* 2.9 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ASP 3.7 17.2 - - - +
10B THR* 3.2 15.3 + - - +
11B ARG 3.2 0.4 - - - -
12B GLU* 1.3 76.4 - - + +
14B ALA* 1.3 55.4 + - - +
16B GLY* 3.6 1.7 - - - -
17B GLU* 2.7 35.0 + - - +
25B GLY* 6.1 2.2 - - - -
26B ILE* 3.3 35.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B THR 2.9 14.0 + - - +
11B ARG* 3.0 8.3 + - - +
13B GLN* 1.3 73.7 - - - +
15B ASN* 1.3 65.4 + - - +
17B GLU* 3.3 13.9 + - - +
18B ARG* 3.9 3.5 + - - +
26B ILE* 3.4 9.1 - - + +
68B VAL* 3.7 23.8 - - + -
69B VAL 3.4 21.9 - - - +
70B PHE* 3.8 23.9 - - + -
71B LYS 5.0 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ARG* 2.7 19.4 + - - +
12B GLU* 3.7 12.1 - - - +
14B ALA* 1.3 75.8 - - - +
16B GLY* 1.3 62.4 + - - +
17B GLU 3.4 0.2 + - - -
18B ARG* 3.5 18.0 + - - +
19B TRP* 3.8 15.8 + - - -
69B VAL 3.8 6.8 + - - +
70B PHE* 5.9 0.2 - - - +
71B LYS* 4.9 18.9 - - - +
3C G 4.4 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLU 2.9 16.9 + - - -
13B GLN* 3.6 2.5 - - - -
15B ASN* 1.3 74.4 + - - +
17B GLU* 1.3 64.5 + - - +
18B ARG 3.1 2.9 - - - -
19B TRP* 2.9 29.8 + - - +
20B ASP* 3.6 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLN 2.7 22.2 + - - +
14B ALA* 3.4 12.9 - - - +
15B ASN 3.2 0.8 - - - -
16B GLY* 1.3 74.5 - - - +
18B ARG* 1.3 62.4 + - - +
19B TRP 3.2 0.5 + - - -
20B ASP* 3.4 22.3 + - - +
23B SER* 5.7 0.5 - - - -
24B GLY* 4.6 17.3 + - - -
25B GLY 6.1 0.2 - - - +
26B ILE* 4.1 20.6 - - + +
28B SER* 3.1 29.4 + - - -
70B PHE* 3.9 8.5 - - + +
71B LYS 5.5 0.2 + - - -
72B ARG* 2.8 44.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ALA 3.9 2.0 + - - +
15B ASN* 3.5 13.7 + - - +
16B GLY 3.1 0.2 - - - -
17B GLU* 1.3 81.2 + - - +
19B TRP* 1.3 91.6 + - + +
20B ASP 3.0 11.1 + - - +
34B ASP* 3.1 38.0 + - + +
36B SER* 4.1 3.4 - - - -
60B LYS* 3.8 14.8 - - - +
71B LYS* 3.5 46.5 + - + +
72B ARG* 3.6 12.3 + - - +
73B TYR* 3.7 27.0 - - - +
1C U 3.8 1.6 - - - +
2C C 2.7 38.2 + - - -
3C G 4.6 6.6 + - - -
----------------------------------------------------------
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