Contacts of the helix formed by residues 2 - 15 (chain B) in PDB entry 3NAV
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 2 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B ALA 3.4 3.2 + - - -
1B MET* 1.3 78.3 - - - +
3B ARG* 1.3 64.3 + - - +
4B TYR* 2.9 11.0 + - - +
5B GLN* 2.7 57.8 + - - +
6B ALA* 3.1 19.3 + - - +
124B ASP* 5.8 0.2 - - - +
149B GLN* 3.6 43.7 - - - +
171B LYS* 5.1 5.3 - - - +
172B GLY 4.6 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 3 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ASN* 1.3 73.8 - - - +
4B TYR* 1.3 57.6 + - - +
6B ALA* 3.5 6.5 + - - +
7B LEU* 3.0 26.7 + - - +
89B ARG* 3.3 45.4 - - - +
93B PRO* 2.8 26.8 + - - +
94B GLU* 3.8 18.7 - - - +
95B THR 3.8 1.3 - - - -
96B PRO* 3.7 15.1 - - + +
122B GLY* 3.7 8.7 + - - -
123B VAL 5.3 0.4 + - - -
124B ASP* 2.8 45.8 + - - +
149B GLN* 4.9 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 4 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ASN* 2.9 6.3 + - - +
3B ARG* 1.3 77.2 - - - +
5B GLN* 1.3 60.5 + - + +
7B LEU* 3.3 9.6 + - + +
8B PHE* 2.9 44.0 + + + -
47B ALA* 4.3 9.2 - - + -
48B LEU 4.7 1.6 + - - -
96B PRO* 3.6 22.9 - - + -
97B ILE 3.8 0.5 - - - -
98B GLY* 3.4 19.4 + - - -
124B ASP* 3.6 17.3 - - + -
125B SER* 2.4 40.3 + - - -
149B GLN* 3.3 18.2 - - - -
172B GLY* 3.9 28.0 - - - +
173B TYR* 3.3 36.9 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 5 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B ALA 3.9 3.3 - - - +
1B MET* 3.2 29.3 - - + +
2B ASN* 2.7 57.8 + - - +
4B TYR* 1.3 73.6 - - + +
6B ALA* 1.3 62.3 + - - +
8B PHE* 3.3 7.0 + - + +
9B GLN* 3.1 23.6 + - - +
172B GLY* 6.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 6 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.7 26.2 - - + +
2B ASN 3.1 15.9 + - - +
3B ARG* 3.9 6.7 - - - +
5B GLN* 1.3 77.4 - - - +
7B LEU* 1.3 63.4 + - - +
9B GLN* 3.4 3.7 + - - +
10B ARG* 3.2 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ARG 3.0 15.5 + - - +
4B TYR* 3.4 16.4 - - + +
6B ALA* 1.3 73.3 - - - +
8B PHE* 1.3 65.7 + - + +
10B ARG* 3.1 44.4 + - - +
11B LEU* 2.8 50.9 + - + +
18B ALA* 5.1 4.7 - - + -
46B ASP* 3.5 40.8 - - + +
47B ALA* 4.5 5.8 - - + -
96B PRO* 3.9 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TYR* 2.9 43.3 + + + +
5B GLN* 3.3 5.8 + - - +
7B LEU* 1.3 79.2 - - + +
9B GLN* 1.3 56.4 + - - +
11B LEU* 3.9 13.7 - - + +
12B SER* 2.9 31.8 + - - -
18B ALA* 4.1 22.2 - - + -
172B GLY 3.4 22.7 - - - -
173B TYR* 4.2 17.0 - + + -
207B PRO* 3.8 35.4 - - + -
209B LEU* 4.5 8.7 - - + -
229B ALA* 4.2 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.6 31.5 - - - +
5B GLN 3.1 13.9 + - - +
6B ALA* 3.5 9.3 + - - +
7B LEU 3.1 0.2 - - - -
8B PHE* 1.3 76.8 - - - +
10B ARG* 1.3 61.5 + - + +
12B SER* 3.4 6.0 + - - -
13B ALA* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ALA 3.2 9.3 + - - +
7B LEU* 3.1 47.8 + - - +
9B GLN* 1.3 78.3 - - - +
11B LEU* 1.3 72.7 + - - +
13B ALA* 3.3 6.9 + - - +
14B ALA* 3.0 24.4 + - - +
46B ASP* 4.1 12.5 + - - +
94B GLU* 5.7 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 2.8 41.7 + - + +
8B PHE* 3.9 14.6 - - + +
10B ARG* 1.3 84.5 - - - +
12B SER* 1.3 63.6 + - - +
14B ALA* 3.1 4.6 + - + -
15B GLN 2.9 19.1 + - - -
16B GLN* 3.1 44.3 + - + +
17B GLY 4.0 2.2 - - - +
18B ALA* 3.7 35.9 - - + +
46B ASP* 3.7 19.5 - - - +
229B ALA 5.4 0.2 - - - +
263B LYS* 3.8 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE 2.9 19.4 + - - -
9B GLN* 3.6 6.5 - - - -
10B ARG 3.2 0.2 - - - -
11B LEU* 1.3 78.0 - - - +
13B ALA* 1.3 59.4 + - - +
15B GLN* 3.3 22.5 + - - +
16B GLN 4.8 2.0 - - - -
268B ILE* 6.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLN* 3.1 13.8 + - + +
10B ARG* 3.7 9.6 - - - +
11B LEU 3.3 0.2 - - - -
12B SER* 1.3 75.0 - - - +
14B ALA* 1.3 60.1 + - - +
15B GLN* 3.3 7.9 + - - +
----------------------------------------------------------
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 ARG 3.0 16.9 + - - +
11B LEU* 3.1 5.1 + - + +
13B ALA* 1.3 76.4 - - - +
15B GLN* 1.3 72.4 + - - +
16B GLN* 3.2 28.4 + - - +
267B LYS* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU 2.9 4.4 + - - -
12B SER 3.3 14.1 + - - +
13B ALA* 3.3 8.4 - - - +
14B ALA* 1.3 83.6 - - - +
16B GLN* 1.3 60.7 + - - +
267B LYS* 3.9 1.9 - - - +
268B ILE* 3.0 57.9 + - + +
----------------------------------------------------------
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