Contacts of the strand formed by residues 17 - 23 (chain C) in PDB entry 2NVX
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 17 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C GLU 3.6 2.0 - - - +
13C ALA* 3.3 4.2 - - - -
14C SER* 2.9 44.5 + - - +
16C ASP* 1.3 93.3 - - - +
18C VAL* 1.3 63.9 + - - +
19C ASP 4.0 0.4 - - - -
231C ASN* 3.8 19.9 + - - +
232C VAL 3.5 2.9 - - - -
233C GLU* 3.5 23.5 + - - +
240C VAL* 3.7 1.8 - - - +
42J LYS* 4.6 16.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 4.2 14.8 - - + -
12C GLU 3.7 1.1 - - - +
13C ALA* 4.5 4.9 - - + -
17C ASN* 1.3 71.8 - - - +
19C ASP* 1.3 60.2 + - - +
20C PHE* 3.4 15.8 - - + -
231C ASN* 3.2 6.7 + - - -
232C VAL* 3.0 36.7 + - + +
240C VAL* 3.3 43.1 - - + +
241C ASP 4.5 0.9 - - - +
244C VAL* 4.6 4.5 - - + -
105K PHE* 4.0 23.6 - - + -
109K TRP* 4.1 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 3.5 2.9 - - - -
11C ARG* 2.7 78.5 + - - +
12C GLU* 2.7 36.3 + - + +
17C ASN* 4.0 0.4 - - + -
18C VAL* 1.3 71.3 - - - +
20C PHE* 1.3 55.4 + - - +
177C GLU* 5.6 0.9 - - - +
205C LYS* 5.6 1.0 - - - +
229C TYR 5.4 0.2 - - - -
230C MET 3.2 13.6 - - - +
231C ASN* 3.4 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C VAL* 3.9 15.0 - - + -
9C LYS 3.2 12.1 - - - +
10C ILE* 3.8 14.4 - - + -
11C ARG* 4.3 0.7 - - - +
18C VAL* 3.4 25.1 - - + -
19C ASP* 1.3 76.9 - - - +
21C ILE* 1.3 76.0 + - - +
22C LEU* 3.8 26.7 - - + -
33C LEU* 5.3 5.4 - - + -
37C MET* 5.3 0.7 - - + -
228C PHE 3.7 0.2 - - - +
229C TYR* 3.8 1.6 - - - -
230C MET* 3.0 58.2 + - + +
232C VAL* 3.9 22.2 - - + -
244C VAL* 4.5 8.3 - - + -
101K LEU* 6.2 0.4 - - + -
105K PHE* 3.9 25.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C GLN 3.5 0.4 - - - +
8C VAL* 3.3 10.0 - - - +
9C LYS* 2.9 50.9 + - + +
11C ARG* 3.6 31.4 - - + +
20C PHE* 1.3 76.5 - - - +
22C LEU* 1.3 63.2 + - - +
23C SER* 3.7 12.8 - - - +
209C TYR* 5.2 5.8 - - + -
227C THR* 3.6 30.3 - - + -
228C PHE 3.4 4.3 - - - +
229C TYR* 3.4 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C PRO* 4.4 10.5 - - + -
7C GLN 3.3 4.9 - - - +
8C VAL* 4.5 10.3 - - + -
20C PHE* 3.8 27.1 - - + -
21C ILE* 1.3 74.2 - - - +
23C SER* 1.3 64.9 + - - +
25C VAL* 3.4 44.2 - - + +
30C ALA* 5.3 4.5 - - + -
33C LEU* 3.9 24.5 - - + -
227C THR* 3.4 2.6 - - - -
228C PHE* 2.8 42.5 + - + +
230C MET* 3.9 13.5 - - + -
101K LEU* 4.5 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C PRO* 3.5 2.3 - - - +
7C GLN* 2.6 51.6 + - - +
9C LYS* 4.8 13.4 + - - +
21C ILE* 3.7 17.7 - - - +
22C LEU* 1.3 75.4 - - - +
24C ASN* 1.3 70.1 + - - +
25C VAL* 3.5 3.8 + - - +
227C THR* 4.2 16.2 + - - +
----------------------------------------------------------
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