Contacts of the strand formed by residues 265 - 272 (chain S) in PDB entry 6NZO
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 CYS 265 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206S ILE* 4.3 13.7 - - - -
263S PRO* 3.5 12.5 - - - +
264S ASN* 1.3 88.4 + - - +
266S TYR* 1.3 69.2 + - - +
280S ILE* 5.0 5.6 - - + -
281S PHE 3.2 20.9 - - - +
282S ALA* 3.9 15.7 - - - +
292S LEU* 3.6 35.9 - - + -
293S VAL 4.2 0.4 + - - -
294S PHE* 3.3 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 266 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E HIS* 4.1 19.7 - - + +
42E ARG* 4.9 17.5 - - + +
203S ASN* 4.1 11.6 + - - -
263S PRO* 5.8 0.7 - - + -
265S CYS* 1.3 78.7 - - - +
267S VAL* 1.3 71.3 + - - +
268S ASP* 4.3 21.1 - - + -
280S ILE* 3.1 9.0 - - - +
281S PHE* 2.9 68.1 + + + +
282S ALA 3.4 22.6 + - - -
283S ALA* 3.7 20.9 - - + -
294S PHE* 4.1 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 267 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E PRO* 3.8 25.1 - - + -
39E HIS* 3.4 34.3 + - - +
209S TYR* 5.6 2.5 - - + -
237S MET* 5.3 5.8 - - + -
266S TYR* 1.3 79.3 - - - +
268S ASP* 1.3 64.7 + - - +
278S MET* 3.7 33.2 - - + -
279S GLY 3.3 16.8 - - - +
280S ILE* 3.7 17.5 - - + -
294S PHE* 5.0 15.0 - - + -
295S ASN 5.2 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 268 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E HIS* 4.8 3.5 - - - +
40E ARG 3.7 22.4 - - - +
41E TYR* 3.9 8.3 - - - -
42E ARG* 4.6 13.7 + - - +
155S LYS* 3.4 28.9 - - - -
266S TYR* 4.3 22.4 - - + -
267S VAL* 1.3 75.4 - - - +
269S LYS* 1.3 84.3 + - - +
270S TRP* 3.6 14.4 - - - +
278S MET* 3.8 1.7 - - - -
279S GLY 2.9 32.3 + - - +
281S PHE* 5.2 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 269 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E PRO* 4.3 12.8 + - + +
39E HIS 2.4 37.6 + - - +
40E ARG* 3.5 14.1 - - - +
41E TYR* 3.2 46.5 - - + +
84J G 5.6 1.1 - - - -
155S LYS* 3.7 3.8 - - - +
239S LEU 4.0 19.0 + - - +
268S ASP* 1.3 82.2 + - - +
270S TRP* 1.3 67.4 + - - +
276S LEU* 3.7 21.8 - - + -
277S ARG 3.4 7.6 - - - +
278S MET* 3.8 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 270 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E TYR* 4.6 1.1 - - - -
152S ARG* 3.9 24.7 - - + -
155S LYS* 3.5 47.7 - - + +
156S ILE 3.9 1.8 - - - -
157S GLU* 3.5 33.7 - - + +
171S ASN* 3.7 20.9 - - - -
173S ARG* 3.5 18.4 - - - -
174S PHE* 4.4 16.6 - + + -
268S ASP* 3.6 16.9 + - - +
269S LYS* 1.3 85.3 - - - +
271S VAL* 1.3 64.4 + - - +
276S LEU* 3.3 8.4 - - - +
277S ARG* 2.9 31.2 + - - +
279S GLY* 5.1 3.1 - - - -
281S PHE* 3.3 40.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 271 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E TYR* 4.7 1.1 - - - +
49E ARG* 4.0 19.7 - - - +
122S SER* 3.6 32.3 - - - +
124S HIS* 5.5 13.7 - - + +
155S LYS 3.3 16.2 + - - +
156S ILE* 3.8 24.9 - - + -
157S GLU* 3.2 27.4 + - - +
270S TRP* 1.3 79.7 - - - +
272S VAL* 1.3 61.2 + - - +
274S ASP* 5.8 1.8 - - - -
275S LYS 3.5 3.4 - - - +
276S LEU* 4.4 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 272 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157S GLU* 3.3 21.1 - - + +
174S PHE* 3.8 15.9 - - + -
175S GLN* 3.4 37.2 - - + +
271S VAL* 1.3 75.6 - - - +
273S GLY* 1.3 63.2 + - - +
274S ASP 3.3 0.6 - - - +
275S LYS* 2.9 34.9 + - - +
277S ARG* 3.5 49.0 + - + +
----------------------------------------------------------
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