Contacts of the strand formed by residues 263 - 271 (chain B) in PDB entry 2P82
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 263 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B GLY* 3.3 16.8 - - - -
260B LYS* 2.9 27.7 + - + +
261B PRO 3.1 20.8 + - - -
262B ASN* 1.3 85.7 - - - +
264B ALA* 1.3 62.3 + - - +
265B TYR* 3.6 26.3 + - + +
281B HIS* 3.7 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B CYS* 3.4 11.0 - - - +
78B MET* 3.6 49.1 - - + +
81B CYS* 3.5 5.1 - - - -
145B TRP* 4.1 5.2 - - + +
258B GLY 3.2 12.3 - - - +
259B GLY* 4.2 1.6 - - - -
260B LYS 3.8 0.9 + - - -
263B ASN* 1.3 75.2 - - - +
265B TYR* 1.3 60.8 - - - +
280B PRO* 3.4 9.4 - - - +
281B HIS* 3.2 18.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B CYS* 3.3 9.7 - - - +
256B ALA 3.9 0.9 - - - +
257B LEU* 4.0 1.9 - - - -
258B GLY 2.9 27.7 + - - +
259B GLY* 4.9 3.4 - - - -
263B ASN* 3.6 34.9 + - + +
264B ALA* 1.3 78.5 - - - +
266B TYR* 1.3 61.2 + - - +
267B PHE* 3.7 28.8 - + + -
277B PHE* 3.6 40.2 - + + -
278B LEU 3.9 1.1 - - - -
279B ASP* 3.3 33.5 + - - -
281B HIS* 3.6 11.8 + + - -
309B MET* 4.5 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 4.0 4.7 - - + +
52B ARG* 5.8 2.5 - - + -
53B LEU 5.7 0.7 - - - -
81B CYS* 3.5 16.0 - - + -
84B MET* 3.5 43.3 - - + -
85B MET* 3.7 29.3 - - + -
88B GLN* 3.7 19.4 - - + +
254B LEU* 2.6 32.4 + - - -
256B ALA 3.6 7.9 - - - -
257B LEU* 4.4 3.8 - - + -
265B TYR* 1.3 71.9 - - - +
267B PHE* 1.3 68.6 + - - +
268B ILE* 3.4 25.9 + - + +
277B PHE* 3.1 3.6 - - - -
278B LEU* 2.8 54.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B PHE* 5.6 0.2 - + - -
248B PHE* 3.4 19.5 - - + -
255B GLY* 3.2 6.2 - - - -
256B ALA* 2.9 48.3 + - + +
257B LEU 4.5 0.7 - - - -
258B GLY* 3.8 17.3 - - - -
265B TYR* 3.7 26.9 - + + -
266B TYR* 1.3 71.2 - - - +
268B ILE* 1.3 61.6 + - - +
269B GLY 3.7 0.7 - - - -
275B LEU* 3.8 28.5 - - + -
276B ILE 3.5 3.8 - - - +
277B PHE* 3.7 22.0 - + + -
309B MET* 3.9 24.5 - - + -
314B LEU* 3.1 40.6 - - + -
318B VAL* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ILE* 3.4 11.6 - - + -
32B LEU* 2.8 50.7 + - + +
49B ILE* 4.0 38.1 - - + -
52B ARG* 4.7 6.7 - - + -
248B PHE* 3.7 7.0 - - - -
266B TYR* 3.4 44.2 - - + +
267B PHE* 1.3 73.9 - - - +
269B GLY* 1.3 59.1 + - - +
276B ILE* 2.8 28.5 + - + +
277B PHE* 4.5 3.4 - - - -
278B LEU* 4.2 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TRP 3.0 15.5 - - - -
31B ILE* 4.2 2.9 - - - -
248B PHE* 3.6 19.1 - - - -
267B PHE 3.7 0.4 - - - -
268B ILE* 1.3 82.0 + - - +
270B PHE* 1.3 61.5 + - - +
275B LEU* 3.4 8.3 - - - +
276B ILE* 2.8 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU 4.5 2.4 - - - +
29B VAL* 3.6 4.0 - - - +
30B TRP* 3.0 48.3 + + + -
245B LYS* 3.2 58.6 - - + -
248B PHE* 4.0 13.9 - + + -
249B LYS* 3.9 26.9 - - + -
269B GLY* 1.3 74.2 - - - +
271B LEU* 1.3 61.8 + - - +
272B GLY* 3.6 23.8 - - - +
274B GLU 3.2 14.4 - - - +
275B LEU* 3.9 14.4 - - + -
276B ILE* 4.0 7.7 - - - +
311B ILE* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLU* 3.4 36.3 - - + +
28B LEU 4.6 5.8 - - - +
29B VAL* 3.8 26.9 - - + -
38B LEU* 3.8 23.6 - - + -
45B LEU* 5.8 0.2 - - + -
270B PHE* 1.3 74.7 - - - +
272B GLY* 1.3 67.1 + - - +
273B ASP 3.1 0.3 + - - -
274B GLU* 2.9 30.8 + - + +
276B ILE* 4.3 7.3 - - + +
308B ARG* 3.5 39.0 - - - +
----------------------------------------------------------
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