Contacts of the helix formed by residues 263 - 273 (chain B) in PDB entry 1PVS
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 TRP 263 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ILE* 4.7 21.8 - - + +
91B VAL* 4.6 20.1 - - + +
94B ALA* 3.8 29.2 - - + +
95B LEU* 4.3 9.2 - - + +
231B LYS* 3.1 44.0 - - + -
260B TRP 2.9 13.1 + - - +
261B LYS 5.1 0.2 - - - -
262B PRO* 1.3 113.3 - - + +
264B ARG* 1.3 64.3 + - - +
266B TYR* 3.1 34.3 + + + +
267B ALA* 3.1 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B LYS 3.2 1.0 + - - -
232B ASP* 2.8 57.8 + - - +
233B VAL 3.3 10.5 - - - +
234B PHE* 3.6 26.5 - - + +
254B ARG* 5.5 6.2 + - - +
257B ALA* 3.6 27.8 + - - +
258B GLU* 4.6 19.3 + - - +
260B TRP* 3.6 7.8 + - + -
261B LYS* 3.1 36.5 - - - +
263B TRP* 1.3 76.5 - - - +
265B SER* 1.3 56.6 + - - +
267B ALA* 3.1 7.6 + - - +
268B LEU* 2.8 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 4.2 9.9 - - - +
225B LEU* 3.8 13.9 - - - +
230B ALA 2.5 28.6 + - - -
231B LYS* 2.9 16.6 + - - -
233B VAL* 2.9 32.3 + - - +
264B ARG* 1.3 76.2 - - - +
266B TYR* 1.3 63.8 + - - +
268B LEU* 3.3 5.2 + - - +
269B LEU* 3.2 27.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
83B ASP* 2.7 28.5 + - - -
85B GLN* 3.4 10.2 + - - -
86B CYS* 3.6 18.7 - - - -
91B VAL* 3.9 36.6 - - + -
95B LEU* 4.0 7.2 - - + -
105B LEU* 4.5 12.1 - - + -
106B ARG* 4.4 4.3 - - - -
107B LEU* 3.9 18.2 - - + -
231B LYS* 3.2 44.1 - - + -
263B TRP* 3.1 27.2 + + + +
265B SER* 1.3 76.6 - - - +
267B ALA* 1.3 64.1 + - - +
269B LEU* 3.5 7.7 + - + +
270B HIS* 2.9 34.1 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 4.2 5.3 - - + +
98B LEU* 4.1 12.3 - - + +
234B PHE* 4.5 0.4 - - + -
260B TRP* 3.6 48.9 - - + -
263B TRP 3.1 6.1 + - - +
264B ARG* 3.1 11.9 + - - +
266B TYR* 1.3 74.5 - - - +
268B LEU* 1.3 66.8 + - - +
270B HIS* 3.2 4.9 + - - +
271B ILE* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LEU* 3.4 31.6 - - + -
233B VAL 4.3 2.0 - - - +
234B PHE* 3.6 16.8 - - + -
235B LEU* 3.7 41.5 - - + +
241B ILE* 3.5 33.7 - - + -
264B ARG 2.8 12.7 + - - +
265B SER 3.5 8.3 - - - +
267B ALA* 1.3 76.5 - - - +
269B LEU* 1.3 59.2 + - + +
271B ILE* 3.2 4.9 + - - +
272B TRP* 2.9 49.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TRP* 3.9 21.1 - - + -
18B PHE* 4.4 7.2 - - + -
105B LEU* 3.4 19.5 - - + -
106B ARG 3.2 26.0 - - - +
107B LEU* 3.6 32.5 - - + +
108B PRO* 3.8 7.2 - - + -
225B LEU* 5.6 3.1 - - + -
265B SER 3.2 10.4 + - - +
266B TYR* 3.7 10.3 - - + +
267B ALA 3.2 0.2 - - - -
268B LEU* 1.3 81.7 - - + +
270B HIS* 1.3 63.6 + - - +
272B TRP* 3.1 26.6 + - + +
273B TYR* 3.0 25.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B VAL* 5.6 0.9 - - + -
92B ASN* 4.5 6.6 + - - -
95B LEU* 4.1 17.9 - - + +
98B LEU* 3.1 39.0 - - + +
99B GLY* 3.8 10.4 + - - -
101B ALA* 4.9 2.7 - - + -
102B ARG* 2.9 39.0 + - + +
103B PRO 5.7 0.7 - - - -
105B LEU* 3.9 32.6 - - + +
266B TYR* 2.9 26.6 + + + +
267B ALA 3.2 7.6 + - - +
269B LEU* 1.3 77.9 - - - +
271B ILE* 1.3 60.9 + - - +
273B TYR* 3.3 2.2 + - - +
274B THR* 2.7 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 4.1 17.5 - - + -
234B PHE* 3.7 16.2 - - + -
241B ILE* 4.2 11.9 - - + -
244B ARG* 2.9 50.0 + - + -
245B PHE* 4.3 7.4 - - + -
260B TRP* 3.3 41.5 - - + -
267B ALA 3.0 15.7 + - - +
268B LEU* 3.6 6.3 - - - +
270B HIS* 1.3 75.1 - - - +
272B TRP* 1.3 61.0 + - - +
273B TYR 3.3 0.5 + - - -
274B THR* 3.3 8.4 + - - +
277B TRP* 4.0 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B PHE* 4.6 12.3 - + - -
22B ARG* 4.5 15.3 - - - -
218B TRP* 5.4 2.2 - + - -
222B TYR* 4.0 31.0 - + - -
225B LEU* 6.4 0.7 - - + -
235B LEU* 4.0 13.9 - - + -
238B ASP* 2.9 42.3 + - - -
240B LEU* 3.5 35.4 - - + +
241B ILE* 3.5 26.1 - - + +
244B ARG* 3.4 18.5 + - + +
268B LEU* 2.9 24.1 + - + +
269B LEU* 3.3 28.3 - - + +
271B ILE* 1.3 79.2 - - - +
273B TYR* 1.3 71.4 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TRP* 3.0 50.5 - + - +
17B GLY 5.4 0.8 - - - -
18B PHE* 3.3 33.8 - + + -
22B ARG* 3.9 12.6 + - - -
102B ARG* 3.3 40.1 + - - +
105B LEU* 4.7 1.1 - - + -
269B LEU* 3.0 20.6 + - + +
270B HIS 3.3 0.9 + - - +
271B ILE 3.2 0.2 - - - -
272B TRP* 1.3 94.3 - + + +
274B THR* 1.4 61.4 + - - +
275B GLU 3.8 3.0 + - - -
----------------------------------------------------------
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