Contacts of the strand formed by residues 1171 - 1181 (chain B) in PDB entry 1VDV
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 HIS1171 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B ARG* 2.8 19.2 + - - -
1162B VAL* 4.3 2.5 - - + -
1163B GLU 3.1 11.0 - - - +
1164B ILE* 3.8 15.7 - - + -
1169B GLY 4.6 2.8 + - - +
1170B ASP* 1.3 83.3 + - - +
1172B LYS* 1.3 65.0 + - - +
1173B ASN* 3.0 35.0 + - - -
1207B THR* 4.5 6.2 + - - -
1208B LEU* 4.4 23.3 - - + -
1270B VAL* 4.3 1.8 - - - +
1274B ILE* 3.7 32.4 - - + +
1300B ALA 5.3 0.4 - - - -
1302B PRO* 6.1 1.8 - - - +
1305B ILE* 4.2 11.0 - - + +
5008B GOL 3.0 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B ARG* 4.5 5.6 - - - +
549B PHE* 3.3 31.6 - - + -
550B GLN* 2.6 34.0 + - - +
551B LYS* 4.2 3.1 - - - +
552B HIS* 2.7 40.0 + - + +
1162B VAL* 3.2 10.6 - - - +
1163B GLU* 2.8 44.7 + - + +
1171B HIS* 1.3 74.4 - - - +
1173B ASN* 1.3 63.8 + - - +
1174B LEU* 3.5 15.0 - - + -
1237B THR* 6.0 1.3 - - - +
5008B GOL 3.5 24.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B ARG* 5.6 1.2 - - - +
1161B GLU 4.0 5.6 - - - +
1162B VAL* 3.6 2.5 - - + +
1171B HIS* 3.0 29.5 + - - -
1172B LYS* 1.3 70.7 - - - +
1174B LEU* 1.3 60.5 + - - +
1175B ARG 3.5 1.6 - - - -
1176B THR* 5.6 0.4 - - - +
1203B LEU* 3.7 21.8 - - - +
1208B LEU* 6.0 1.0 - - - +
1234B SER* 2.7 26.7 + - - +
1235B ILE 3.9 2.6 + - - +
1236B PRO* 3.1 20.8 - - + +
1237B THR* 2.9 28.3 + - - -
1270B VAL* 3.3 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B HIS* 3.8 33.0 - - + +
996B ARG* 3.5 40.4 - - - +
1161B GLU* 3.0 37.3 + - + +
1162B VAL 4.0 12.6 - - - -
1163B GLU* 4.0 9.9 - - + +
1172B LYS* 3.5 14.1 - - + -
1173B ASN* 1.3 72.8 - - - +
1175B ARG* 1.3 63.4 + - + +
1237B THR* 3.6 8.9 + - - +
1238B GLU* 3.0 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
974B SER 3.1 19.8 + - - -
975B SER* 3.7 5.2 + - - +
976B GLN* 4.8 12.1 - - - +
980B ARG* 3.5 39.8 + - - +
1159B CYS 3.9 0.6 - - - +
1160B SER* 3.2 3.8 - - - -
1161B GLU* 2.8 30.3 + - + +
1173B ASN* 3.5 1.4 - - - -
1174B LEU* 1.3 84.9 - - + +
1176B THR* 1.3 67.1 + - - +
1177B ASP* 2.8 37.7 + - - +
1236B PRO* 4.1 2.7 - - - -
1238B GLU* 3.2 42.1 + - + +
1240B ARG* 3.4 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1158B ALA* 5.0 0.7 - - + -
1159B CYS 3.1 6.1 - - - +
1160B SER* 2.7 22.7 + - - +
1173B ASN* 5.6 1.0 - - - +
1175B ARG* 1.3 75.1 + - - +
1177B ASP* 1.3 66.1 + - - +
1178B ILE* 3.7 21.5 - - + -
1199B PHE* 3.6 28.9 - - + -
1236B PRO* 3.6 22.6 - - - +
1238B GLU 2.9 7.9 + - - +
1239B PHE* 3.7 7.7 - - + -
1240B ARG* 2.9 26.9 + - - +
1270B VAL* 4.4 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
971B CYS* 3.6 11.0 - - - +
974B SER* 3.8 8.0 + - - +
975B SER* 3.4 27.4 + - - +
980B ARG* 3.2 14.2 + - - -
1158B ALA* 3.2 4.0 - - - +
1159B CYS 2.8 33.5 + - - +
1175B ARG* 2.8 45.4 + - - +
1176B THR* 1.3 74.1 - - - +
1178B ILE* 1.3 61.9 + - - +
1179B VAL* 6.2 0.2 - - + -
1240B ARG* 3.3 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1157B VAL 3.3 9.9 - - - +
1158B ALA* 3.8 8.3 - - + -
1176B THR* 3.7 15.0 - - + -
1177B ASP* 1.3 80.1 - - - +
1179B VAL* 1.3 71.7 + - - +
1180B MET* 4.4 3.8 - - + +
1195B VAL* 4.0 25.8 - - + -
1199B PHE* 3.5 39.7 - - + -
1239B PHE* 4.2 10.8 - - + -
1240B ARG 2.8 13.4 + - - +
1241B VAL* 3.5 7.4 - - + -
1242B SER* 2.7 33.6 + - - -
1263B PRO* 6.4 0.2 - - + -
1266B LEU* 3.9 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967B CYS* 3.8 31.2 - - + +
970B GLU* 3.8 30.1 - - + +
971B CYS* 3.5 35.4 - - + +
974B SER* 4.5 5.4 - - - +
1156B GLY* 3.2 2.8 - - - -
1157B VAL 2.9 32.7 + - - +
1178B ILE* 1.3 79.0 - - - +
1180B MET* 1.3 62.1 + - - +
1242B SER* 3.3 11.4 - - - +
1244B LEU* 4.1 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967B CYS* 4.6 0.4 - - - -
1003B THR* 4.6 2.7 - - + -
1154B THR* 3.9 16.2 - - + -
1155B TYR* 3.3 23.8 - - - +
1156B GLY* 3.8 4.3 - - - +
1178B ILE* 4.5 6.3 - - + -
1179B VAL* 1.3 75.1 - - - +
1181B ASP* 1.3 61.6 + - - +
1182B VAL* 3.5 16.2 + - + -
1195B VAL* 3.9 25.6 - - + -
1241B VAL* 5.7 0.2 - - + -
1242B SER 2.8 12.7 + - - +
1243B LEU* 3.3 12.1 - - + +
1244B LEU* 2.9 26.4 + - - -
1262B PRO* 3.9 7.4 - - + +
1263B PRO* 3.8 36.8 - - + -
1266B LEU* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963B SER* 2.7 32.6 + - - +
967B CYS* 4.0 10.4 - - - -
1154B THR* 3.4 22.2 - - - +
1155B TYR* 2.8 20.8 + - - +
1180B MET* 1.3 69.8 - - - +
1182B VAL* 1.3 58.5 + - - +
1183B GLY* 3.1 16.6 + - - -
1244B LEU* 4.0 9.6 - - + -
1247B CYS* 3.3 18.0 - - - +
1257B LYS* 2.7 32.0 + - - +
----------------------------------------------------------
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