Contacts of the strand formed by residues 1171 - 1181 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427A ARG* 2.8 20.8 + - - -
1162A VAL* 4.2 3.4 - - + -
1163A GLU 3.0 10.1 - - - +
1164A ILE* 3.8 14.8 - - + -
1169A GLY 4.7 2.4 + - - +
1170A ASP* 1.3 83.0 + - - +
1172A LYS* 1.3 67.0 + - - +
1173A ASN* 2.9 34.3 + - - -
1207A THR* 4.5 16.8 - - - -
1208A LEU* 5.0 12.6 - - + -
1270A VAL* 4.2 2.0 - - - +
1274A ILE* 3.7 33.2 - - + +
1300A ALA 5.4 0.4 - - - -
1302A PRO* 6.1 2.2 - - + +
1305A ILE* 4.3 8.8 - - + +
5001A GOL 3.0 11.0 - - - -
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Residues in contact with LYS1172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A ARG* 4.5 5.6 - - - +
549A PHE* 3.5 30.7 - - + -
550A GLN* 2.8 34.8 + - - +
551A LYS 5.2 1.0 - - - -
552A HIS* 5.3 8.3 - - + +
1162A VAL* 3.1 11.1 - - - +
1163A GLU* 2.7 47.4 + - + +
1171A HIS* 1.3 76.5 - - - +
1173A ASN* 1.3 60.8 + - - +
1174A LEU* 3.4 26.1 + - + +
1237A THR* 6.0 2.2 - - - +
5001A GOL 3.2 24.4 + - - -
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Residues in contact with ASN1173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A ARG* 5.6 1.6 - - - +
1161A GLU 4.0 4.9 - - - -
1162A VAL* 3.9 2.1 - - + +
1171A HIS* 2.9 30.1 + - - -
1172A LYS* 1.3 72.0 - - - +
1174A LEU* 1.3 58.4 + - - +
1175A ARG 3.6 2.2 - - - -
1176A THR* 5.6 0.9 - - - +
1203A LEU* 3.8 17.6 - - - +
1207A THR* 5.7 0.4 + - - -
1234A SER* 2.6 29.4 + - - +
1235A ILE 4.0 2.5 + - - +
1236A PRO* 3.2 19.6 - - + +
1237A THR* 3.0 27.4 + - - -
1270A VAL* 3.3 23.8 - - + +
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Residues in contact with LEU1174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A HIS* 6.0 9.6 - - + -
996A ARG* 3.6 38.1 - - - +
1161A GLU* 2.9 42.3 + - + +
1162A VAL 3.9 18.4 - - - +
1163A GLU* 4.1 5.4 - - + +
1172A LYS* 3.4 28.9 + - + +
1173A ASN* 1.3 72.8 - - - +
1175A ARG* 1.3 64.3 + - + +
1237A THR* 3.6 11.2 + - - +
1238A GLU* 3.1 22.7 + - - +
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Residues in contact with ARG1175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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974A SER 3.2 12.5 + - - -
975A SER* 3.7 5.0 + - - +
976A GLN* 4.5 11.5 + - - -
980A ARG* 3.5 42.6 + - - +
1159A CYS 3.8 0.8 - - - +
1160A SER* 3.2 2.9 - - - -
1161A GLU* 2.8 34.6 + - + +
1173A ASN 3.6 1.0 - - - -
1174A LEU* 1.3 86.0 - - + +
1176A THR* 1.3 69.4 + - - +
1177A ASP* 2.7 34.0 + - - +
1236A PRO* 4.2 2.0 - - - -
1238A GLU* 2.9 47.1 + - + +
1240A ARG* 2.9 32.9 - - + +
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Residues in contact with THR1176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1158A ALA* 4.9 1.1 - - + -
1159A CYS 3.2 6.7 - - - +
1160A SER* 2.8 22.1 + - - +
1173A ASN* 5.6 0.7 - - - +
1175A ARG* 1.3 76.4 + - - +
1177A ASP* 1.3 67.7 - - - +
1178A ILE* 3.7 22.7 - - + -
1199A PHE* 3.5 31.4 - - + -
1236A PRO* 3.7 22.1 - - - +
1238A GLU 3.0 9.0 + - - +
1239A PHE* 3.8 3.7 - - + -
1240A ARG* 3.0 25.8 + - - +
1270A VAL* 4.4 3.1 - - - +
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Residues in contact with ASP1177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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971A CYS* 3.5 9.8 - - - -
974A SER* 3.9 8.9 + - - +
975A SER* 3.5 28.3 + - - +
980A ARG* 3.4 13.5 + - - -
1158A ALA* 3.2 4.0 - - - +
1159A CYS 2.9 32.2 + - - +
1175A ARG* 2.7 45.6 + - - +
1176A THR* 1.3 75.4 - - - +
1178A ILE* 1.3 61.0 + - - +
1179A VAL* 6.2 0.2 - - + -
1240A ARG* 3.2 22.7 - - + +
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Residues in contact with ILE1178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1157A VAL 3.4 8.5 - - - +
1158A ALA* 3.9 8.5 - - + -
1176A THR* 3.7 11.0 - - + -
1177A ASP* 1.3 78.1 - - - +
1179A VAL* 1.3 75.7 + - - +
1180A MET* 4.3 3.8 - - + +
1195A VAL* 4.0 29.4 - - + -
1199A PHE* 3.7 33.7 - - + -
1239A PHE* 4.0 18.2 - - + -
1240A ARG 2.9 13.5 + - - +
1241A VAL* 3.6 8.1 - - + -
1242A SER* 2.8 28.6 + - - -
1266A LEU* 4.0 18.2 - - + -
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Residues in contact with VAL1179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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967A CYS* 3.6 35.9 - - + +
970A GLU* 4.1 21.3 - - + +
971A CYS* 3.6 33.7 - - + +
974A SER* 4.5 7.0 - - - +
1156A GLY* 3.2 2.4 - - - -
1157A VAL 2.8 35.1 + - - +
1177A ASP* 6.2 0.4 - - + -
1178A ILE* 1.3 78.7 - - - +
1180A MET* 1.3 61.7 + - - +
1242A SER* 3.4 16.6 - - - +
1244A LEU* 4.3 9.6 - - + +
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Residues in contact with MET1180 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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967A CYS* 4.5 0.4 - - - -
1003A THR* 4.7 2.0 - - + -
1154A THR* 3.9 5.6 - - + -
1155A TYR* 3.3 25.1 - - - +
1156A GLY* 3.8 3.6 - - - +
1178A ILE* 4.5 7.0 - - + -
1179A VAL* 1.3 74.9 - - - +
1181A ASP* 1.3 60.6 + - - +
1182A VAL* 3.6 13.8 + - + -
1195A VAL* 4.0 24.9 - - + -
1241A VAL* 5.7 0.4 - - + -
1242A SER 2.9 11.0 + - - +
1243A LEU* 3.4 10.5 - - + +
1244A LEU* 2.8 29.2 + - - -
1262A PRO* 3.9 23.8 - - + +
1263A PRO* 3.9 30.3 - - + -
1266A LEU* 3.7 26.2 - - + -
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Residues in contact with ASP1181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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961A GLY 4.9 0.2 - - - +
963A SER* 2.7 29.8 + - - +
967A CYS* 4.0 3.5 - - - -
1154A THR* 3.5 21.3 - - - +
1155A TYR* 2.8 19.9 + - - +
1180A MET* 1.3 71.6 - - - +
1182A VAL* 1.3 59.0 + - - +
1183A GLY* 3.0 16.5 + - - -
1244A LEU* 3.8 19.5 - - + -
1247A CYS* 3.1 17.2 - - - +
1257A LYS* 2.6 33.2 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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