Contacts of the strand formed by residues 1152 - 1165 (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 TYR1152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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957B GLN* 5.1 1.1 - - - +
960B GLU 6.0 2.2 - - - +
1007B ILE* 2.9 49.6 + - + +
1084B ASP* 2.5 31.4 + - - -
1150B PHE* 3.3 3.9 - - - +
1151B HIS* 1.3 104.1 - + + +
1153B PHE* 1.3 86.4 + - - +
1154B THR* 3.9 5.6 - - - -
1249B ASN* 3.7 27.5 + - - +
1251B LYS* 4.2 9.4 - - + -
1252B ALA* 4.3 2.4 - - + +
1257B LYS* 3.6 25.3 - - + +
1258B ALA* 2.9 22.7 + - - +
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Residues in contact with PHE1153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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883B PHE 5.8 0.2 - - - -
884B HIS* 5.4 1.1 - - - -
953B THR* 4.6 1.3 - - + -
955B PHE* 3.9 17.3 - + - -
957B GLN* 3.7 26.2 - - + -
958B ARG 4.8 3.1 - - - -
959B LEU* 3.8 19.7 - - + -
960B GLU 5.9 2.8 + - - -
1004B LYS* 3.7 28.7 - - + -
1005B PHE 3.3 7.6 - - - +
1006B GLY* 3.6 19.1 - - - -
1150B PHE* 3.7 29.4 - + - -
1152B TYR* 1.3 86.9 - - - +
1154B THR* 1.3 63.3 + - - +
1155B TYR* 3.4 36.0 + - + +
1257B LYS* 2.9 23.9 + - - -
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Residues in contact with THR1154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003B THR* 4.6 0.7 - - - +
1004B LYS* 3.4 3.3 - - - -
1005B PHE* 3.0 32.7 + - - +
1007B ILE* 3.6 13.9 - - - +
1152B TYR* 3.9 8.0 - - - -
1153B PHE* 1.3 74.0 - - - +
1155B TYR* 1.3 62.0 + - - +
1180B MET* 3.9 10.9 - - + +
1181B ASP 3.4 19.3 - - - +
1182B VAL* 5.0 4.3 - - + -
1257B LYS* 4.1 3.8 - - - +
1258B ALA 2.8 28.9 + - - +
1259B VAL* 5.1 0.7 - - - -
1262B PRO* 3.6 30.8 - - + +
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Residues in contact with TYR1155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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959B LEU* 3.9 10.0 - - - +
960B GLU 4.4 7.4 + - - -
961B GLY 3.5 19.4 + - - -
962B PHE* 3.4 35.8 - + - +
963B SER* 3.3 27.4 - - - +
964B VAL* 3.3 28.9 - - + +
967B CYS* 4.6 0.9 - - - -
1003B THR 3.4 6.5 - - - +
1004B LYS* 3.4 30.3 - - + -
1153B PHE* 3.4 39.8 + - + +
1154B THR* 1.3 75.3 - - - +
1156B GLY* 1.3 59.4 + - - +
1180B MET* 3.3 12.3 - - - +
1181B ASP* 2.8 36.6 + - + +
1257B LYS* 4.1 1.1 - - - -
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Residues in contact with GLY1156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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964B VAL* 5.3 1.3 - - - +
967B CYS* 4.4 4.4 - - - +
1002B PRO* 3.4 0.7 - - - +
1003B THR* 2.9 32.4 + - - +
1155B TYR* 1.3 78.5 - - - +
1157B VAL* 1.3 67.4 + - - +
1179B VAL 3.2 12.6 - - - -
1180B MET* 3.8 15.8 - - - +
1266B LEU* 3.8 7.1 - - - +
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Residues in contact with VAL1157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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964B VAL* 4.1 7.0 - - + +
967B CYS* 3.6 28.0 - - + +
968B TRP* 3.6 21.3 - - + +
971B CYS* 3.8 15.8 - - + -
1000B ILE* 3.7 25.8 - - + -
1001B ILE 3.3 11.2 - - - +
1002B PRO* 4.0 15.7 - - + -
1156B GLY* 1.3 81.5 - - - +
1158B ALA* 1.3 66.1 + - - +
1177B ASP 3.9 0.2 - - - +
1178B ILE* 3.3 5.0 - - - +
1179B VAL 2.9 31.5 + - - +
1266B LEU* 4.0 2.2 - - - +
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Residues in contact with ALA1158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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971B CYS* 4.3 0.2 - - - -
1000B ILE* 3.4 3.2 - - - -
1001B ILE 2.8 38.7 + - - -
1157B VAL* 1.3 77.3 - - - +
1159B CYS* 1.3 60.4 + - - +
1176B THR* 5.0 0.7 - - + -
1177B ASP 3.2 4.7 - - - -
1178B ILE* 3.8 17.5 - - + -
1199B PHE* 4.5 2.7 - - + -
1266B LEU* 3.7 38.4 - - + +
1269B SER* 3.6 11.1 - - - +
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Residues in contact with CYS1159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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971B CYS* 3.9 17.7 - - - -
975B SER* 3.9 20.6 - - - +
977B TYR* 3.9 16.6 - - - -
980B ARG* 3.9 10.0 + - - -
998B LEU* 3.6 26.7 - - - -
999B CYS 3.4 8.1 - - - -
1000B ILE* 4.0 9.0 - - + +
1158B ALA* 1.3 71.9 - - - +
1160B SER* 1.3 63.7 + - - +
1175B ARG 3.9 0.5 - - - +
1176B THR* 3.1 3.8 - - - -
1177B ASP* 2.8 37.2 + - - +
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Residues in contact with SER1160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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980B ARG* 5.3 0.4 - - - -
998B LEU* 3.5 5.2 - - - +
999B CYS 3.1 30.3 + - - +
1159B CYS* 1.3 75.3 - - - +
1161B GLU* 1.3 61.8 + - - +
1162B VAL* 5.2 0.4 - - - -
1175B ARG 3.2 4.9 - - - -
1176B THR* 2.7 27.0 + - - +
1199B PHE* 3.9 0.2 - - - -
1269B SER* 2.7 34.7 + - - -
1270B VAL* 3.7 20.0 - - - +
1273B ALA* 3.5 7.4 - - - +
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Residues in contact with GLU1161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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980B ARG* 3.0 41.2 + - - +
983B GLU* 3.2 28.5 - - - +
984B VAL* 3.8 12.8 - - + +
996B ARG* 3.6 6.1 + - - -
997B GLY 3.2 17.5 - - - +
998B LEU* 3.8 8.3 - - + -
1160B SER* 1.3 74.6 - - - +
1162B VAL* 1.3 69.2 + - - +
1173B ASN* 3.8 1.2 - - - -
1174B LEU* 3.0 46.1 + - + +
1175B ARG* 2.8 16.6 + - - +
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Residues in contact with VAL1162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996B ARG* 3.1 8.1 - - - +
997B GLY 2.9 32.6 + - - +
1160B SER* 5.2 0.2 - - - -
1161B GLU* 1.3 81.7 - - - +
1163B GLU* 1.3 61.3 + - - +
1164B ILE* 4.5 8.7 - - + -
1171B HIS* 4.3 4.9 - - + -
1172B LYS 3.2 10.8 - - - +
1173B ASN* 3.6 23.1 - - - +
1174B LEU* 4.0 7.1 - - - +
1270B VAL* 3.9 20.4 - - + +
1273B ALA* 3.8 18.2 - - + +
1274B ILE* 3.8 33.9 - - + +
1277B ALA* 4.5 0.7 - - + -
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Residues in contact with GLU1163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987B PHE* 3.1 20.0 - - + -
994B LYS* 3.8 12.7 - - + -
995B LYS 3.3 9.6 - - - +
996B ARG* 2.9 44.7 + - + +
1162B VAL* 1.3 75.8 - - - +
1164B ILE* 1.3 69.9 + - - +
1171B HIS* 3.1 3.0 - - - -
1172B LYS* 2.8 53.6 + - + +
1174B LEU* 4.0 10.0 - - + +
5008B GOL 2.9 25.7 + - - +
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Residues in contact with ILE1164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994B LYS* 3.4 9.7 - - - +
995B LYS 2.8 36.9 + - - +
1162B VAL* 4.5 5.8 - - + -
1163B GLU* 1.3 79.3 - - - +
1165B ASP* 1.3 58.1 + - - +
1166B CYS* 4.2 9.4 - - - +
1170B ASP 3.6 6.7 - - - +
1171B HIS* 3.9 13.5 - - + -
1274B ILE* 4.3 19.1 - - + -
1277B ALA* 3.7 41.5 - - + +
1278B ILE* 3.8 16.4 - - + +
1305B ILE* 4.4 11.7 - - + -
1309B CYS* 4.1 17.5 - - - -
5008B GOL 4.6 1.6 - - - -
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Residues in contact with ASP1165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518B LYS* 4.9 6.6 + - - -
993B TRP 4.0 5.2 - - - +
994B LYS* 3.4 23.7 + - - -
1164B ILE* 1.3 74.1 - - - +
1166B CYS* 1.3 57.9 + - - +
1167B LEU* 2.9 25.1 + - - +
1168B THR* 3.2 31.3 + - - +
1169B GLY* 3.0 25.8 + - - -
1170B ASP* 2.8 15.2 + - + +
1305B ILE* 4.9 1.6 - - - +
5008B GOL 3.7 23.2 + - - -
5009B GOL 5.1 2.1 + - - -
5022B GOL 5.1 2.4 + - - -
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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