Contacts of the strand formed by residues 1152 - 1165 (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 TYR1152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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957A GLN* 5.2 0.4 - - - +
960A GLU 6.0 2.2 - - - +
1007A ILE* 2.9 51.0 + - + +
1084A ASP* 2.5 32.0 + - - -
1150A PHE* 3.4 3.4 - - - +
1151A HIS* 1.3 103.0 - + + +
1153A PHE* 1.3 87.8 + - - +
1154A THR* 3.8 4.5 - - - -
1249A ASN* 3.6 19.1 - - - +
1251A LYS* 3.8 17.3 - - + -
1252A ALA* 4.2 3.1 - - + +
1257A LYS* 3.4 30.5 - - + -
1258A ALA* 2.8 22.7 + - - +
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Residues in contact with PHE1153 (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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883A PHE 6.0 0.2 - - - -
884A HIS* 5.5 1.1 - - - -
953A THR* 4.5 1.6 - - + -
955A PHE* 3.9 16.6 - + - -
957A GLN* 3.7 24.9 - - + -
958A ARG 4.7 5.6 - - - -
959A LEU* 3.7 22.0 - - + -
960A GLU 5.9 2.4 + - - -
1004A LYS* 3.9 27.4 - - + -
1005A PHE 3.3 6.5 - - - +
1006A GLY* 3.6 18.8 - - - -
1150A PHE* 3.8 30.5 - + - -
1152A TYR* 1.3 84.5 - - - +
1154A THR* 1.3 63.4 + - - +
1155A TYR* 3.3 37.8 + - + +
1257A LYS* 2.8 27.2 + - - -
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Residues in contact with THR1154 (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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1003A THR* 4.6 0.7 - - - +
1004A LYS* 3.4 3.6 - - - -
1005A PHE* 3.0 33.1 + - - +
1007A ILE* 3.6 13.2 - - - +
1152A TYR* 3.8 8.3 - - - -
1153A PHE* 1.3 73.4 - - - +
1155A TYR* 1.3 62.9 + - - +
1180A MET* 3.9 10.4 - - + +
1181A ASP 3.5 15.7 - - - +
1182A VAL* 5.1 3.8 - - + -
1257A LYS* 4.0 6.8 - - - +
1258A ALA 3.0 27.4 + - - +
1259A VAL* 5.1 0.9 - - - -
1262A PRO* 3.5 32.2 - - + +
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Residues in contact with TYR1155 (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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959A LEU* 4.0 7.1 - - - +
960A GLU 4.5 5.7 + - - -
961A GLY 3.6 18.9 + - - -
962A PHE* 3.3 37.8 + + - +
963A SER* 3.2 28.3 - - - +
964A VAL* 3.3 28.7 - - + +
967A CYS* 4.5 1.3 - - - -
1003A THR* 3.5 5.6 - - - +
1004A LYS* 3.4 25.6 - - + -
1153A PHE* 3.3 44.4 + - + +
1154A THR* 1.3 75.6 - - - +
1156A GLY* 1.3 60.2 + - - +
1180A MET* 3.3 14.0 - - - +
1181A ASP* 2.8 35.6 + - + +
1257A LYS* 3.8 1.6 - - - -
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Residues in contact with GLY1156 (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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964A VAL* 5.3 0.9 - - - +
967A CYS* 4.3 4.4 - - - -
1002A PRO 3.5 0.3 - - - -
1003A THR* 3.0 31.7 + - - +
1155A TYR* 1.3 79.6 - - - +
1157A VAL* 1.3 68.6 + - - +
1179A VAL 3.2 12.8 - - - -
1180A MET* 3.8 14.5 - - - +
1266A LEU* 4.1 7.0 - - - -
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Residues in contact with VAL1157 (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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964A VAL* 4.2 4.7 - - + +
967A CYS* 3.7 16.2 - - + +
968A TRP* 3.6 32.3 - - + +
971A CYS* 3.7 11.7 - - + -
1000A ILE* 3.6 31.9 - - + -
1001A ILE 3.3 10.8 - - - +
1002A PRO* 3.9 17.3 - - + -
1156A GLY* 1.3 79.8 - - - +
1158A ALA* 1.3 65.2 + - - +
1177A ASP 3.9 0.3 - - - +
1178A ILE* 3.4 4.0 - - - +
1179A VAL 2.8 32.3 + - - +
1266A LEU* 4.0 3.9 - - - +
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Residues in contact with ALA1158 (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* 4.3 0.4 - - - -
1000A ILE* 3.3 3.6 - - - -
1001A ILE 2.8 36.3 + - - +
1157A VAL* 1.3 76.5 - - - +
1159A CYS* 1.3 60.5 + - - +
1176A THR* 4.9 1.3 - - + -
1177A ASP 3.2 8.5 - - - +
1178A ILE* 3.9 13.2 - - + -
1199A PHE* 4.5 2.5 - - + -
1266A LEU* 3.8 37.7 - - + +
1269A SER* 3.7 12.0 - - - +
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Residues in contact with CYS1159 (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* 3.9 17.2 - - - -
975A SER* 4.0 11.9 - - - +
977A TYR* 3.7 21.5 - - - -
980A ARG* 3.9 14.3 + - - -
998A LEU* 3.6 27.1 - - - -
999A CYS 3.2 8.5 - - - +
1000A ILE* 4.0 8.5 - - + -
1158A ALA* 1.3 73.0 - - - +
1160A SER* 1.3 65.2 + - - +
1175A ARG 3.8 0.7 - - - +
1176A THR* 3.2 3.5 - - - -
1177A ASP* 2.9 33.4 + - - +
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Residues in contact with SER1160 (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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998A LEU* 3.4 4.4 - - - -
999A CYS 2.9 31.0 + - - +
1159A CYS* 1.3 74.4 - - - +
1161A GLU* 1.3 61.7 + - - +
1162A VAL* 5.2 0.2 - - - -
1175A ARG 3.2 4.5 - - - -
1176A THR* 2.8 26.6 + - - +
1269A SER* 2.6 34.6 + - - -
1270A VAL* 3.6 21.1 - - - +
1273A ALA* 3.4 8.5 - - - +
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Residues in contact with GLU1161 (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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980A ARG* 2.9 39.7 + - - +
983A GLU* 3.1 23.8 - - - +
984A VAL* 3.9 12.7 - - + +
996A ARG* 3.7 10.9 + - - -
997A GLY 3.1 15.3 - - - +
998A LEU* 3.8 9.2 - - + +
1160A SER* 1.3 73.6 - - - +
1162A VAL* 1.3 68.9 + - - +
1173A ASN* 3.8 1.0 - - - -
1174A LEU* 2.9 47.8 + - + +
1175A ARG* 2.8 16.3 + - - +
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Residues in contact with VAL1162 (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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996A ARG* 3.1 9.9 - - - +
997A GLY 3.0 29.6 + - - +
1161A GLU* 1.3 80.8 - - - +
1163A GLU* 1.3 63.8 + - - +
1164A ILE* 4.4 7.9 - - + -
1171A HIS* 4.2 4.5 - - + -
1172A LYS 3.1 15.9 - - - +
1173A ASN* 3.9 16.8 - - - +
1174A LEU* 3.9 6.8 - - - +
1270A VAL* 3.9 20.6 - - + +
1273A ALA* 3.9 17.3 - - + +
1274A ILE* 3.8 34.5 - - + +
1277A ALA* 4.5 1.1 - - + -
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Residues in contact with GLU1163 (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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987A PHE* 3.2 19.8 - - + -
994A LYS* 3.6 11.9 - - + +
995A LYS 3.3 11.0 - - - +
996A ARG* 3.0 40.4 + - + -
1162A VAL* 1.3 76.5 - - - +
1164A ILE* 1.3 69.6 + - - +
1171A HIS* 3.0 3.5 - - - -
1172A LYS* 2.7 55.0 + - + +
1174A LEU* 4.1 11.9 - - + +
5001A GOL 2.9 26.0 + - - +
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Residues in contact with ILE1164 (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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994A LYS* 3.3 10.7 - - - +
995A LYS 2.8 36.8 + - - +
1162A VAL* 4.4 8.1 - - + -
1163A GLU* 1.3 79.8 - - - +
1165A ASP* 1.3 59.1 + - - +
1166A CYS* 4.1 9.2 - - - +
1170A ASP 3.6 6.3 - - - +
1171A HIS* 3.8 13.9 - - + -
1274A ILE* 4.5 11.0 - - + -
1277A ALA* 3.8 40.6 - - + +
1278A ILE* 3.9 8.7 - - + +
1305A ILE* 4.2 16.2 - - + -
1309A CYS* 4.0 25.8 - - - -
5001A GOL 4.5 2.0 - - - -
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Residues in contact with ASP1165 (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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518A LYS* 4.8 7.4 + - - +
993A TRP 4.0 5.3 - - - +
994A LYS* 3.3 21.7 + - - -
1164A ILE* 1.3 71.3 - - - +
1166A CYS* 1.3 59.0 + - - +
1167A LEU* 2.8 36.1 + - - +
1168A THR* 3.1 33.4 + - - +
1169A GLY* 3.0 25.8 + - - -
1170A ASP* 2.9 14.8 + - + +
1305A ILE* 5.1 1.4 - - - +
1306A ARG* 5.7 0.2 - - - -
1309A CYS* 5.5 0.2 - - - -
5001A GOL 3.9 22.1 + - - -
5003A GOL 5.1 2.6 + - - -
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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