Contacts of the strand formed by residues 1135 - 1145 (chain B) in PDB entry 1W21
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 CYS1135 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1106B LEU* 5.5 3.1 - - - -
1128B LEU* 5.2 1.3 - - + -
1129B SER 3.6 4.0 - - - +
1130B CYS* 2.0 46.0 - - - -
1134B GLY* 1.3 74.4 - - - -
1136B ARG* 1.3 71.0 + - - +
1168B GLU* 4.9 1.4 - - - +
1169B MET* 3.3 45.7 + - + +
1416B PHE* 4.7 8.7 - - + -
1418B ASP* 4.2 14.4 - - - -
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Residues in contact with ARG1136 (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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1128B LEU* 3.3 8.9 - - - +
1129B SER 2.9 30.9 + - - +
1131B ASP* 4.7 13.9 - - - +
1134B GLY 5.6 0.9 - - - -
1135B CYS* 1.3 80.6 - - - +
1137B MET* 1.3 63.5 + - - +
1138B PHE* 3.5 20.1 - - + -
1166B SER* 2.8 44.0 + - - -
1167B TRP* 3.4 15.5 - - - +
1168B GLU* 3.6 21.6 - - - +
1169B MET 4.1 1.3 - - - +
1177B ASN 5.4 0.8 + - - -
1179B ARG* 3.7 34.0 - - - +
1181B GLU* 5.0 0.8 + - - -
1196B ARG* 5.5 5.8 - - - +
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Residues in contact with MET1137 (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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1107B SER* 3.4 33.2 - - - +
1108B LYS 4.4 1.6 - - - +
1109B ASP* 4.0 16.6 - - + +
1127B TYR 3.6 4.3 - - - +
1128B LEU* 3.6 18.2 - - + -
1136B ARG* 1.3 73.2 - - - +
1138B PHE* 1.3 62.8 + - - +
1166B SER* 3.2 4.9 - - - -
1167B TRP* 2.9 65.8 + - + +
1169B MET* 3.9 7.6 - - + -
1170B GLY 3.5 15.5 - - - +
1171B GLN 3.9 4.7 - - - +
1451B ILE* 4.0 38.4 - - + -
1453B ALA* 5.5 0.7 - - + -
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Residues in contact with PHE1138 (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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1126B PRO* 3.0 4.5 - - - +
1127B TYR* 2.7 64.3 + + + +
1129B SER* 3.6 23.1 - - - -
1136B ARG* 3.5 33.7 - - + -
1137B MET* 1.3 77.7 - - - +
1139B ALA* 1.3 67.3 + - - +
1164B LEU* 4.0 12.8 - - + -
1165B ILE 3.3 6.1 - - - -
1166B SER* 3.5 24.7 - - - -
1167B TRP* 3.8 5.6 - - - -
1181B GLU* 3.9 13.9 - - + -
1189B SER* 3.7 16.8 - - - -
1196B ARG* 3.8 26.9 - - - -
1451B ILE* 4.4 0.7 - - - +
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Residues in contact with ALA1139 (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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1123B THR* 3.9 17.7 - - + +
1124B ARG 3.9 5.4 - - - +
1125B GLU 3.7 11.0 - - - -
1126B PRO* 3.7 16.2 - - + -
1138B PHE* 1.3 79.3 - - - +
1140B LEU* 1.3 61.2 + - - +
1141B SER 3.8 0.2 - - - -
1164B LEU* 3.4 10.2 - - - +
1165B ILE* 2.9 33.7 + - - +
1167B TRP* 3.8 18.3 - - + -
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Residues in contact with LEU1140 (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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1123B THR* 3.2 2.9 - - - -
1124B ARG 3.1 20.6 + - - +
1125B GLU* 3.6 30.3 - - + +
1139B ALA* 1.3 73.8 - - - +
1141B SER* 1.3 62.0 + - - +
1162B ARG* 2.9 33.7 + - - +
1163B ALA 3.4 2.0 - - - -
1164B LEU* 3.9 24.5 - - + +
1184B GLY 4.0 15.0 - - - +
1185B TRP* 3.4 30.1 - - - +
1186B SER* 3.8 8.7 - - - +
1187B SER* 4.0 22.9 - - - +
1200B CYS* 5.3 0.2 - - - -
1234B GLU* 4.0 5.8 - - - +
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Residues in contact with SER1141 (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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1121B LEU* 4.0 16.7 - - - +
1122B VAL 3.3 11.3 + - - -
1123B THR* 4.1 4.5 - - - -
1139B ALA 3.7 2.8 + - - -
1140B LEU* 1.3 77.8 - - - +
1142B GLN* 1.3 61.7 + - - +
1143B GLY* 3.0 16.1 + - - -
1161B PHE 5.4 0.2 - - - -
1162B ARG* 3.1 27.6 + - - +
1163B ALA* 2.9 19.7 + - - -
1165B ILE* 3.9 25.5 - - - +
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Residues in contact with GLN1142 (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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113A ARG* 2.9 22.7 + - - -
1122B VAL* 2.8 36.1 + - + +
1123B THR* 4.7 2.5 - - - +
1124B ARG* 5.4 2.4 - - - +
1141B SER* 1.3 74.2 - - - +
1143B GLY* 1.3 59.4 + - - +
1144B THR* 3.4 1.6 - - + -
1154B THR* 3.1 39.3 - - + +
1156B HIS 3.1 16.1 + - - +
1159B SER* 4.3 1.2 + - - -
1161B PHE* 3.6 7.7 - - - +
1162B ARG* 3.2 42.2 + - - +
1447B THR 5.3 0.2 - - - +
2479B GOL 2.7 39.4 + - - +
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Residues in contact with GLY1143 (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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110A ASN* 4.3 12.1 - - - +
113A ARG* 2.8 36.3 + - - +
114A ILE* 3.8 13.5 - - - +
1141B SER* 3.0 12.1 + - - -
1142B GLN* 1.3 79.4 - - - +
1144B THR* 1.3 58.2 + - - +
1161B PHE 3.4 15.9 + - - -
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Residues in contact with THR1144 (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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113A ARG* 3.8 10.5 + - - +
114A ILE* 4.0 12.4 - - - +
1121B LEU* 3.4 11.9 - - - +
1122B VAL* 2.9 46.5 + - + +
1142B GLN 3.8 4.9 - - - +
1143B GLY* 1.3 80.6 - - - +
1145B THR* 1.3 68.8 + - - +
1148B GLY* 4.5 3.1 - - - -
1150B HIS* 3.3 44.1 + - - +
1151B ALA* 3.4 4.6 + - - -
1154B THR* 4.0 5.4 - - + -
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Residues in contact with THR1145 (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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113A ARG 5.4 0.2 + - - -
114A ILE* 4.5 10.2 + - + +
117A ASP* 2.7 32.8 + - - +
118A ALA* 4.1 22.9 - - + -
1119B HIS* 4.4 8.7 - - + -
1120B ILE 3.1 17.3 - - - +
1122B VAL* 3.5 2.0 - - - -
1144B THR* 1.3 88.1 + - - +
1146B LEU* 1.3 66.9 + - - +
1147B ARG 4.3 0.9 - - - -
1148B GLY* 3.1 19.4 + - - -
1151B ALA* 3.4 7.8 - - - +
1175B PRO* 4.2 17.5 - - + -
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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