Contacts of the strand formed by residues 1121 - 1130 (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 LEU1121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A ILE* 4.2 20.4 - - + -
1120B ILE* 1.3 84.7 - - - +
1122B VAL* 1.3 65.5 + - - +
1123B THR* 3.7 14.2 + - + +
1141B SER* 4.0 18.6 - - - +
1144B THR 3.4 21.8 - - - +
1145B THR 4.5 0.7 - - - +
1146B LEU* 5.1 1.7 - - - +
1165B ILE* 3.9 20.4 - - + -
1173B PRO* 2.8 14.3 + - - +
1174B SER 3.6 22.2 - - - +
1175B PRO* 3.8 27.8 - - + -
1178B THR* 3.9 10.5 - - - +
1448B SER* 4.3 3.3 + - - -
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Residues in contact with VAL1122 (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* 1.3 71.5 - - - +
1123B THR* 1.3 66.6 + - - +
1141B SER* 3.3 2.3 + - - -
1142B GLN* 2.8 40.4 + - + -
1144B THR* 2.9 22.4 + - + +
1145B THR 3.5 11.4 - - - +
1146B LEU* 3.5 32.8 - - + +
1151B ALA* 3.7 14.6 - - + -
1154B THR* 3.8 11.7 - - - +
1446B TRP* 5.3 0.4 - - + -
1447B THR 3.2 27.4 - - - +
1448B SER* 3.7 9.2 - - - -
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Residues in contact with THR1123 (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* 3.7 11.2 + - + +
1122B VAL* 1.3 81.4 - - - +
1124B ARG* 1.3 73.2 + - - +
1139B ALA* 3.9 16.3 - - + +
1140B LEU 3.2 10.5 - - - -
1141B SER* 4.1 11.7 - - - -
1142B GLN* 4.8 1.2 - - - +
1162B ARG* 4.2 2.7 - - - -
1165B ILE* 4.2 12.8 - - + -
1167B TRP* 5.4 0.9 - - - -
1173B PRO* 4.1 21.3 - - + +
1447B THR 4.0 2.8 - - - +
1448B SER* 3.2 18.4 + - - -
1449B ASN* 2.7 34.1 + - - -
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Residues in contact with ARG1124 (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* 1.3 80.0 - - - +
1125B GLU* 1.3 102.3 + - - +
1126B PRO* 3.4 2.9 - - - -
1139B ALA* 3.9 1.0 - - - +
1140B LEU 3.1 21.5 + - - +
1142B GLN* 5.4 2.2 - - - +
1154B THR 6.0 1.3 - - - +
1155B ILE 6.2 0.2 - - - -
1157B ASP* 4.5 6.9 + - - -
1162B ARG* 3.6 6.7 - - - +
1378B ARG* 3.9 4.6 - - - +
1412B TYR* 3.4 32.5 - - - -
1433B GLU* 2.9 35.6 + - - +
1435B ILE* 3.7 19.1 - - - +
1447B THR* 3.9 28.7 - - + +
1448B SER 4.5 5.8 - - - -
1449B ASN* 3.1 11.2 - - - +
2477B SIA 3.0 23.2 + - - +
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Residues in contact with GLU1125 (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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1124B ARG* 1.3 101.3 + - - +
1126B PRO* 1.3 65.1 - - - +
1127B TYR* 3.8 11.3 - - - -
1139B ALA* 3.7 9.0 - - - -
1140B LEU* 3.6 22.0 + - + +
1157B ASP* 4.4 1.9 - - - +
1162B ARG* 2.9 36.6 + - - -
1234B GLU* 4.2 19.6 - - + +
1412B TYR* 3.9 28.0 - - + -
1433B GLU* 2.8 15.4 + - - -
2477B SIA 3.1 28.1 + - - +
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Residues in contact with PRO1126 (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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1124B ARG 3.4 3.5 - - - -
1125B GLU* 1.3 94.9 - - - +
1127B TYR* 1.3 63.9 + - - +
1138B PHE 3.0 15.7 - - - +
1139B ALA* 3.7 7.4 - - + -
1234B GLU 3.7 0.9 - - - +
1412B TYR* 5.4 1.0 - - + +
1431B TYR* 2.9 31.6 + - + -
1433B GLU* 3.2 35.7 - - + +
1449B ASN* 3.6 15.0 - - - +
1451B ILE* 3.7 27.4 - - + -
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Residues in contact with TYR1127 (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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1125B GLU 3.8 9.4 - - - -
1126B PRO* 1.3 79.6 - - - +
1128B LEU* 1.3 76.6 + - - +
1129B SER* 4.9 1.1 - - - -
1137B MET* 3.6 1.4 - - - +
1138B PHE* 2.7 57.6 + + + +
1140B LEU* 6.3 0.2 - - + -
1164B LEU* 3.4 16.8 - - + +
1187B SER* 3.1 27.0 + - - -
1188B THR* 3.4 18.6 - - - -
1189B SER* 3.6 16.0 - - - -
1234B GLU* 3.2 22.4 - - - -
1235B SER* 3.3 18.4 - - - -
1236B GLU* 3.5 16.6 - - + -
1415B ALA 6.0 0.2 - - - +
1431B TYR* 3.3 27.4 - - + -
1451B ILE* 4.9 0.3 - - - +
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Residues in contact with LEU1128 (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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1127B TYR* 1.3 87.5 - - - +
1129B SER* 1.3 63.9 + - - +
1135B CYS* 5.2 0.9 - - + -
1136B ARG 3.3 12.3 - - - +
1137B MET* 3.6 26.9 - - + -
1138B PHE* 4.4 0.9 - - - -
1169B MET* 4.1 26.0 - - + -
1236B GLU* 3.7 9.7 + - - +
1415B ALA 4.9 0.2 - - - +
1416B PHE* 3.4 50.7 - - + +
1431B TYR* 3.6 30.9 - - + -
1451B ILE* 4.0 17.0 - - + -
1453B ALA* 4.2 7.6 - - + -
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Residues in contact with SER1129 (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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1127B TYR* 4.8 2.5 - - - -
1128B LEU* 1.3 79.0 - - - +
1130B CYS* 1.3 66.6 + - - +
1136B ARG* 2.9 29.8 + - - +
1138B PHE* 3.6 14.0 - - - -
1189B SER 3.9 5.3 + - - -
1190B CYS* 3.9 3.6 - - - -
1191B HIS 4.5 0.2 + - - -
1196B ARG* 2.8 40.8 + - - -
1236B GLU* 3.0 26.2 + - - -
1416B PHE* 4.9 0.7 - - - -
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Residues in contact with CYS1130 (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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1129B SER* 1.3 77.9 + - - +
1131B ASP* 1.3 63.0 + - - +
1134B GLY 3.2 5.6 - - - +
1135B CYS* 2.0 45.8 - - - -
1191B HIS* 3.6 3.1 + - - +
1196B ARG* 3.2 13.2 + - - -
1236B GLU* 3.8 4.9 + - - +
1416B PHE* 4.0 18.6 - - - -
1417B ILE 4.0 5.1 + - - +
1418B ASP* 3.8 33.0 - - - +
1420B TRP* 3.1 19.3 - - + -
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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