Contacts of the strand formed by residues 1140 - 1149 (chain B) in PDB entry 1Q6S
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 LEU1140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1096B TRP* 3.5 16.8 - - + +
1097B GLU* 3.4 37.2 - - + +
1100B TRP* 4.4 16.4 - - + -
1134B ILE* 3.4 4.3 - - - +
1135B PHE* 2.8 42.0 + - + -
1138B THR* 3.6 25.6 - - - +
1139B ASN* 1.3 77.3 - - - +
1141B LYS* 1.3 61.0 + - - +
1160B LEU* 4.2 15.7 - - + -
1161B GLU 3.3 15.7 - - - +
1162B ASN* 3.6 21.5 - - + +
1163B LEU* 4.1 3.1 - - - +
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Residues in contact with LYS1141 (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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1132B GLU* 3.9 27.6 + - + -
1133B MET 3.3 8.1 - - - +
1134B ILE* 4.2 17.2 - - + +
1140B LEU* 1.3 76.0 - - - +
1142B LEU* 1.3 62.8 - - - +
1143B THR* 4.2 14.1 - - - +
1159B GLU 3.5 1.7 - - - +
1160B LEU* 3.4 5.3 - - - +
1161B GLU* 2.8 55.4 + - + +
1163B LEU* 3.8 24.0 - - + -
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Residues in contact with LEU1142 (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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1096B TRP* 3.4 42.6 - - + +
1124B TYR 3.7 6.3 - - - +
1125B TRP* 3.8 2.7 - - + -
1126B PRO* 3.5 28.2 - - + +
1132B GLU* 3.4 4.0 - - - +
1133B MET* 2.7 39.8 + - + +
1135B PHE* 3.9 16.6 - - + -
1141B LYS* 1.3 75.4 - - - +
1143B THR* 1.3 61.4 + - - +
1158B LEU* 3.8 29.2 - - + -
1159B GLU 3.3 15.9 - - - +
1160B LEU* 4.2 16.2 - - + -
1171B ILE* 5.6 0.2 - - + -
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Residues in contact with THR1143 (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* 3.8 4.3 - - - -
1129B GLU* 3.9 15.7 - - + +
1132B GLU* 3.5 17.9 - - + +
1141B LYS* 4.2 14.0 - - - +
1142B LEU* 1.3 78.0 - - - +
1144B LEU* 1.3 74.8 + - - +
1145B ILE* 3.4 15.1 + - + +
1158B LEU* 3.2 7.7 - - - +
1159B GLU* 2.8 43.2 + - - +
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Residues in contact with LEU1144 (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* 3.4 31.4 - - + +
1127B GLN* 3.4 27.8 - - - +
1128B LYS 4.0 0.7 - - - +
1129B GLU* 3.4 44.4 + - - +
1143B THR* 1.3 82.4 - - - +
1145B ILE* 1.3 60.8 + - - +
1146B SER* 3.1 35.9 - - - +
1147B GLU* 3.9 20.2 - - + +
1156B ARG* 4.7 7.6 - - + +
1157B GLN 3.6 3.8 - - - +
1158B LEU* 3.8 13.5 - - + -
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Residues in contact with ILE1145 (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 GLU* 4.0 11.9 - - - +
1143B THR* 4.0 17.5 - - + +
1144B LEU* 1.3 82.2 - - - +
1146B SER* 1.3 60.4 + - - +
1157B GLN* 2.7 46.5 + - + +
1158B LEU 4.1 2.5 - - - -
1159B GLU* 4.0 34.3 - - + +
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Residues in contact with SER1146 (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 GLU* 4.5 7.4 - - - -
1144B LEU* 3.1 13.7 - - - +
1145B ILE* 1.3 81.1 - - - +
1147B GLU* 1.3 64.0 + - - +
1157B GLN* 2.7 52.3 + - - +
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Residues in contact with GLU1147 (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 GLN* 4.1 7.3 - - - +
1129B GLU* 5.3 3.2 + - - +
1144B LEU* 3.9 22.0 - - + +
1146B SER* 1.3 81.0 - - - +
1148B ASP* 1.3 58.7 - - - +
1149B ILE* 3.8 24.5 + - + +
1154B THR* 3.7 9.8 - - + +
1155B VAL 3.4 5.4 - - - +
1156B ARG* 3.1 40.5 + - + -
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Residues in contact with ASP1148 (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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1147B GLU* 1.3 71.3 - - - +
1149B ILE* 1.3 64.0 + - - +
1150B LYS* 2.9 40.8 + - - +
1153B TYR 4.2 0.3 - - - +
1154B THR* 3.4 4.6 - - - -
1155B VAL* 2.8 43.3 + - + +
1197B LYS* 5.6 2.8 + - - -
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Residues in contact with ILE1149 (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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1147B GLU* 3.8 27.4 + - + +
1148B ASP* 1.3 76.7 + - - +
1150B LYS* 1.3 70.7 + - - +
1154B THR* 3.7 29.6 - - + +
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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