Contacts of the strand formed by residues 1148 - 1154 (chain B) in PDB entry 6X34
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 VAL1148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1091B GLU* 6.4 1.1 - - + -
1092B PHE 3.3 6.7 - - - +
1093B GLU* 3.8 17.7 - - + +
1146B GLY 3.8 2.6 + - - +
1147B ASP* 1.3 73.9 - - - +
1149B VAL* 1.3 63.7 + - - +
1150B GLY 3.7 1.6 + - - -
1165B ASN* 3.7 25.3 + - - +
1166B GLY 4.7 1.7 + - - -
1212B ARG* 5.3 14.1 - - + -
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Residues in contact with VAL1149 (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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1090B PHE 4.2 0.2 - - - +
1091B GLU* 3.8 0.9 - - - +
1092B PHE* 2.6 48.1 + - + +
1102B VAL* 4.7 8.3 - - + -
1124B PHE* 6.0 0.4 - - + -
1143B TRP* 3.8 38.1 - - + -
1147B ASP* 4.0 2.9 + - + +
1148B VAL* 1.3 73.4 - - - +
1150B GLY* 1.3 58.5 + - - +
1151B CYS* 5.1 1.1 - - - -
1163B THR 3.5 7.4 - - - +
1164B LEU* 4.2 14.4 - - + +
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Residues in contact with GLY1150 (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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1089B TYR* 4.4 12.8 - - - -
1090B PHE 3.3 7.0 - - - -
1091B GLU* 4.5 1.8 - - - -
1148B VAL 3.7 2.4 + - - -
1149B VAL* 1.3 74.9 - - - +
1151B CYS* 1.3 65.7 + - - -
1162B PHE* 3.5 2.9 - - - +
1163B THR* 2.5 55.3 + - - +
1164B LEU* 5.2 0.2 - - - +
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Residues in contact with CYS1151 (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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1089B TYR* 3.3 6.8 - - - -
1090B PHE* 2.5 56.7 + - + +
1102B VAL* 3.6 33.7 - - - -
1103B GLY* 4.2 4.5 - - - -
1104B TRP* 3.5 19.4 - - + +
1149B VAL* 5.1 0.7 - - - -
1150B GLY* 1.3 81.5 - - - -
1152B MET* 1.3 61.0 + - - +
1161B ILE 3.9 4.3 - - - -
1162B PHE* 3.6 27.1 - - + +
1163B THR* 5.0 0.4 - - - -
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Residues in contact with MET1152 (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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1088B TRP 3.3 13.5 - - - +
1089B TYR* 4.3 13.7 - - + -
1104B TRP* 3.8 3.3 - - - +
1151B CYS* 1.3 75.8 - - - +
1153B ILE* 1.3 61.3 + - - +
1161B ILE* 2.9 49.6 + - + +
1163B THR* 5.0 4.7 - - - +
1221B GLU* 6.2 2.2 - - + -
1223B PHE* 4.6 11.0 - - + -
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Residues in contact with ILE1153 (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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1086B GLY 5.3 1.3 - - - +
1087B ARG* 3.3 25.9 - - - +
1088B TRP* 3.6 9.1 + - + +
1104B TRP* 3.4 49.1 - - + +
1122B TYR* 5.8 0.2 - - + -
1152B MET* 1.3 74.7 - - - +
1154B ASP* 1.3 67.6 + - - +
1155B LEU* 4.7 8.7 - - + +
1159B THR 3.8 4.0 - - - +
1160B ILE* 3.7 33.4 - - + +
1182B ILE* 4.7 4.9 - - + -
1188B PHE* 3.8 35.2 - - + -
1223B PHE* 5.2 0.2 - - - +
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Residues in contact with ASP1154 (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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1087B ARG* 4.4 9.9 - - + -
1152B MET 4.3 0.2 + - - -
1153B ILE* 1.3 74.0 - - - +
1155B LEU* 1.3 60.8 + - - +
1156B THR* 3.3 6.1 - - - +
1157B GLU* 4.1 20.0 - - + +
1158B ASN* 2.9 24.1 + - - -
1159B THR* 3.0 22.7 + - - +
1161B ILE* 5.0 10.3 - - + -
1182B ILE* 5.1 0.5 - - - +
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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