Contacts of the helix formed by residues 1091 - 1105 (chain B) in PDB entry 6KJV
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 ASP1091 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B THR* 6.0 3.6 - - + +
344B ASP* 4.0 13.5 - - - +
1089B SER 3.9 1.4 + - - -
1090B LEU* 1.3 73.6 - - - +
1092B ALA* 1.3 57.2 + - - +
1093B VAL* 3.1 14.7 + - + +
1094B ARG* 2.7 62.2 + - - +
1095B ARG* 2.6 37.4 + - - +
1125B TRP* 4.8 2.9 - - - -
1155B GLY* 4.4 3.1 - - - +
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Residues in contact with ALA1092 (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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339B LEU 5.1 8.3 - - - +
344B ASP* 3.5 31.1 + - + +
1091B ASP* 1.3 73.5 - - - +
1093B VAL* 1.3 60.4 + - + +
1095B ARG* 3.3 14.1 - - - +
1096B ALA* 2.9 28.2 + - - +
1157B TRP* 5.1 1.1 - - - -
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Residues in contact with VAL1093 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ASP* 6.1 1.6 - - + +
345B ILE* 4.1 22.4 - - + -
1091B ASP* 3.2 7.8 - - + +
1092B ALA* 1.3 79.6 - - + +
1094B ARG* 1.3 63.3 + - - +
1096B ALA* 3.1 7.1 + - - +
1097B ALA 3.1 16.5 + - - -
1151B THR* 3.7 20.3 - - + +
1155B GLY 3.3 37.2 - - - +
1156B THR 3.7 8.1 - - - +
1157B TRP* 3.8 33.2 - - + +
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Residues in contact with ARG1094 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090B LEU* 3.7 20.6 - - + +
1091B ASP* 2.7 32.8 + - - +
1093B VAL* 1.3 76.1 - - - +
1095B ARG* 1.3 62.2 + - - +
1097B ALA* 3.2 9.9 + - - +
1098B LEU 3.0 17.8 + - - -
1125B TRP* 3.5 51.7 - - - +
1151B THR 3.6 17.0 - - - +
1152B PHE* 2.8 49.0 + - + +
1153B ARG 3.6 6.9 + - - -
1154B THR 3.5 7.5 + - - -
1155B GLY* 3.3 25.3 - - - +
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Residues in contact with ARG1095 (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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341B CYS* 5.8 8.6 - - - -
1087B TYR* 3.1 63.8 + - + +
1088B ASP* 3.9 26.5 + - - +
1090B LEU* 3.2 21.1 + - + +
1091B ASP 2.6 26.4 + - - +
1092B ALA* 3.3 15.0 - - - +
1094B ARG* 1.3 73.5 - - - +
1096B ALA* 1.3 63.1 + - - +
1098B LEU* 3.1 3.9 + - - +
1099B ILE* 2.9 30.3 + - + +
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Residues in contact with ALA1096 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002B ILE* 3.4 35.5 - - + +
1005B MET* 3.9 2.9 - - - +
1092B ALA 2.9 12.5 + - - +
1093B VAL 3.1 8.7 + - - +
1095B ARG* 1.3 75.3 - - - +
1097B ALA* 1.3 57.8 + - - +
1099B ILE* 3.4 8.0 + - + +
1100B ASN* 2.9 26.3 + - - +
1157B TRP* 3.5 26.0 - - + -
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Residues in contact with ALA1097 (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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1005B MET* 4.1 11.8 - - + +
1093B VAL 3.1 6.4 + - - +
1094B ARG* 3.3 9.6 - - - +
1095B ARG 3.2 0.2 - - - -
1096B ALA* 1.3 76.8 - - - +
1098B LEU* 1.3 63.1 + - - +
1100B ASN* 3.1 5.4 + - - +
1101B MET* 3.1 18.5 + - - +
1148B VAL* 3.7 14.7 - - + +
1151B THR* 3.9 24.5 - - + -
1152B PHE* 3.5 28.5 - - + -
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Residues in contact with LEU1098 (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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1077B ILE* 4.5 11.9 - - + -
1083B LEU* 4.3 12.6 - - + +
1086B VAL* 4.2 14.1 - - + -
1087B TYR* 3.9 37.5 - - + -
1090B LEU* 4.2 12.3 - - + -
1094B ARG 3.0 12.6 + - - +
1095B ARG* 3.1 7.6 + - - +
1097B ALA* 1.3 75.1 - - - +
1099B ILE* 1.3 64.3 + - - +
1101B MET* 3.2 15.7 + - - +
1102B VAL* 3.0 22.1 + - + +
1110B VAL* 5.0 7.9 - - + -
1117B LEU* 4.4 20.9 - - + -
1120B LEU* 5.5 1.3 - - + -
1152B PHE* 3.5 17.8 - - + -
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Residues in contact with ILE1099 (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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1002B ILE* 4.2 25.8 - - + -
1006B LEU* 5.3 2.0 - - + -
1070B VAL* 4.9 6.7 - - + -
1073B ALA* 4.0 22.4 - - + -
1074B VAL* 3.7 24.5 - - + -
1077B ILE* 3.9 14.1 - - + -
1087B TYR* 3.9 24.2 - - + +
1095B ARG* 2.9 21.2 + - + +
1096B ALA* 3.7 10.3 - - - +
1098B LEU* 1.3 76.3 - - - +
1100B ASN* 1.3 58.0 + - - +
1102B VAL* 3.2 2.3 + - - +
1103B PHE* 2.8 29.7 + - + +
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Residues in contact with ASN1100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002B ILE* 4.3 1.5 - - + +
1005B MET* 3.7 24.3 - - + +
1006B LEU* 3.4 26.8 - - + +
1009B ASP* 3.1 22.4 + - - -
1096B ALA 2.9 13.9 + - - +
1097B ALA 3.1 10.1 + - - +
1099B ILE* 1.3 76.6 - - - +
1101B MET* 1.3 64.6 + - - +
1103B PHE* 3.1 3.8 + - - +
1104B GLN* 3.0 19.2 + - - +
1137B TRP* 5.7 0.3 - - - -
1144B ARG* 2.8 32.8 + - - +
1148B VAL* 3.6 17.3 - - + +
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Residues in contact with MET1101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1097B ALA 3.1 10.9 + - - +
1098B LEU* 3.2 15.5 + - + +
1100B ASN* 1.3 81.5 + - - +
1102B VAL* 1.3 58.0 + - - +
1104B GLN* 3.1 6.5 + - - -
1105B MET* 2.8 40.1 + - - +
1110B VAL* 3.7 19.7 - - + -
1113B PHE* 3.8 35.7 - - + -
1117B LEU* 6.4 0.9 - - - -
1132B LEU* 4.6 7.6 - - + -
1137B TRP* 3.9 42.4 - - + -
1148B VAL* 4.0 3.8 - - + -
1152B PHE* 3.9 24.7 - - - -
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Residues in contact with VAL1102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073B ALA* 4.2 28.9 - - + +
1077B ILE* 3.6 25.6 - - + -
1083B LEU* 4.3 5.4 - - + -
1098B LEU* 3.0 16.0 + - + +
1099B ILE* 3.2 6.9 + - - +
1101B MET* 1.3 75.3 - - - +
1103B PHE* 1.3 63.2 + - - +
1105B MET 3.8 0.2 - - - -
1106B GLY* 3.0 27.0 + - - +
1107B GLU* 4.0 21.1 - - + +
1110B VAL* 3.6 24.2 - - + -
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Residues in contact with PHE1103 (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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1006B LEU* 3.6 35.2 - - + -
1010B GLU* 3.7 26.8 - - + +
1028B ILE 3.6 20.4 - - - -
1029B GLY* 3.6 22.4 - - - +
1031B LEU* 6.1 1.0 - - - +
1066B PHE* 4.1 8.3 - + - -
1069B ASP* 3.5 42.4 - - + -
1070B VAL* 4.0 9.2 - - + -
1073B ALA* 4.6 10.5 - - + +
1099B ILE* 2.8 17.2 + - + +
1100B ASN 3.1 5.3 + - - +
1102B VAL* 1.3 78.5 - - - +
1104B GLN* 1.3 61.5 + - - +
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Residues in contact with GLN1104 (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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1010B GLU* 4.2 5.8 - - - +
1031B LEU* 6.0 2.4 - - - +
1100B ASN 3.0 9.8 + - - +
1101B MET* 3.9 4.2 - - - +
1103B PHE* 1.3 81.1 - - - +
1105B MET* 1.3 67.5 + - + +
1137B TRP* 3.0 30.1 + - - -
1141B THR* 3.3 33.1 + - - +
1144B ARG* 3.3 44.6 + - - +
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Residues in contact with MET1105 (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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1101B MET* 2.8 22.7 + - - +
1102B VAL 3.8 0.2 - - - -
1104B GLN* 1.3 82.9 - - + +
1106B GLY* 1.3 57.8 + - - +
1109B GLY* 4.6 12.3 - - - +
1110B VAL* 3.8 22.0 - - + +
1113B PHE* 3.8 27.4 - - + -
1136B ARG* 4.1 21.5 - - + +
1137B TRP* 4.0 32.8 - - + +
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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
------------------------------------------------------------
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