Contacts of the helix formed by residues 1091 - 1105 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A THR* 6.0 3.8 - - + +
344A ASP* 3.9 14.6 - - - +
1089A SER 3.9 1.2 + - - -
1090A LEU* 1.3 73.9 - - - +
1092A ALA* 1.3 56.5 + - - +
1093A VAL* 3.1 13.4 + - + +
1094A ARG* 2.7 61.5 + - - +
1095A ARG* 2.6 37.5 + - - +
1125A TRP* 4.7 3.5 - - - -
1155A GLY* 4.5 2.8 - - - +
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Residues in contact with ALA1092 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A LEU 4.8 11.4 - - - +
340A MET* 6.3 0.2 - - + -
344A ASP* 3.6 28.9 + - + +
1091A ASP* 1.3 74.5 - - - +
1093A VAL* 1.3 61.2 + - + +
1095A ARG* 3.3 15.0 - - - +
1096A ALA* 2.9 28.1 + - - +
1157A TRP* 5.3 0.8 - - - -
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Residues in contact with VAL1093 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ASP* 6.3 1.6 - - + -
345A ILE* 4.2 21.3 - - + -
1091A ASP* 3.2 8.9 - - + +
1092A ALA* 1.3 80.1 - - + +
1094A ARG* 1.3 62.3 + - - +
1096A ALA* 3.1 6.9 + - - +
1097A ALA 3.0 16.3 + - - -
1151A THR* 3.7 20.5 - - + +
1155A GLY 3.3 36.8 - - - +
1156A THR 3.7 10.5 - - - +
1157A TRP* 3.9 30.1 - - + +
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Residues in contact with ARG1094 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090A LEU* 3.7 21.0 - - + +
1091A ASP* 2.7 33.0 + - - +
1093A VAL* 1.3 73.3 - - - +
1095A ARG* 1.3 64.9 + - - +
1097A ALA* 3.2 9.8 + - - +
1098A LEU 3.0 18.7 + - - -
1125A TRP* 3.5 52.5 - - - +
1151A THR 3.6 16.6 - - - +
1152A PHE* 2.7 48.8 + - + +
1153A ARG 3.6 7.1 + - - -
1154A THR 3.5 10.5 + - - -
1155A GLY* 3.4 22.3 - - - +
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Residues in contact with ARG1095 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A ASN 5.9 1.0 + - - -
341A CYS* 6.1 3.6 - - - -
1087A TYR* 3.1 65.4 + - + +
1088A ASP* 3.9 24.2 + - - +
1090A LEU* 3.2 19.8 + - + +
1091A ASP 2.6 26.6 + - - +
1092A ALA* 3.3 14.8 - - - +
1094A ARG* 1.3 72.8 - - - +
1096A ALA* 1.3 63.2 + - - +
1098A LEU* 3.2 3.9 + - - +
1099A ILE* 2.9 30.7 + - + +
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Residues in contact with ALA1096 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002A ILE* 3.4 31.8 - - + +
1005A MET* 4.0 2.4 - - - +
1092A ALA 2.9 12.5 + - - +
1093A VAL 3.1 8.5 + - - +
1095A ARG* 1.3 75.5 - - - +
1097A ALA* 1.3 58.1 + - - +
1099A ILE* 3.4 10.4 + - + +
1100A ASN* 2.9 26.0 + - - +
1157A TRP* 3.6 26.2 - - + -
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Residues in contact with ALA1097 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005A MET* 4.2 9.3 - - - +
1093A VAL 3.0 6.4 + - - +
1094A ARG* 3.4 9.9 - - - +
1095A ARG 3.2 0.2 - - - -
1096A ALA* 1.3 77.0 - - - +
1098A LEU* 1.3 63.2 + - - +
1100A ASN* 3.1 13.0 + - - +
1101A MET* 3.1 11.1 + - - +
1148A VAL* 3.7 17.9 - - + +
1151A THR* 3.9 23.1 - - + -
1152A PHE* 3.5 29.2 - - + -
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Residues in contact with LEU1098 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1077A ILE* 4.4 13.5 - - + -
1083A LEU* 4.4 20.9 - - + +
1086A VAL* 4.4 10.5 - - + -
1087A TYR* 3.9 40.2 - - + +
1090A LEU* 4.2 11.4 - - + -
1094A ARG 3.0 12.4 + - - +
1095A ARG* 3.2 8.7 + - - +
1097A ALA* 1.3 76.0 - - - +
1099A ILE* 1.3 63.2 + - - +
1101A MET* 3.2 14.0 + - - +
1102A VAL* 3.0 24.9 + - + +
1110A VAL* 4.8 10.5 - - + -
1117A LEU* 4.5 12.3 - - + -
1120A LEU* 5.6 1.8 - - + -
1152A PHE* 3.5 16.0 - - + -
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Residues in contact with ILE1099 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002A ILE* 4.2 25.6 - - + -
1006A LEU* 5.4 1.8 - - + -
1070A VAL* 4.7 7.6 - - + -
1073A ALA* 4.1 21.8 - - + -
1074A VAL* 3.7 23.8 - - + -
1077A ILE* 3.9 21.8 - - + -
1087A TYR* 4.0 17.5 - - + +
1095A ARG* 2.9 24.9 + - + +
1096A ALA* 3.7 10.3 - - - +
1098A LEU* 1.3 76.5 - - - +
1100A ASN* 1.3 58.1 + - - +
1102A VAL* 3.2 2.5 + - - +
1103A PHE* 2.8 30.0 + - + +
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Residues in contact with ASN1100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002A ILE* 4.1 1.8 - - + +
1005A MET* 3.6 24.5 - - + +
1006A LEU* 3.4 26.2 - - - +
1009A ASP* 3.2 21.6 + - - -
1096A ALA 2.9 14.2 + - - +
1097A ALA 3.1 10.3 + - - +
1099A ILE* 1.3 77.4 - - - +
1101A MET* 1.3 64.2 + - - +
1103A PHE* 3.1 4.0 + - - +
1104A GLN* 3.0 19.1 + - - +
1137A TRP* 5.6 0.5 - - - -
1144A ARG* 2.9 33.0 + - - -
1148A VAL* 3.6 17.3 - - + +
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Residues in contact with MET1101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097A ALA 3.1 9.6 + - - +
1098A LEU* 3.2 14.3 + - + +
1100A ASN* 1.3 79.5 + - - +
1102A VAL* 1.3 59.2 + - - +
1104A GLN* 3.1 5.4 + - - -
1105A MET* 2.8 37.9 + - - +
1110A VAL* 3.6 20.0 - - + -
1113A PHE* 3.8 34.1 - - + -
1132A LEU* 4.5 9.9 - - + -
1137A TRP* 3.9 44.6 - - + -
1148A VAL* 4.1 3.1 - - + -
1152A PHE* 3.8 28.5 - - - -
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Residues in contact with VAL1102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1073A ALA* 4.1 28.5 - - + +
1077A ILE* 3.7 25.4 - - + -
1083A LEU* 4.6 3.4 - - + -
1098A LEU* 3.0 16.0 + - + +
1099A ILE* 3.2 6.9 + - - +
1101A MET* 1.3 76.3 - - - +
1103A PHE* 1.3 64.3 + - - +
1106A GLY* 3.1 26.6 + - - +
1107A GLU* 3.9 22.0 - - + +
1110A VAL* 3.6 25.1 - - + -
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Residues in contact with PHE1103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006A LEU* 3.6 33.4 - - + -
1010A GLU* 3.7 28.0 - - + +
1028A ILE 3.7 20.0 - - - -
1029A GLY 3.7 21.1 - - - +
1066A PHE* 4.1 7.9 - + - -
1069A ASP* 3.4 40.6 - - + -
1070A VAL* 4.0 14.6 - - + -
1073A ALA* 4.8 7.8 - - + +
1099A ILE* 2.8 17.4 + - + +
1100A ASN 3.1 5.6 + - - +
1102A VAL* 1.3 78.1 - - - +
1104A GLN* 1.3 61.4 + - - +
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Residues in contact with GLN1104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010A GLU* 4.3 7.4 - - - +
1031A LEU* 6.1 1.0 - - - +
1100A ASN 3.0 10.2 + - - +
1101A MET* 3.9 3.7 - - - +
1103A PHE* 1.3 81.4 - - - +
1105A MET* 1.3 67.5 + - + +
1137A TRP* 3.0 31.2 + - - -
1141A THR* 3.2 33.1 + - - +
1144A ARG* 3.3 42.2 + - - +
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Residues in contact with MET1105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101A MET* 2.8 20.9 + - - +
1102A VAL 3.8 0.4 - - - -
1104A GLN* 1.3 82.1 - - + +
1106A GLY* 1.3 58.9 + - - +
1109A GLY* 4.6 13.2 - - - +
1110A VAL* 3.9 21.5 - - + +
1113A PHE* 3.8 27.1 - - + -
1136A ARG* 4.0 22.0 - - + +
1137A TRP* 4.0 35.2 - - + +
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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