Contacts of the helix formed by residues 1082 - 1095 (chain C) in PDB entry 6M6A
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 PRO1082 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1050C GLN* 6.2 0.2 - - - +
1079C PRO* 6.5 0.2 - - + -
1080C SER 3.2 9.4 - - - +
1081C VAL* 1.3 85.6 - - + +
1083C GLU* 1.3 64.2 + - - +
1084C SER* 4.0 2.2 - - - +
1085C PHE* 3.3 19.2 + - + +
1086C ARG* 2.9 27.6 + - - +
1468D LEU* 3.1 31.2 - - + +
1469D GLY* 4.0 5.4 - - - +
1470D ARG* 3.7 31.0 - - + +
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Residues in contact with GLU1083 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1054C THR* 2.7 34.9 + - - +
1059C ASP* 3.1 32.7 - - - +
1061C GLU* 4.2 8.4 - - - +
1079C PRO* 5.8 3.3 - - - +
1081C VAL 3.5 4.2 + - - +
1082C PRO* 1.3 73.9 - - - +
1084C SER* 1.3 65.4 + - - +
1085C PHE 3.3 0.4 - - - -
1086C ARG* 3.3 25.4 - - + +
1087C VAL* 2.9 27.4 + - - +
87D ARG* 5.6 1.1 + - - +
88D TYR* 5.1 6.2 - - - +
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Residues in contact with SER1084 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082C PRO* 4.0 1.6 - - - +
1083C GLU* 1.3 86.2 - - - +
1085C PHE* 1.3 59.9 + - - +
1087C VAL* 3.1 15.1 + - - +
1088C LEU* 3.0 30.6 + - - +
617D ASN 5.5 2.2 - - - -
618D LEU* 4.3 17.0 - - - +
1467D ILE 4.0 2.6 + - - -
1468D LEU 2.6 31.7 + - - -
1469D GLY* 4.8 0.5 - - - -
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Residues in contact with PHE1085 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1081C VAL* 4.6 4.0 - - + -
1082C PRO* 3.3 37.1 + - + +
1083C GLU 3.3 0.2 - - - -
1084C SER* 1.3 81.2 + - - +
1086C ARG* 1.3 62.2 + - - +
1088C LEU* 3.2 17.0 + - + +
1089C VAL* 3.0 40.7 + - + +
1099C VAL* 5.8 0.4 - - + -
1101C THR* 3.9 26.0 - - + -
1111C ILE* 3.8 31.0 - - + -
5D VAL* 5.2 9.9 - - + -
8D VAL* 5.3 12.8 - - + -
1468D LEU* 3.9 38.4 - - + +
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Residues in contact with ARG1086 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1081C VAL* 3.8 13.8 + - + +
1082C PRO 2.9 15.8 + - - +
1083C GLU* 3.3 27.4 - - - +
1085C PHE* 1.3 76.7 - - - +
1087C VAL* 1.3 59.7 + - - +
1089C VAL* 3.1 6.0 + - - +
1090C LYS* 2.9 31.3 + - - +
1111C ILE* 2.4 77.2 + - + +
1112C PHE* 3.3 32.2 - - + +
1115C LEU* 4.6 9.9 - - - +
88D TYR* 3.9 23.3 + - + -
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Residues in contact with VAL1087 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083C GLU 2.9 15.4 + - - +
1084C SER* 3.1 21.9 + - - +
1086C ARG* 1.3 72.8 - - - +
1088C LEU* 1.3 61.0 + - - +
1090C LYS* 4.1 5.2 - - - -
1091C GLU* 2.9 33.4 + - + +
87D ARG* 3.7 14.1 - - - +
88D TYR* 5.9 2.5 - - + -
524D LEU* 3.7 35.9 - - + -
613D ARG* 4.3 32.8 - - - +
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Residues in contact with LEU1088 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084C SER 3.0 18.7 + - - +
1085C PHE* 3.3 25.4 - - + +
1087C VAL* 1.3 76.2 - - - +
1089C VAL* 1.3 60.6 + - + +
1091C GLU* 2.8 29.3 - - + +
1092C LEU* 2.9 21.9 + - + +
607D LEU* 5.5 1.3 - - + -
613D ARG* 3.7 33.2 - - + -
614D PHE* 5.7 7.0 - - + -
618D LEU* 4.6 9.4 - - + -
1435D LEU* 5.7 4.7 - - + -
1467D ILE* 4.4 23.8 - - + +
1468D LEU* 4.5 12.1 - - + -
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Residues in contact with VAL1089 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085C PHE* 3.0 43.7 + - + +
1086C ARG* 3.1 9.2 + - - +
1088C LEU* 1.3 75.7 - - + +
1090C LYS* 1.3 62.9 + - + +
1092C LEU* 3.3 6.7 + - - +
1093C GLN* 3.0 53.5 + - - +
1099C VAL* 3.7 22.4 - - + -
1101C THR* 5.3 6.7 - - + -
1111C ILE* 5.0 5.8 - - + -
1112C PHE* 5.6 5.2 - - + -
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Residues in contact with LYS1090 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086C ARG 2.9 20.2 + - - +
1087C VAL* 3.6 9.2 - - + +
1088C LEU 3.2 0.2 - - - -
1089C VAL* 1.3 80.8 - - - +
1091C GLU* 1.3 56.9 + - - +
1093C GLN* 3.4 17.8 + - - +
1094C ALA* 2.9 25.6 + - - +
1112C PHE* 3.7 26.5 - - - -
1116C ALA 4.9 4.4 + - - -
87D ARG 3.9 4.0 - - - +
88D TYR* 3.2 60.6 + - + +
90D MET* 3.4 26.6 - - - +
520D LEU* 4.8 1.0 - - - +
521D PRO* 5.9 0.2 - - - +
524D LEU* 3.8 21.1 - - + -
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Residues in contact with GLU1091 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087C VAL* 2.9 24.6 + - + +
1088C LEU* 2.8 26.9 - - + +
1090C LYS* 1.3 74.4 - - - +
1092C LEU* 1.3 76.1 + - - +
1094C ALA* 3.1 11.2 + - + +
1095C LEU* 2.9 29.8 + - - +
520D LEU* 5.0 5.6 - - + -
524D LEU* 5.3 1.3 - - + +
606D ILE* 6.4 0.4 - - + -
607D LEU* 3.3 46.6 - - + +
613D ARG* 5.8 4.5 - - + +
614D PHE* 5.9 0.3 - - - -
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Residues in contact with LEU1092 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088C LEU* 2.9 18.9 + - + +
1089C VAL* 3.5 5.6 - - - +
1091C GLU* 1.3 87.6 - - - +
1093C GLN* 1.3 58.0 + - + +
1095C LEU* 3.0 21.7 + - - +
1096C ALA 3.1 8.0 + - - -
1097C LEU* 3.2 59.1 + - + +
1098C ASP 3.7 1.8 - - - +
1099C VAL* 3.7 31.9 - - + +
10D ILE* 3.7 26.9 - - + -
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Residues in contact with GLN1093 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089C VAL* 3.0 38.1 + - - +
1090C LYS* 3.7 16.1 + - - +
1092C LEU* 1.3 76.7 - - + +
1094C ALA* 1.3 60.1 + - - +
1096C ALA* 3.0 18.1 + - - +
1097C LEU 3.9 9.9 - - - +
1099C VAL* 4.3 8.1 - - + +
21D TRP* 3.7 46.5 - - + +
90D MET* 3.3 29.8 - - - +
518D PRO* 3.6 10.9 - - - +
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Residues in contact with ALA1094 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090C LYS 2.9 15.1 + - - +
1091C GLU* 3.1 14.8 + - + +
1093C GLN* 1.3 76.4 - - - +
1095C LEU* 1.3 55.7 + - - +
1096C ALA 3.1 2.0 - - - -
90D MET* 5.6 2.2 - - - -
518D PRO* 3.3 28.0 - - + +
519D VAL 5.6 0.9 - - - +
520D LEU* 3.7 29.4 - - + +
544D TYR* 5.7 2.0 - - - +
603D LEU* 6.0 2.3 - - - +
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Residues in contact with LEU1095 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091C GLU* 2.9 17.2 + - - +
1092C LEU* 3.0 10.5 + - - +
1094C ALA* 1.3 74.8 - - - +
1096C ALA* 1.3 69.6 + - - +
1097C LEU* 3.3 32.1 - - + +
101D HIS* 3.5 34.1 + - + +
103D TRP* 4.5 29.8 - - + -
518D PRO* 5.6 0.2 - - - -
582D LEU* 5.1 5.4 - - + -
603D LEU* 4.7 21.5 - - + -
607D LEU* 6.4 1.6 - - + -
1447D LEU* 5.5 5.6 - - + -
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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