Contacts of the helix formed by residues 1080 - 1096 (chain A) in PDB entry 6S1M
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 TYR1080 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877A ASP* 3.5 17.9 - - - +
878A ILE* 3.6 33.9 + - + -
879A SER* 2.4 40.3 + - - -
882A VAL* 5.2 4.0 - - - +
942A PRO* 6.1 4.3 - - + -
943A LEU* 6.2 0.2 - - + -
946A LEU* 3.6 35.4 - - + -
1074A ARG* 4.2 23.7 + - + -
1075A ASP 6.0 0.2 - - - -
1076A CYS 4.4 5.5 + - - -
1077A PRO 4.6 1.3 - - - -
1078A ILE 3.6 0.6 + - - -
1079A PHE* 1.3 101.4 - + - +
1081A MET* 1.3 58.6 + - - +
1082A ARG* 3.4 5.8 - - - +
1083A LYS* 3.8 24.0 + - + +
1084A LYS* 3.9 18.0 + - - +
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Residues in contact with MET1081 (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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877A ASP* 4.1 17.7 - - + +
1050A ARG* 6.0 5.6 - - + -
1054A LEU* 3.5 26.8 - - + +
1077A PRO* 3.2 29.1 + - - +
1078A ILE* 3.9 5.2 - - - +
1079A PHE 3.0 4.4 + - - -
1080A TYR* 1.3 74.4 - - - +
1082A ARG* 1.3 58.0 + - - +
1083A LYS 3.2 4.7 - - - -
1084A LYS* 3.9 25.3 - - - +
1085A VAL* 3.3 26.7 - - - +
107B ILE* 5.4 8.5 - - + -
108B LEU* 6.4 2.7 - - + -
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Residues in contact with ARG1082 (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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1054A LEU* 4.3 18.1 - - + +
1055A TRP* 3.2 58.5 + - + +
1058A CYS* 3.5 27.2 - - - -
1069A VAL* 4.6 7.8 + - - +
1071A CYS* 2.8 36.4 + - - +
1078A ILE* 3.1 17.4 + - + +
1079A PHE* 3.9 18.8 - - - -
1080A TYR 4.3 1.3 - - - +
1081A MET* 1.3 76.3 - - - +
1083A LYS* 1.3 63.8 + - + +
1084A LYS 3.6 0.2 - - - -
1085A VAL* 4.6 3.1 - - - +
1086A ARG* 4.4 9.5 + - - +
1202A SF4 3.8 9.7 - - - -
106D PRO 3.9 6.3 + - - -
107D LEU* 3.6 36.2 + - - +
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Residues in contact with LYS1083 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946A LEU* 4.6 28.0 - - + +
947A GLU* 5.5 1.1 - - - -
1055A TRP* 5.9 0.4 - - - -
1079A PHE* 6.1 2.5 - - + -
1080A TYR* 3.8 20.8 - - + +
1081A MET 3.2 0.8 - - - -
1082A ARG* 1.3 82.6 - - + +
1084A LYS* 1.3 62.7 + - - +
1085A VAL 3.5 1.2 + - - -
1086A ARG* 3.8 18.4 - - - +
1087A LYS* 4.0 10.5 + - + +
106D PRO* 3.4 43.4 + - + +
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Residues in contact with LYS1084 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A ARG 6.3 1.0 - - - -
876A ILE 5.9 1.1 - - - +
877A ASP* 3.3 35.2 - - - +
1050A ARG* 4.1 21.4 - - - +
1080A TYR 3.9 7.8 + - - +
1081A MET* 3.9 29.3 - - - +
1083A LYS* 1.3 78.4 - - - +
1085A VAL* 1.3 65.1 + - + +
1086A ARG 3.2 0.9 - - - -
1087A LYS* 3.2 9.2 + - - +
1088A ASP* 3.0 36.6 + - - +
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Residues in contact with VAL1085 (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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1047A LEU* 4.0 12.8 - - + +
1050A ARG* 3.7 43.3 - - - +
1051A PHE* 4.0 30.1 - - + +
1054A LEU* 4.0 8.7 - - + -
1055A TRP* 6.4 1.3 - - + -
1081A MET 3.3 21.8 - - - +
1082A ARG* 5.1 2.9 - - - +
1083A LYS 3.5 0.8 - - - +
1084A LYS* 1.3 80.8 - - + +
1086A ARG* 1.3 59.9 + - - +
1088A ASP* 4.2 8.5 - - + -
1089A LEU* 2.9 30.6 + - + +
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Residues in contact with ARG1086 (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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1051A PHE* 3.8 22.4 - - + -
1055A TRP* 3.4 38.5 - - - +
1082A ARG 4.4 10.4 + - - +
1083A LYS* 3.8 12.6 + - - +
1084A LYS 3.2 0.2 - - - -
1085A VAL* 1.3 78.2 - - - +
1087A LYS* 1.3 72.0 + - - +
1089A LEU* 3.8 4.3 - - - +
1090A GLU* 2.9 27.9 + - - +
46B PHE* 5.8 3.9 - - + +
47B SER* 3.5 38.1 + - - +
48B ARG* 3.3 30.1 + - - +
49B GLN* 4.4 2.8 + - - +
107D LEU 4.5 11.5 + - - -
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Residues in contact with LYS1087 (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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1083A LYS 4.2 10.5 - - - +
1084A LYS* 3.2 10.7 + - - +
1086A ARG* 1.3 112.5 + - - +
1088A ASP* 1.3 60.0 + - - +
1090A GLU* 3.5 18.7 + - + +
1091A ASP* 2.9 32.4 + - - +
47B SER* 5.3 5.3 - - - -
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Residues in contact with ASP1088 (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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1047A LEU* 3.6 22.3 - - + +
1050A ARG* 3.9 17.7 + - - -
1084A LYS* 3.0 29.8 + - - +
1085A VAL* 3.5 6.0 + - + +
1087A LYS* 1.3 74.3 - - - +
1089A LEU* 1.3 58.8 + - - +
1091A ASP* 2.3 40.2 - - - +
1092A GLN* 3.0 10.0 + - - +
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Residues in contact with LEU1089 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1044A LEU* 4.0 22.4 - - + -
1047A LEU* 3.7 30.4 - - + +
1048A GLU* 4.1 14.6 - - + +
1051A PHE* 4.0 26.0 - - + -
1085A VAL* 2.9 17.5 + - + +
1086A ARG* 3.8 4.0 - - - +
1088A ASP* 1.3 73.4 - - - +
1090A GLU* 1.3 61.6 + - - +
1092A GLN* 4.6 0.4 - - - +
1093A GLU* 3.0 35.7 + - + +
46B PHE* 3.6 51.1 - - + -
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Residues in contact with GLU1090 (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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1086A ARG 2.9 19.7 + - - +
1087A LYS* 3.5 23.6 + - + +
1089A LEU* 1.3 77.4 - - - +
1091A ASP* 1.3 60.9 + - - +
1093A GLU* 4.2 5.3 - - - +
1094A GLN* 3.4 42.3 + - + +
45B SER* 5.7 1.2 + - - -
46B PHE* 5.7 5.4 + - - +
47B SER* 6.0 1.4 - - - -
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Residues in contact with ASP1091 (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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1047A LEU* 4.9 0.3 - - - +
1087A LYS 2.9 21.0 + - - +
1088A ASP* 2.3 32.3 - - - +
1090A GLU* 1.3 76.7 - - - +
1092A GLN* 1.3 89.6 + - - +
1093A GLU 3.3 0.4 - - - -
1094A GLN* 3.4 5.3 + - - +
1095A LEU* 3.2 27.5 + - - +
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Residues in contact with GLN1092 (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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1040A GLU* 3.2 33.0 - - - +
1043A HIS* 3.2 28.2 + - + -
1044A LEU* 3.9 29.6 - - + -
1047A LEU* 3.8 10.8 - - + -
1088A ASP 3.0 11.7 + - - +
1089A LEU 4.3 1.3 - - - +
1091A ASP* 1.3 89.5 + - - +
1093A GLU* 1.3 63.0 + - - +
1095A LEU* 3.7 22.5 + - - +
1096A LEU* 3.4 22.9 + - - +
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Residues in contact with GLU1093 (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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1044A LEU* 4.3 15.4 - - + +
1089A LEU* 3.0 21.3 + - + +
1090A GLU* 4.2 5.7 - - - +
1092A GLN* 1.3 80.0 - - - +
1094A GLN* 1.3 76.6 + - - +
1096A LEU* 3.5 10.6 + - - +
1097A ARG* 3.4 30.9 + - + +
43B GLU 4.1 5.0 - - - +
44B ARG* 3.5 45.0 - - + +
46B PHE* 5.7 6.5 - - + -
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Residues in contact with GLN1094 (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 GLU* 3.4 32.8 + - + +
1091A ASP* 3.4 6.3 + - - +
1092A GLN 3.4 0.4 - - - -
1093A GLU* 1.3 86.6 + - - +
1095A LEU* 1.3 64.3 + - - +
1096A LEU 3.3 0.2 - - - -
1097A ARG* 3.4 44.2 + - - +
1098A ARG* 4.1 8.1 + - - -
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Residues in contact with LEU1095 (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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1013A ILE* 3.8 20.5 - - + +
1040A GLU* 3.3 35.9 - - + +
1091A ASP 3.2 16.2 + - - +
1092A GLN* 4.1 22.9 - - - +
1093A GLU 3.3 0.8 - - - -
1094A GLN* 1.3 79.0 - - - +
1096A LEU* 1.3 57.4 + - + +
1097A ARG 3.3 0.2 - - - -
1098A ARG* 3.4 33.3 - - - +
1099A PHE* 4.4 3.6 - - - -
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Residues in contact with LEU1096 (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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1037A TYR* 3.9 32.3 - - + +
1040A GLU* 3.5 34.1 - - + +
1041A VAL* 4.7 11.2 - - + -
1044A LEU* 3.8 36.8 - - + -
1092A GLN* 3.4 25.5 + - - +
1093A GLU* 3.5 7.9 + - - +
1094A GLN 3.3 0.6 - - - -
1095A LEU* 1.3 74.6 - - - +
1097A ARG* 1.3 57.8 + - + +
1098A ARG 3.1 5.3 + - - -
1099A PHE* 3.3 26.6 + - + +
1100A GLY 4.5 2.4 - - - +
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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