Contacts of the helix formed by residues 1002 - 1018 (chain A) in PDB entry 4G34
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 HIS1002 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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928A HIS* 3.2 60.4 + + + +
932A LEU 4.9 2.0 - - - +
933A MET* 3.8 19.5 - - + -
1001A SER* 1.3 80.0 - - - +
1003A LYS* 1.3 73.7 - - + +
1004A VAL 3.0 7.2 + - - -
1005A ASP* 3.0 14.0 + - - +
1006A ILE* 4.0 3.2 + - + -
1066A GLU* 2.6 39.9 + - - -
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Residues in contact with LYS1003 (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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993A GLU* 5.0 0.4 - - - +
1001A SER* 2.9 17.8 + - - +
1002A HIS* 1.3 87.3 - - + +
1004A VAL* 1.3 60.6 + - - +
1005A ASP 3.2 0.4 - - - -
1006A ILE* 3.3 18.4 + - + +
1007A PHE 3.5 0.3 + - - -
1061A PRO* 3.3 39.0 - - + +
1062A MET* 4.1 11.0 + - - +
1064A ARG* 2.7 55.8 + - + +
1065A PRO 3.9 4.8 - - - -
1066A GLU* 2.6 36.6 + - - +
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Residues in contact with VAL1004 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
933A MET* 3.0 33.0 - - + -
935A ARG* 4.7 4.3 - - - -
991A SER* 3.4 12.5 - - - +
993A GLU* 3.4 19.7 - - + +
994A GLN* 3.4 23.7 - - + +
1000A TYR* 3.5 26.9 - - + -
1001A SER 3.0 10.3 + - - +
1002A HIS 3.0 1.0 - - - -
1003A LYS* 1.3 78.2 - - - +
1005A ASP* 1.3 70.0 + - - +
1006A ILE 3.4 0.5 + - - -
1007A PHE* 3.4 5.9 + - - +
1008A SER* 3.4 21.4 + - - -
1064A ARG* 3.9 7.0 - - - +
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Residues in contact with ASP1005 (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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924A VAL* 4.0 6.0 - - + +
928A HIS* 2.9 27.8 + - + +
933A MET* 3.5 7.7 - - - +
934A HIS* 2.8 32.5 + - - +
935A ARG* 2.8 28.5 + - - -
937A LEU* 3.8 16.9 - - + +
1002A HIS 3.0 9.8 + - - +
1004A VAL* 1.3 76.4 - - - +
1006A ILE* 1.3 60.8 + - - +
1008A SER* 3.3 8.2 + - - -
1009A LEU* 2.9 31.1 + - - +
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Residues in contact with ILE1006 (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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928A HIS* 4.1 17.0 - - + -
1002A HIS* 4.3 2.7 - - + +
1003A LYS* 3.6 27.8 - - + +
1004A VAL 3.2 0.8 - - - -
1005A ASP* 1.3 75.4 - - - +
1007A PHE* 1.3 64.9 + - - +
1009A LEU* 3.0 13.0 + - + +
1010A GLY 3.0 18.5 + - - -
1056A MET* 3.6 19.5 - - + +
1064A ARG* 4.0 13.0 - - + -
1065A PRO* 3.5 29.6 - - + +
1066A GLU* 4.7 0.7 - - - -
1067A ALA* 3.8 26.5 - - + +
1070A ILE* 3.8 20.0 - - + -
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Residues in contact with PHE1007 (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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989A TYR* 4.2 6.3 - - - -
991A SER* 3.7 23.8 - - - -
992A PRO* 3.6 21.5 - - + -
1003A LYS 3.5 2.4 + - - -
1004A VAL 3.4 10.5 + - - +
1006A ILE* 1.3 77.5 - - - +
1008A SER* 1.3 63.6 + - - +
1010A GLY 3.1 10.2 + - - -
1011A LEU* 3.4 6.0 + - + +
1034A ARG* 3.8 52.5 - - + -
1056A MET 3.4 10.4 + - - -
1057A LEU* 3.3 57.0 - - + +
1058A SER 4.1 3.4 - - - -
1059A PRO* 5.2 0.9 - - + -
1064A ARG* 3.7 28.7 - - - +
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Residues in contact with SER1008 (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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935A ARG 5.6 2.6 + - - -
937A LEU* 3.7 34.1 + - - +
989A TYR* 2.6 29.1 + - - +
990A MET* 4.7 1.9 - - - -
994A GLN* 5.3 1.7 + - - -
1004A VAL 3.4 10.7 + - - -
1005A ASP* 3.3 12.2 + - - -
1006A ILE 3.3 0.2 - - - -
1007A PHE* 1.3 79.2 - - - +
1009A LEU* 1.3 63.3 + - - +
1010A GLY 3.4 0.2 + - - -
1011A LEU* 3.5 3.8 + - - +
1012A ILE* 3.2 28.8 + - - +
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Residues in contact with LEU1009 (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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917A PHE* 3.2 33.3 - - + -
920A ILE* 3.8 29.2 - - + -
921A ALA* 4.5 15.5 - - + -
924A VAL* 4.3 22.7 - - + -
937A LEU* 4.3 5.4 - - + -
1005A ASP 2.9 19.6 + - - +
1006A ILE* 3.0 28.2 + - + +
1008A SER* 1.3 76.4 - - - +
1010A GLY* 1.3 62.4 + - - +
1012A ILE* 3.2 6.9 + - + -
1013A LEU* 2.9 19.4 + - - +
1056A MET* 4.3 4.5 - - - -
1067A ALA* 5.1 2.5 - - + -
1070A ILE* 4.4 11.9 - - + -
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Residues in contact with GLY1010 (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 ILE 3.0 11.3 + - - -
1007A PHE 3.1 4.8 + - - -
1009A LEU* 1.3 75.0 - - - +
1011A LEU* 1.3 62.0 + - - +
1013A LEU* 3.1 5.2 + - - +
1014A PHE 3.0 18.5 + - - -
1053A VAL* 3.7 17.8 - - - +
1056A MET* 3.8 30.5 - - - -
1057A LEU* 4.3 4.5 - - - -
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Residues in contact with LEU1011 (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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988A LEU* 3.2 28.3 - - + +
989A TYR* 4.0 24.5 - - + -
1007A PHE* 3.4 11.6 + - + +
1008A SER* 4.0 7.4 - - - +
1009A LEU 3.4 0.2 - - - -
1010A GLY* 1.3 75.9 - - - +
1012A ILE* 1.3 57.0 + - - +
1014A PHE* 3.5 3.8 + - + +
1015A GLU* 2.9 31.2 + - - +
1030A LEU* 3.8 34.5 - - + +
1033A VAL* 3.7 31.9 - - + -
1034A ARG* 4.0 16.2 - - + +
1057A LEU* 4.0 14.1 - - + +
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Residues in contact with ILE1012 (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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895A LEU* 4.2 19.5 - - + -
899A MET* 6.0 0.7 - - - -
917A PHE* 4.7 3.8 - - + -
920A ILE* 4.3 11.0 - - + -
937A LEU* 4.0 25.4 - - + +
938A LYS* 4.2 1.6 - - - +
939A PRO* 4.5 6.5 - - + -
942A ILE* 3.9 21.3 - - + -
989A TYR* 4.0 17.5 - - + -
1008A SER 3.2 21.6 + - - +
1009A LEU* 3.7 11.9 - - + +
1010A GLY 3.2 0.6 - - - -
1011A LEU* 1.3 73.4 - - - +
1013A LEU* 1.3 61.7 + - - +
1015A GLU* 3.3 6.7 + - + +
1016A LEU* 2.9 46.6 + - + +
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Residues in contact with LEU1013 (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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913A CYS 5.7 0.4 - - - +
914A LEU* 4.0 18.8 - - + -
917A PHE* 3.7 39.0 - - + -
1009A LEU 2.9 13.0 + - - +
1010A GLY 3.1 8.5 + - - +
1012A ILE* 1.3 73.6 - - - +
1014A PHE* 1.3 66.8 + - - +
1016A LEU* 3.3 6.2 + - + +
1017A LEU* 3.2 45.5 + - + +
1049A GLU* 4.4 14.6 - - + +
1052A MET* 4.6 7.9 - - + -
1053A VAL* 3.9 12.8 - - + -
1056A MET* 3.6 27.1 - - + -
1076A PHE* 5.0 2.7 - - + -
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Residues in contact with PHE1014 (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 GLY 3.0 13.0 + - - +
1011A LEU 3.7 5.8 - - - +
1013A LEU* 1.3 76.0 - - - +
1015A GLU* 1.3 64.6 + - - +
1017A LEU* 2.9 15.1 + - - +
1018A TYR* 3.0 40.3 + + + +
1020A PHE* 4.0 16.2 - + - -
1029A THR* 3.8 3.1 - - + -
1030A LEU* 3.6 26.0 - - + -
1033A VAL* 3.7 35.4 - - + -
1038A PHE* 4.5 2.7 - + - -
1039A PRO* 3.8 18.6 - - + -
1042A PHE* 3.7 49.1 - + - -
1053A VAL* 4.1 13.8 - - + +
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Residues in contact with GLU1015 (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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899A MET* 3.8 26.3 - - + +
908A ARG* 2.5 34.1 + - - +
939A PRO* 3.7 5.4 - - + +
989A TYR* 2.5 36.3 + - - -
1011A LEU 2.9 16.9 + - - +
1012A ILE* 3.8 4.7 - - - +
1014A PHE* 1.3 81.1 - - - +
1016A LEU* 1.3 53.4 + - - +
1018A TYR 3.4 8.3 - - - +
1020A PHE* 4.1 17.6 - - + -
1026A ARG* 2.9 31.4 + - - -
1030A LEU* 3.8 12.2 - - + +
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Residues in contact with LEU1016 (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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895A LEU* 4.1 18.8 - - + -
898A TRP* 4.0 26.5 - - + -
899A MET* 4.2 9.4 - - - -
908A ARG* 3.1 24.0 + - - +
913A CYS* 3.4 33.7 - - + +
916A ILE* 4.2 13.2 - - + -
917A PHE* 3.8 33.7 - - + +
920A ILE* 4.8 1.1 - - + -
1012A ILE* 2.9 37.4 + - + +
1013A LEU* 3.7 6.5 - - + +
1015A GLU* 1.3 76.5 - - - +
1017A LEU* 1.3 60.5 + - + +
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Residues in contact with LEU1017 (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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905A ILE* 5.8 2.9 - - - +
908A ARG* 5.3 4.5 - - - +
910A ARG* 4.6 7.0 - - + -
913A CYS* 4.2 21.5 - - + -
914A LEU* 4.3 14.6 - - + -
1013A LEU* 3.4 30.1 - - + +
1014A PHE 2.9 6.9 + - - +
1016A LEU* 1.3 76.7 - - + +
1018A TYR* 1.3 59.3 + - - +
1019A PRO* 3.5 10.3 - - - +
1042A PHE* 3.9 16.6 - - + -
1046A TYR* 3.7 47.1 + - + +
1049A GLU* 3.7 32.1 - - + +
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Residues in contact with TYR1018 (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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908A ARG* 3.7 3.3 + - - -
1014A PHE* 3.0 38.3 + + + +
1015A GLU 3.4 9.7 - - - +
1016A LEU 3.4 1.2 - - - -
1017A LEU* 1.3 79.5 - - - +
1019A PRO* 1.3 73.1 - - + +
1020A PHE* 3.5 42.6 - + - -
1025A GLU* 4.1 11.8 + - - -
1029A THR* 4.3 8.3 + - + +
1039A PRO* 3.6 29.7 - - + +
1041A LEU* 5.1 9.8 - - + +
1042A PHE* 4.1 24.2 - + + -
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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