Contacts of the helix formed by residues 1003 - 1019 (chain A) in PDB entry 4X7J
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 HIS1003 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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929A HIS* 3.1 55.9 + + + +
933A LEU 5.0 1.1 - - - +
934A MET* 3.5 24.7 - - + +
1002A SER* 1.3 81.6 - - - +
1004A LYS* 1.3 78.5 + - + +
1005A VAL* 3.1 1.6 - - - -
1006A ASP* 3.1 14.1 + - - +
1007A ILE* 4.0 1.1 + - + -
1067A GLU* 2.8 37.4 + - - -
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Residues in contact with LYS1004 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994A GLU* 5.0 0.2 - - - +
1002A SER* 2.9 18.2 + - - +
1003A HIS* 1.3 86.0 - - + +
1005A VAL* 1.3 62.9 + - - +
1006A ASP 3.2 0.4 - - - -
1007A ILE* 3.2 30.6 + - + +
1008A PHE 3.4 1.6 + - - -
1062A PRO* 3.1 39.7 + - + +
1063A MET* 3.5 16.3 + - - +
1065A ARG* 2.6 50.8 + - + +
1066A PRO 4.2 2.5 - - - -
1067A GLU* 3.5 33.4 + - - +
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Residues in contact with VAL1005 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934A MET* 4.4 5.4 - - - -
936A ARG* 4.4 10.3 - - - -
992A SER* 3.3 20.4 - - - +
994A GLU* 3.4 12.8 - - - +
995A GLN* 3.4 23.2 - - - +
1001A TYR* 3.4 32.1 - - + -
1002A SER 3.1 19.1 + - - +
1003A HIS 4.2 2.0 - - - +
1004A LYS* 1.3 77.6 - - - +
1006A ASP* 1.3 75.6 + - - +
1008A PHE* 3.3 13.5 + - - +
1009A SER* 3.4 14.3 + - - -
1065A ARG* 3.8 6.5 - - - +
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Residues in contact with ASP1006 (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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925A VAL* 4.0 12.7 - - + +
928A LEU* 5.7 0.3 - - - +
929A HIS* 2.9 27.0 + - + +
934A MET* 3.5 4.0 - - - +
935A HIS* 2.8 33.2 + - - +
936A ARG* 2.9 28.8 + - - -
938A LEU* 4.0 8.4 - - + +
1003A HIS 3.1 10.3 + - - +
1005A VAL* 1.3 78.2 - - - +
1007A ILE* 1.3 61.9 + - - +
1009A SER* 3.4 8.7 + - - -
1010A LEU* 3.1 30.5 + - - +
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Residues in contact with ILE1007 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929A HIS* 4.2 15.5 - - + +
1003A HIS* 4.4 2.7 - - + +
1004A LYS* 3.2 28.1 + - + +
1006A ASP* 1.3 74.7 - - - +
1008A PHE* 1.3 64.2 + - - +
1010A LEU* 3.4 19.6 + - + +
1011A GLY 3.2 16.1 + - - -
1057A MET* 3.5 28.7 - - + +
1065A ARG* 3.9 18.4 - - + -
1066A PRO* 3.4 29.2 - - + +
1067A GLU* 4.7 0.9 - - - +
1068A ALA* 3.8 26.5 - - + +
1071A ILE* 4.1 4.7 - - + -
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Residues in contact with PHE1008 (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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990A TYR 3.9 8.5 - - - -
991A MET 4.0 2.0 - - - -
992A SER* 3.8 15.5 - - - -
993A PRO* 3.5 22.0 - - + -
1004A LYS 3.4 2.2 + - - -
1005A VAL 3.3 11.3 + - - +
1006A ASP 3.3 0.2 - - - -
1007A ILE* 1.3 76.1 - - - +
1009A SER* 1.3 67.8 + - - +
1011A GLY 3.2 9.7 + - - -
1012A LEU* 3.5 16.1 + - + +
1035A ARG* 3.5 47.6 - - - -
1057A MET 3.4 7.7 + - - -
1058A LEU* 3.3 56.9 - - + +
1059A SER 4.5 0.9 - - - -
1060A PRO* 5.4 0.4 - - + -
1065A ARG* 3.8 30.5 - - - +
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Residues in contact with SER1009 (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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936A ARG 5.6 2.3 + - - -
938A LEU* 3.5 40.8 + - - +
990A TYR* 2.8 26.4 + - - -
991A MET* 4.5 2.9 - - - -
995A GLN* 5.5 0.7 + - - -
1005A VAL 3.4 8.7 + - - -
1006A ASP* 3.4 11.5 + - - -
1007A ILE 3.4 0.2 - - - -
1008A PHE* 1.3 77.1 - - - +
1010A LEU* 1.3 62.7 + - - +
1012A LEU* 3.3 5.7 + - - +
1013A ILE* 3.1 27.8 + - - +
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Residues in contact with LEU1010 (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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918A PHE* 3.3 31.6 - - + -
921A ILE* 3.6 31.4 - - + -
922A ALA* 4.2 15.0 - - + +
925A VAL* 4.1 24.0 - - + -
938A LEU* 3.8 11.2 - - + -
1006A ASP 3.1 17.9 + - - +
1007A ILE* 3.5 22.9 - - + +
1008A PHE 3.2 0.2 - - - -
1009A SER* 1.3 76.1 - - - +
1011A GLY* 1.3 56.6 + - - +
1013A ILE* 3.2 5.4 + - + +
1014A LEU* 2.9 26.5 + - - +
1057A MET* 4.1 4.5 - - - -
1068A ALA* 5.2 1.6 - - + -
1071A ILE* 4.2 13.7 - - + -
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Residues in contact with GLY1011 (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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1007A ILE 3.2 4.8 + - - -
1008A PHE 3.2 8.6 + - - -
1010A LEU* 1.3 79.3 - - - +
1012A LEU* 1.3 61.5 + - - +
1014A LEU* 3.5 3.2 + - - +
1015A PHE* 3.2 17.5 + - - +
1054A VAL* 3.6 20.5 - - - +
1057A MET* 3.7 26.8 - - - -
1058A LEU* 4.1 7.6 - - - -
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Residues in contact with LEU1012 (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 LEU 3.3 24.7 - - - +
990A TYR* 3.9 24.0 - - + +
1008A PHE* 3.5 36.3 + - + +
1009A SER 3.3 6.7 + - - +
1011A GLY* 1.3 75.3 - - - +
1013A ILE* 1.3 57.7 + - - +
1015A PHE* 3.5 7.1 + - - +
1016A GLU* 2.9 30.4 + - - +
1031A LEU* 3.7 41.0 - - + +
1034A VAL* 4.1 15.9 - - + -
1035A ARG* 3.9 9.6 - - + +
1058A LEU* 3.9 9.6 - - + +
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Residues in contact with ILE1013 (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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896A LEU* 4.4 9.9 - - + -
900A MET* 5.3 1.1 - - + +
918A PHE* 4.5 4.7 - - + -
921A ILE* 4.0 24.9 - - + -
938A LEU* 4.0 31.4 - - + +
939A LYS* 4.2 11.7 - - - -
940A PRO* 4.3 18.2 - - + -
943A ILE* 4.1 12.6 - - + -
990A TYR* 4.3 6.5 - - + -
1009A SER 3.1 19.5 + - - +
1010A LEU* 3.7 8.1 - - + +
1012A LEU* 1.3 74.5 - - - +
1014A LEU* 1.3 59.6 + - - +
1016A GLU* 3.7 6.1 - - + +
1017A LEU* 2.8 40.3 + - + +
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Residues in contact with LEU1014 (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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914A CYS 5.4 1.6 - - - +
915A LEU* 4.1 16.8 - - + -
918A PHE* 3.6 38.5 - - + -
1010A LEU 2.9 17.0 + - - +
1011A GLY* 3.8 4.9 - - - +
1012A LEU 3.4 0.2 - - - -
1013A ILE* 1.3 79.7 - - - +
1015A PHE* 1.3 62.9 + - - +
1017A LEU* 3.3 6.1 + - + +
1018A LEU* 3.2 38.3 + - + +
1050A GLU* 4.5 4.7 - - + +
1053A MET* 4.0 18.4 - - + -
1054A VAL* 3.8 20.4 - - + -
1057A MET* 4.0 21.3 - - + -
1077A PHE* 5.3 1.3 - - + -
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Residues in contact with PHE1015 (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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1011A GLY 3.2 11.0 + - - +
1012A LEU 3.7 7.0 - - - +
1013A ILE 3.3 0.2 - - - -
1014A LEU* 1.3 79.9 - - - +
1016A GLU* 1.3 59.4 + - - +
1018A LEU* 3.2 3.6 + - - +
1019A TYR* 3.0 53.8 + + + +
1021A PHE* 4.0 5.4 - + - -
1030A THR* 3.8 20.9 - - + -
1031A LEU* 3.8 23.1 - - + -
1034A VAL* 3.7 39.5 - - + -
1039A PHE* 4.4 3.4 - + - -
1040A PRO* 4.0 11.2 - - + -
1043A PHE* 3.7 49.4 - + + -
1054A VAL* 4.3 7.8 - - + +
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Residues in contact with GLU1016 (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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900A MET* 3.7 26.9 - - + +
909A ARG* 2.8 21.3 + - - +
940A PRO* 3.7 6.6 - - - +
990A TYR* 2.4 36.0 + - - -
1012A LEU 2.9 16.5 + - - +
1013A ILE* 3.2 5.7 + - - +
1015A PHE* 1.3 81.6 - - - +
1017A LEU* 1.3 58.3 + - - +
1019A TYR 3.2 13.0 - - - +
1021A PHE* 4.0 17.3 - - + -
1027A ARG* 2.9 31.2 + - - -
1031A LEU* 4.0 11.6 - - + +
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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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896A LEU* 4.0 26.2 - - + -
899A TRP* 4.1 16.6 - - + -
900A MET* 4.0 12.3 - - - -
909A ARG* 2.8 23.4 + - - +
914A CYS* 3.3 46.1 - - + +
917A ILE* 4.2 12.3 - - + -
918A PHE* 3.8 26.7 - - + +
921A ILE* 4.5 1.3 - - + -
1013A ILE* 2.8 33.8 + - + +
1014A LEU* 3.5 6.5 - - + +
1016A GLU* 1.3 77.4 - - - +
1018A LEU* 1.3 57.3 + - - +
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Residues in contact with LEU1018 (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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906A ILE* 4.6 5.5 - - - +
909A ARG* 4.4 7.6 - - - +
911A ARG* 4.3 15.9 - - + +
914A CYS* 3.8 24.9 - - + -
915A LEU* 4.9 4.3 - - + -
1014A LEU* 3.2 25.5 + - + +
1015A PHE 3.2 7.0 + - - +
1017A LEU* 1.3 76.8 - - - +
1019A TYR* 1.3 59.1 + - - +
1020A PRO* 3.5 9.6 - - - +
1043A PHE* 4.0 17.0 - - + -
1047A TYR* 4.0 47.3 + - + +
1050A GLU* 3.8 34.1 - - + -
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Residues in contact with TYR1019 (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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906A ILE* 6.0 4.3 - - + -
909A ARG* 3.9 1.0 + - - -
1015A PHE* 3.0 39.9 + + + +
1016A GLU 3.2 14.2 - - - +
1017A LEU 3.4 0.6 - - - -
1018A LEU* 1.3 79.8 - - - +
1020A PRO* 1.4 74.7 - - + +
1021A PHE* 3.5 42.4 + + - -
1026A GLU* 4.2 9.5 + - - -
1030A THR* 4.3 9.4 - - + +
1040A PRO* 3.8 29.5 - - + +
1042A LEU* 5.6 5.9 - - + +
1043A PHE* 4.2 21.8 - + + -
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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