Contacts of the helix formed by residues 1076 - 1100 (chain A) in PDB entry 4RGW
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 VAL1076 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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991A ASN 4.1 13.0 - - - +
992A LYS* 3.9 20.2 - - - +
1075A SER* 1.3 76.7 - - - +
1077A ALA* 1.3 63.8 + - + +
1078A GLU 3.3 0.2 - - - -
1079A HIS* 3.8 6.7 - - + -
1080A GLN* 3.6 29.5 + - - +
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Residues in contact with ALA1077 (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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1075A SER 3.3 5.3 - - - +
1076A VAL* 1.3 82.9 - - + +
1078A GLU* 1.3 57.8 + - - +
1079A HIS 3.4 0.4 - - - -
1080A GLN* 4.2 3.3 - - - +
1081A GLU* 3.2 28.5 + - - +
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Residues in contact with GLU1078 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1075A SER* 3.7 26.7 + - - +
1077A ALA* 1.3 78.7 - - - +
1079A HIS* 1.3 58.7 + - - +
1081A GLU* 3.8 12.2 - - - +
1082A ARG* 2.9 66.4 + - + +
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Residues in contact with HIS1079 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968A LEU* 3.8 18.3 - - + +
989A ILE* 4.5 12.1 - - + +
990A PRO* 3.5 20.2 - - + +
991A ASN 3.4 8.3 + - - -
992A LYS* 3.3 36.5 - - + +
1075A SER 3.2 18.2 + - - +
1076A VAL* 3.9 11.7 - - + +
1077A ALA 3.4 0.2 - - - -
1078A GLU* 1.3 78.4 - - - +
1080A GLN* 1.3 62.8 + - - +
1082A ARG* 3.6 6.8 + - + +
1083A TYR* 3.3 19.2 + - - +
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Residues in contact with GLN1080 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968A LEU* 4.4 27.5 - - + +
991A ASN* 4.6 15.3 + - - +
1076A VAL* 3.6 22.4 + - - +
1077A ALA* 3.9 3.7 + - - +
1079A HIS* 1.3 79.9 - - - +
1081A GLU* 1.3 61.7 + - - +
1083A TYR* 3.3 10.8 + - + +
1084A LYS* 3.0 30.3 + - - +
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Residues in contact with GLU1081 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077A ALA 3.2 21.5 + - - +
1078A GLU* 3.4 11.7 + - + +
1080A GLN* 1.3 77.2 - - - +
1082A ARG* 1.3 58.0 - - + +
1084A LYS* 3.9 6.2 - - + +
1085A GLU* 2.9 47.6 + - + +
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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
----------------------------------------------------------
1078A GLU* 2.9 49.8 + - + +
1079A HIS* 3.9 6.3 - - - +
1081A GLU* 1.3 75.2 - - + +
1083A TYR* 1.3 64.4 + - - +
1085A GLU* 3.6 17.8 + - - +
1086A GLU* 3.1 26.9 + - - +
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Residues in contact with TYR1083 (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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752A LEU* 4.7 6.6 - - - +
962A ALA* 4.6 6.6 - - - +
968A LEU* 3.8 36.5 - - + +
969A LEU* 3.3 61.7 + - - +
971A VAL* 3.7 15.9 - - + -
989A ILE* 5.2 2.9 - - + -
1079A HIS 3.3 11.1 + - - +
1080A GLN* 3.3 10.9 + - + +
1082A ARG* 1.3 79.2 - - - +
1084A LYS* 1.3 67.9 + - + +
1086A GLU* 3.3 3.6 + - - +
1087A CYS* 2.9 46.8 + - - -
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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
----------------------------------------------------------
752A LEU 3.0 27.6 + - - +
753A GLY* 3.6 4.2 - - - -
754A SER* 4.4 14.4 - - - -
1080A GLN 3.0 17.3 + - - +
1081A GLU* 3.9 7.0 - - + +
1083A TYR* 1.3 86.2 - - + +
1085A GLU* 1.3 58.2 + - - +
1087A CYS* 3.4 2.6 + - + -
1088A GLN* 2.8 51.1 + - - +
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Residues in contact with GLU1085 (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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1081A GLU* 2.9 43.6 + - + +
1082A ARG* 3.6 20.9 + - - +
1083A TYR 3.3 0.2 - - - -
1084A LYS* 1.3 76.5 - - - +
1086A GLU* 1.3 60.8 + - - +
1088A GLN* 3.3 7.1 + - - +
1089A ARG* 3.0 28.2 + - - +
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Residues in contact with GLU1086 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970A GLU 5.8 0.4 - - - +
971A VAL* 4.1 16.4 - - + -
972A THR* 4.0 18.3 + - - +
1082A ARG 3.1 15.7 + - - +
1083A TYR* 3.8 4.7 - - - +
1085A GLU* 1.3 78.2 - - - +
1087A CYS* 1.3 67.7 + - - +
1089A ARG* 2.5 45.5 + - - +
1090A ILE* 3.1 23.9 + - - +
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Residues in contact with CYS1087 (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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752A LEU* 3.3 40.2 - - + +
971A VAL* 3.7 25.1 - - - +
984A PHE* 3.7 11.3 - - - -
1083A TYR* 2.9 44.6 + - - +
1084A LYS* 3.6 6.5 - - - +
1086A GLU* 1.3 75.7 - - - +
1088A GLN* 1.3 58.3 + - - +
1090A ILE 3.3 0.2 + - - -
1091A PHE* 2.8 32.7 + - - +
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Residues in contact with GLN1088 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A GLY* 4.2 0.4 - - - -
754A SER* 2.8 51.6 + - - +
756A HIS* 3.8 8.9 + - - +
1084A LYS* 2.8 28.2 + - - +
1085A GLU* 3.4 8.1 - - - +
1087A CYS* 1.3 77.2 - - - +
1089A ARG* 1.3 56.5 + - - +
1091A PHE* 3.3 8.0 + - - +
1092A ASP* 2.9 65.9 + - - +
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Residues in contact with ARG1089 (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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972A THR* 4.3 5.9 + - - -
981A GLY* 4.8 4.0 + - - -
1085A GLU 3.0 16.3 + - - +
1086A GLU* 2.5 35.5 + - - +
1088A GLN* 1.3 77.3 - - - +
1090A ILE* 1.3 82.8 + - - +
1092A ASP* 3.4 6.3 + - - +
1093A LEU* 2.9 44.3 + - + +
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Residues in contact with ILE1090 (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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971A VAL* 3.4 35.7 - - + +
972A THR* 4.5 4.9 - - - +
981A GLY* 4.0 12.3 - - - +
982A GLU 4.1 5.2 - - - +
983A GLY 3.8 37.7 - - - +
984A PHE* 3.7 25.4 - - + -
1086A GLU* 3.1 9.2 + - + +
1089A ARG* 1.3 99.0 - - - +
1091A PHE* 1.3 60.5 + - - +
1093A LEU* 3.5 5.6 - - - +
1094A GLN* 2.9 29.8 + - - +
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Residues in contact with PHE1091 (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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751A PHE* 3.6 30.5 - + + -
752A LEU 4.8 0.7 - - - -
753A GLY* 3.6 31.6 - - - +
754A SER 3.6 20.9 - - - -
755A LEU* 3.9 15.7 - - + -
759A GLN* 4.5 4.9 - - - -
761A LEU* 3.7 18.4 - - + -
772A PRO* 6.0 2.0 - - + -
984A PHE* 3.7 15.8 - + + -
1087A CYS 2.8 18.2 + - - +
1088A GLN* 3.5 6.5 - - - +
1090A ILE* 1.3 76.9 - - - +
1092A ASP* 1.3 74.9 + - - +
1094A GLN* 3.9 8.2 + - - +
1095A ASN* 3.1 51.2 + - - +
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Residues in contact with ASP1092 (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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756A HIS* 3.0 32.9 + - - -
759A GLN* 5.2 1.2 + - - -
1088A GLN* 2.9 42.5 + - - +
1089A ARG* 3.8 5.8 - - - +
1091A PHE* 1.3 80.9 - - - +
1093A LEU* 1.3 65.9 + - - +
1095A ASN* 3.5 7.3 + - - +
1096A LYS* 3.1 25.6 + - - +
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Residues in contact with LEU1093 (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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980A CYS 5.7 0.4 - - - +
981A GLY 3.5 25.4 - - - +
982A GLU* 3.9 17.9 - - + +
1089A ARG* 2.9 33.6 + - + +
1090A ILE* 3.2 6.7 + - - +
1092A ASP* 1.3 76.6 - - - +
1094A GLN* 1.3 63.0 + - - +
1096A LYS* 3.2 11.0 + - + +
1097A VAL* 3.0 48.8 + - + +
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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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705A SER* 4.8 0.9 + - - -
772A PRO* 3.8 20.4 - - - +
774A TYR* 3.5 13.1 + - - +
804A GLY* 3.5 6.0 - - - -
805A GLN* 2.9 36.1 + - - +
982A GLU* 3.9 23.4 + - - +
984A PHE* 4.4 18.8 - - + -
1090A ILE* 2.9 18.2 + - + +
1091A PHE* 3.9 8.2 + - - +
1093A LEU* 1.3 76.0 - - - +
1095A ASN* 1.3 64.6 + - - +
1097A VAL* 4.9 2.5 - - - -
1098A LEU* 2.9 41.0 + - + +
147B ARG* 4.7 5.3 + - - +
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Residues in contact with ASN1095 (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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759A GLN* 3.8 16.8 - - - +
761A LEU* 3.9 16.7 - - + +
772A PRO* 4.4 2.1 - - - +
774A TYR* 2.5 39.5 + - + -
1091A PHE* 3.1 52.9 + - - +
1092A ASP* 3.8 6.4 + - - +
1094A GLN* 1.3 77.8 + - - +
1096A LYS* 1.3 53.4 - - - +
1099A SER* 2.7 38.2 + - - -
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Residues in contact with LYS1096 (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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1092A ASP 3.1 17.9 + - - +
1093A LEU* 3.7 12.6 - - + +
1095A ASN* 1.3 79.5 - - - +
1097A VAL* 1.3 63.6 + - + +
1099A SER* 3.5 6.1 + - - -
1100A SER* 3.3 24.8 + - - -
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Residues in contact with VAL1097 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982A GLU* 3.6 28.9 - - + +
1093A LEU* 3.0 37.6 + - + +
1094A GLN* 4.0 2.9 - - - +
1096A LYS* 1.3 80.9 - - + +
1098A LEU* 1.3 73.6 + - + +
1100A SER* 3.5 14.3 + - - -
139B PRO* 3.4 18.1 - - + +
146B ARG* 4.0 13.7 - - - +
147B ARG* 4.5 0.7 - - - +
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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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705A SER* 4.2 5.4 - - - +
774A TYR* 3.6 25.3 - - + +
776A HIS* 2.8 23.2 + - - -
802A VAL* 4.1 18.6 - - + +
804A GLY* 3.7 24.2 - - - -
1094A GLN* 2.9 40.1 + - + +
1097A VAL* 1.3 79.2 - - + +
1099A SER* 1.3 57.6 + - - +
139B PRO* 3.3 21.0 - - + +
140B LEU* 4.5 6.7 - - + -
147B ARG* 3.5 36.6 - - - +
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Residues in contact with SER1099 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774A TYR* 3.9 18.6 - - - -
775A LEU 5.7 0.5 - - - +
776A HIS* 3.9 11.7 - - - -
1095A ASN 2.7 25.2 + - - -
1096A LYS* 3.5 6.6 + - - -
1098A LEU* 1.3 76.9 - - - +
1100A SER* 1.3 65.9 + - - +
1101A THR* 3.6 6.4 + - - +
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Residues in contact with SER1100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776A HIS* 3.5 12.6 - - - -
1096A LYS* 3.3 19.6 + - - -
1097A VAL* 3.7 10.8 - - - -
1098A LEU 3.4 1.8 - - - -
1099A SER* 1.3 79.2 - - - +
1101A THR* 1.3 61.7 + - - +
1102A GLU* 3.1 28.4 + - - +
138B LEU* 4.2 1.9 - - - +
139B PRO* 3.6 13.9 - - - +
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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
------------------------------------------------------------
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