Contacts of the helix formed by residues 984 - 1004 (chain A) in PDB entry 3VF0
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 ASN 984 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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980A SER 3.8 15.0 + - - +
981A SER 3.0 13.2 + - - +
983A GLY* 1.3 77.9 - - - +
985A ASP* 1.3 62.5 + - - +
986A ILE* 3.2 14.0 + - - +
987A ILE* 3.2 27.4 + - + +
988A ALA* 3.2 17.0 + - - +
1123A LEU* 3.9 13.1 - - - +
1124A ARG 2.9 26.0 + - - +
1125A TRP* 3.4 34.4 - - - -
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Residues in contact with ASP 985 (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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981A SER 4.8 2.6 - - - +
983A GLY* 4.2 1.5 + - - -
984A ASN* 1.3 74.6 + - - +
986A ILE* 1.3 59.7 + - - +
987A ILE 3.3 0.2 - - - -
988A ALA* 3.7 11.6 - - - +
989A ALA* 3.0 30.5 + - - +
1027A GLU* 3.9 14.3 - - - +
1031A LEU* 3.6 28.6 - - + +
1123A LEU* 4.2 6.0 - - + +
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Residues in contact with ILE 986 (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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984A ASN* 3.2 9.3 + - - +
985A ASP* 1.3 76.5 - - - +
987A ILE* 1.3 55.8 + - + +
989A ALA* 3.3 5.2 + - - +
990A ALA* 2.8 33.1 + - - +
1028A VAL* 3.8 24.4 - - + +
1031A LEU* 3.5 22.3 - - + +
1032A ALA* 3.7 33.0 - - + +
1104A THR* 4.5 4.0 - - + -
1105A VAL* 3.7 31.0 - - + -
1108A ALA* 4.2 11.0 - - + -
1123A LEU* 3.7 23.7 - - + +
1125A TRP* 5.0 2.9 - - + -
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Residues in contact with ILE 987 (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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976A ALA* 3.5 27.6 - - + +
979A TRP* 3.6 41.5 - - + +
980A SER 3.8 5.8 - - - +
981A SER* 3.7 4.0 - - - +
984A ASN* 3.2 34.7 + - + +
986A ILE* 1.3 73.0 - - - +
988A ALA* 1.3 65.1 + - - +
990A ALA* 3.2 4.6 + - - +
991A LYS* 2.9 45.7 + - - +
1105A VAL* 3.8 26.5 - - + -
1125A TRP* 3.8 3.8 - - + -
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Residues in contact with ALA 988 (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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981A SER* 3.9 21.5 + - - +
984A ASN 3.2 12.9 + - - +
985A ASP* 3.7 17.5 - - + +
986A ILE 3.4 0.2 - - - -
987A ILE* 1.3 76.9 - - - +
989A ALA* 1.4 59.2 - - - +
991A LYS* 3.4 6.0 + - - +
992A ARG* 3.2 37.6 + - - +
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Residues in contact with ALA 989 (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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985A ASP 3.0 19.5 + - - +
986A ILE* 3.7 3.1 - - - +
988A ALA* 1.4 72.7 - - - +
990A ALA* 1.3 60.3 + - - +
992A ARG* 3.1 29.3 + - - +
993A MET* 2.9 32.7 + - - +
1024A ALA* 4.0 12.4 - - + +
1027A GLU* 4.0 10.1 - - + +
1028A VAL* 3.7 18.2 - - + -
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Residues in contact with ALA 990 (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 LEU* 3.4 15.3 - - + +
976A ALA* 4.0 17.5 - - + -
986A ILE 2.8 23.0 + - - +
987A ILE* 3.6 4.9 - - - +
989A ALA* 1.3 71.3 - - - +
991A LYS* 1.3 57.6 + - - +
993A MET* 3.3 8.4 + - - -
994A ALA* 3.1 25.5 + - - +
1028A VAL* 4.3 1.0 - - + +
1101A VAL* 3.9 26.5 - - + -
1105A VAL* 4.5 8.3 - - + -
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Residues in contact with LYS 991 (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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973A HIS* 4.9 6.6 + - + +
976A ALA* 3.5 35.2 - - + -
977A THR* 3.8 22.3 - - + +
979A TRP 3.0 16.7 + - - -
981A SER* 2.9 19.3 + - - +
987A ILE* 2.9 16.3 + - - +
988A ALA* 3.5 9.0 - - - +
990A ALA* 1.3 76.2 - - - +
992A ARG* 1.3 60.8 + - + +
994A ALA* 3.5 7.7 + - - +
995A LEU* 3.3 30.6 + - + +
1128A LYS* 5.4 0.8 - - - +
2002A GOL 2.7 29.9 + - - +
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Residues in contact with ARG 992 (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 ALA* 3.2 29.5 + - - +
989A ALA* 3.1 20.5 + - - +
991A LYS* 1.3 73.7 - - + +
993A MET* 1.4 60.7 + - - +
995A LEU* 3.2 10.8 + - + +
996A LEU* 2.9 38.4 + - + +
1024A ALA* 4.3 14.2 - - + +
1027A GLU* 2.8 29.5 + - - -
69B ASP* 4.3 31.3 + - + +
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Residues in contact with MET 993 (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 LEU* 3.9 6.1 - - + -
989A ALA 2.9 12.6 + - - +
990A ALA* 3.5 8.3 - - - +
992A ARG* 1.4 74.8 - - - +
994A ALA* 1.4 51.3 + - - +
996A LEU* 3.2 9.4 + - - +
997A MET* 2.8 36.9 + - - +
1021A ILE* 4.2 12.1 - - + +
1024A ALA* 3.4 23.8 - - + -
1025A SER* 3.6 36.1 - - - +
1028A VAL* 4.4 9.4 - - - -
1097A LEU* 3.8 11.0 - - + -
1098A MET* 3.6 20.6 - - + +
1101A VAL* 3.5 35.7 - - + -
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Residues in contact with ALA 994 (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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969A ALA* 3.4 33.1 - - - +
972A LEU* 4.0 7.7 - - + +
973A HIS* 3.6 29.2 - - + +
990A ALA 3.1 12.6 + - - +
991A LYS* 3.8 9.0 - - - +
992A ARG 3.3 0.4 - - - -
993A MET* 1.4 75.6 - - - +
995A LEU* 1.4 57.9 + - - +
997A MET* 3.3 4.7 + - - -
998A ALA* 2.9 26.0 + - - +
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Residues in contact with LEU 995 (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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973A HIS* 4.6 12.1 - - + +
991A LYS* 3.3 18.6 + - + +
992A ARG* 3.2 11.2 + - + +
994A ALA* 1.4 75.5 - - - +
996A LEU* 1.3 58.1 + - - +
998A ALA* 3.5 9.3 + - + +
999A GLU* 3.1 18.9 + - - +
1002A ARG* 4.8 1.7 + - - -
68B GLY* 3.2 32.2 - - - +
69B ASP* 5.3 2.9 - - - -
70B VAL 6.1 0.2 - - - +
91B LYS* 3.9 35.4 - - + +
92B TYR* 3.6 38.4 - - + -
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Residues in contact with LEU 996 (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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992A ARG* 2.9 27.9 + - + +
993A MET* 3.5 3.6 - - - +
995A LEU* 1.3 74.3 - - - +
997A MET* 1.3 58.1 + - - +
999A GLU* 3.1 9.0 + - - +
1000A MET 2.9 23.0 + - - -
1017A CYS* 3.2 14.7 - - - -
1020A ASP* 3.8 36.6 - - + +
1021A ILE* 3.5 20.4 - - + +
1024A ALA* 5.0 2.9 - - + -
68B GLY* 4.2 2.0 - - - -
69B ASP* 3.6 37.5 - - + +
121B ARG* 3.4 28.9 - - - +
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Residues in contact with MET 997 (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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965A ILE* 3.5 19.6 - - + +
969A ALA* 3.7 14.6 - - + -
993A MET 2.8 20.4 + - - +
994A ALA 3.7 4.7 - - - +
996A LEU* 1.3 71.2 - - - +
998A ALA* 1.3 62.9 + - - +
1000A MET* 3.3 24.8 + - - +
1001A SER* 3.1 17.8 + - - -
1021A ILE* 3.8 21.5 - - + +
1062A LEU* 4.1 7.0 - - + -
1094A ALA* 3.6 34.5 - - + -
1097A LEU* 4.0 14.4 - - + -
1098A MET* 3.6 40.6 - - + -
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Residues in contact with ALA 998 (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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966A LEU* 4.0 17.7 - - + +
969A ALA* 3.6 8.4 - - + +
970A GLN* 6.1 0.7 - - + -
994A ALA 2.9 17.6 + - - +
995A LEU* 3.5 14.4 - - + +
996A LEU 3.3 0.2 - - - -
997A MET* 1.3 76.3 - - - +
999A GLU* 1.4 60.2 + - - +
1001A SER* 2.7 24.9 + - - -
1002A ARG* 3.4 21.9 + - - +
92B TYR* 4.6 9.0 - - + +
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Residues in contact with GLU 999 (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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995A LEU 3.1 11.3 + - - +
996A LEU* 3.1 12.1 + - - +
998A ALA* 1.4 71.9 - - - +
1000A MET* 1.3 60.3 + - - +
1002A ARG* 3.0 32.7 + - - +
1003A LEU* 3.0 47.5 + - + +
1017A CYS* 3.7 3.0 - - - -
65B GLY 4.9 0.3 - - - +
66B LEU 4.1 3.7 - - - +
67B PRO* 3.9 1.7 - - - +
68B GLY* 2.6 32.4 + - - +
121B ARG* 2.8 49.4 + - - +
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Residues in contact with MET1000 (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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965A ILE* 3.8 29.6 - - + -
996A LEU 2.9 11.8 + - - +
997A MET* 3.4 33.9 - - - +
999A GLU* 1.3 76.8 - - - +
1001A SER* 1.4 62.1 + - - +
1003A LEU* 4.2 4.9 - - - -
1004A VAL* 3.1 34.3 + - + +
1014A LEU* 3.6 26.0 - - + -
1017A CYS* 4.0 15.0 - - + -
1018A ALA* 5.2 2.0 - - - -
1021A ILE* 4.3 7.4 - - - -
1062A LEU* 4.0 22.7 - - + -
1066A SER* 4.3 7.9 - - - -
1090A LEU* 4.2 18.2 - - + -
1094A ALA* 4.6 2.9 - - + -
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Residues in contact with SER1001 (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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961A VAL* 3.3 11.7 - - - +
962A ASN 2.9 46.1 + - - +
965A ILE* 3.8 13.0 - - - +
966A LEU* 3.6 31.5 - - - +
997A MET 3.1 6.4 + - - -
998A ALA 2.7 21.4 + - - -
1000A MET* 1.4 73.8 - - - +
1002A ARG* 1.3 58.1 + - - +
1004A VAL* 3.6 10.7 - - - +
1005A ARG* 3.7 1.7 - - - +
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Residues in contact with ARG1002 (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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959A GLN* 4.2 36.3 - - + +
960A PRO 4.1 8.5 - - - +
961A VAL* 3.7 22.0 - - + +
966A LEU* 5.7 2.0 - - - +
995A LEU 4.8 2.6 + - - -
998A ALA* 3.4 18.5 + - - +
999A GLU* 3.0 39.7 + - - +
1001A SER* 1.3 77.0 + - - +
1003A LEU* 1.3 67.2 + - + +
1005A ARG* 3.3 18.4 + - - +
1006A GLY 4.2 5.9 - - - +
1010A THR* 5.4 0.2 - - - +
66B LEU 4.9 2.6 + - - -
68B GLY* 4.9 1.8 - - - -
91B LYS 4.9 2.8 + - - -
92B TYR 2.8 26.7 + - - -
93B LYS* 3.6 40.6 + - - +
94B GLY* 3.8 6.7 - - - +
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Residues in contact with LEU1003 (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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999A GLU* 3.0 44.7 + - + +
1000A MET 3.2 4.5 + - - +
1002A ARG* 1.3 79.3 - - + +
1004A VAL* 1.4 56.6 + - - +
1005A ARG 3.1 0.2 - - - -
1006A GLY* 3.0 20.1 + - - -
1010A THR* 3.8 22.4 - - + -
1013A ALA* 3.7 44.0 - - + +
1014A LEU* 3.8 17.3 - - + -
1017A CYS* 3.8 17.0 - - + -
1073A LEU* 3.6 13.3 - - - +
121B ARG* 5.7 0.9 - - + -
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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
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962A ASN* 3.7 21.8 - - + -
965A ILE* 4.2 15.3 - - + -
1000A MET* 3.1 20.0 + - + +
1001A SER 3.6 12.8 - - - +
1003A LEU* 1.4 73.1 - - - +
1005A ARG* 1.4 60.4 + - + +
1006A GLY 3.1 4.5 + - - -
1014A LEU* 4.1 20.2 - - + -
1069A LYS* 3.4 28.3 + - + +
1073A LEU* 3.7 4.7 - - - +
1087A THR* 4.6 12.6 + - + +
1090A LEU* 3.7 29.8 - - + -
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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
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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