Contacts of the helix formed by residues 1064 - 1084 (chain B) in PDB entry 3QCF
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 VAL1064 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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883B ILE* 3.6 30.5 - - + -
1060B CYS* 3.7 1.0 - - - -
1062B ALA* 3.8 7.0 - - + +
1063B GLY* 1.3 84.6 - - - +
1065B GLY* 1.3 66.0 + - - +
1066B ARG 3.9 0.7 - - - -
1068B GLY 3.1 15.1 + - - -
1099B ARG* 3.7 11.9 - - - +
1100B ASN* 3.2 26.0 - - - +
1101B TYR* 3.8 13.0 - - + +
1102B LEU* 3.1 9.0 - - - +
1103B VAL 3.0 19.6 + - - -
1104B GLN* 3.6 32.8 - - - +
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Residues in contact with GLY1065 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060B CYS* 4.2 2.0 - - - -
1064B VAL* 1.3 83.8 - - - +
1066B ARG* 1.3 60.5 + - - +
1069B THR* 3.0 28.9 + - - -
1103B VAL* 3.7 3.1 - - - -
1104B GLN* 3.7 15.9 + - - -
1108B GLN* 3.4 27.9 - - - +
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Residues in contact with ARG1066 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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950B ILE* 3.1 41.3 + - + +
951B THR* 3.5 6.5 + - - +
955B GLU* 2.9 42.0 + - - -
1026B TRP* 3.1 34.2 - - + -
1031B VAL* 6.0 1.4 - - - +
1032B PRO* 5.6 0.2 - - - +
1060B CYS* 3.9 17.4 - - + +
1065B GLY* 1.3 71.3 - - - +
1067B THR* 1.3 57.7 + - - +
1069B THR* 3.0 9.2 + - - -
1070B TYR* 2.7 35.7 + - - +
1108B GLN* 3.7 5.8 - - - +
2001B NXY 2.9 40.0 + - + +
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Residues in contact with THR1067 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923B ALA* 3.6 31.4 - - + -
950B ILE* 4.3 2.4 - - - +
1058B VAL* 3.7 23.2 - - + +
1059B HIS* 3.3 10.4 + - - -
1060B CYS* 3.1 29.8 + - - -
1063B GLY* 3.5 22.6 - - - +
1064B VAL 4.1 0.2 - - - -
1066B ARG* 1.3 78.0 - - - +
1068B GLY* 1.3 62.0 + - - +
1070B TYR* 3.4 2.3 + - - +
1071B ILE* 3.1 28.0 + - + +
1102B LEU* 4.3 2.5 - - + -
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Residues in contact with GLY1068 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1064B VAL 3.1 19.0 + - - -
1067B THR* 1.3 76.5 - - - +
1069B THR* 1.3 66.7 + - - +
1071B ILE* 3.1 6.2 + - - +
1072B VAL* 2.9 28.6 + - - +
1095B ILE* 5.1 0.7 - - - -
1102B LEU* 3.8 19.3 - - - -
1103B VAL* 3.6 12.8 - - - -
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Residues in contact with THR1069 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065B GLY 3.0 14.7 + - - -
1066B ARG* 3.0 12.3 + - - -
1068B GLY* 1.3 75.2 - - - +
1070B TYR* 1.3 63.7 + - - +
1072B VAL* 3.5 0.9 + - - +
1073B ILE* 3.1 48.9 + - + +
1103B VAL* 3.8 4.3 - - - +
1108B GLN* 3.5 28.0 + - + +
1111B PHE* 4.1 9.2 - - + -
1112B ILE* 3.7 21.5 - - + -
2001B NXY 4.0 19.1 - - + -
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Residues in contact with TYR1070 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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921B TYR* 4.3 6.5 - + - -
948B VAL* 3.8 19.8 - - + +
950B ILE* 3.2 33.4 - - + -
1041B PHE* 4.0 9.6 - + - -
1042B VAL* 4.0 25.5 + - + +
1045B SER* 2.6 32.7 + - - -
1046B SER* 3.8 13.5 + - - -
1056B VAL* 5.2 3.3 - - + +
1058B VAL* 3.9 29.4 - - + -
1066B ARG 2.7 11.0 + - - +
1067B THR 3.6 3.1 - - - +
1069B THR* 1.3 73.3 - - - +
1071B ILE* 1.3 62.7 + - + +
1073B ILE* 3.3 2.4 + - - +
1074B ASP* 2.9 50.7 + - + +
2001B NXY 3.4 13.6 - - + +
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Residues in contact with ILE1071 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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912B VAL* 4.3 14.8 - - + -
913B ASP 4.1 7.9 - - - +
921B TYR* 3.6 57.8 + - + -
923B ALA* 4.4 5.8 - - + -
1058B VAL* 4.5 4.5 - - + -
1067B THR* 3.1 31.1 + - + +
1068B GLY* 3.1 8.6 + - - +
1070B TYR* 1.3 82.6 - - + +
1072B VAL* 1.3 64.8 + - - +
1074B ASP* 4.5 0.2 - - - -
1075B SER* 3.0 24.3 + - - -
1091B PHE* 4.2 10.8 - - + -
1095B ILE* 4.3 10.1 - - + -
1102B LEU* 5.1 2.7 - - + -
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Residues in contact with VAL1072 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068B GLY 2.9 18.8 + - - +
1069B THR 3.9 0.2 - - - +
1071B ILE* 1.3 74.1 - - - +
1073B ILE* 1.3 60.3 + - - +
1075B SER* 3.1 1.9 + - - -
1076B MET* 2.8 44.1 + - + +
1088B VAL* 4.3 11.4 - - + +
1091B PHE* 3.9 15.7 - - + -
1092B LEU* 4.2 10.1 - - + -
1095B ILE* 3.9 21.5 - - + -
1103B VAL* 4.0 13.7 - - + -
1112B ILE* 3.5 36.1 - - + -
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Residues in contact with ILE1073 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038B VAL* 4.8 4.9 - - + -
1039B LEU* 4.7 10.3 - - + -
1042B VAL* 4.2 15.0 - - + -
1069B THR* 3.1 38.1 + - + +
1070B TYR* 3.8 3.1 - - - +
1072B VAL* 1.3 75.8 - - - +
1074B ASP* 1.3 64.5 + - - +
1076B MET* 4.1 0.7 - - - +
1077B LEU* 3.0 42.6 + - + +
1111B PHE* 4.2 11.0 - - + -
1112B ILE* 4.1 24.2 - - + +
1115B ALA* 4.1 18.2 - - + -
1116B LEU* 4.2 12.9 - - + +
2001B NXY 4.4 7.9 - - + -
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Residues in contact with ASP1074 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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921B TYR* 2.6 31.4 + - - +
1042B VAL* 3.8 18.0 - - + +
1046B SER* 2.9 35.3 + - - -
1049B ARG* 5.1 2.8 + - - -
1070B TYR* 2.9 28.4 + - + +
1071B ILE 4.0 0.2 - - - +
1073B ILE* 1.3 78.9 - - - +
1075B SER* 1.3 62.9 + - - +
1077B LEU* 3.3 4.4 + - - +
1078B GLN* 3.2 33.1 + - - +
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Residues in contact with SER1075 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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914B GLY* 3.3 13.3 - - - -
915B TYR* 3.1 37.2 + - - +
921B TYR* 3.4 7.5 + - - -
1071B ILE 3.0 21.0 + - - -
1072B VAL 3.1 2.2 + - - -
1074B ASP* 1.3 78.3 - - - +
1076B MET* 1.3 64.4 + - - +
1078B GLN* 3.4 4.3 + - - -
1079B GLN* 3.0 24.4 + - - +
1091B PHE* 3.6 19.4 - - - -
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Residues in contact with MET1076 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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915B TYR* 5.3 1.8 - - + -
1072B VAL* 2.8 33.0 + - + +
1075B SER* 1.3 82.8 - - - +
1077B LEU* 1.3 60.1 + - - +
1079B GLN* 3.2 29.1 + - - +
1080B ILE* 2.9 36.0 + - - +
1086B VAL* 3.9 10.3 - - + -
1087B ASN 3.4 39.5 - - - +
1088B VAL* 4.2 8.5 - - + -
1091B PHE* 3.9 29.8 - - + -
1116B LEU* 4.0 21.3 - - + -
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Residues in contact with LEU1077 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1039B LEU* 4.5 8.3 - - + -
1042B VAL* 4.2 17.0 - - + -
1043B ARG* 4.2 29.8 - - + +
1073B ILE* 3.0 36.3 + - + +
1074B ASP* 3.3 5.8 + - - +
1076B MET* 1.3 74.9 - - - +
1078B GLN* 1.3 65.7 + - + +
1080B ILE* 3.1 12.6 + - + +
1081B LYS* 3.0 23.3 + - - +
1116B LEU* 4.1 14.4 - - + -
1119B ALA* 3.7 28.9 - - + -
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Residues in contact with GLN1078 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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915B TYR* 3.9 34.2 + - + +
921B TYR* 4.5 3.5 + - - -
1046B SER* 3.8 8.8 + - - +
1049B ARG* 5.7 2.1 + - - -
1074B ASP* 3.2 36.3 + - - +
1075B SER* 3.6 8.0 - - - +
1077B LEU* 1.3 78.0 - - + +
1079B GLN* 1.3 62.0 + - - +
1081B LYS* 3.3 7.1 + - - +
1082B ASP* 3.0 27.2 + - - +
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Residues in contact with GLN1079 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827B ALA* 3.7 16.8 - - - +
915B TYR* 3.6 37.9 - - + +
1075B SER 3.0 15.3 + - - +
1076B MET* 3.2 33.4 - - - +
1077B LEU 3.3 0.2 - - - -
1078B GLN* 1.3 76.2 - - - +
1080B ILE* 1.3 57.4 + - - +
1083B LYS* 3.0 26.1 + - + +
1084B SER 3.3 4.0 + - - -
1085B THR* 3.1 31.0 + - - +
1086B VAL* 3.8 12.8 + - - -
1087B ASN* 3.9 6.0 + - - +
1091B PHE* 5.7 0.8 - - - +
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Residues in contact with ILE1080 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830B VAL* 4.2 17.0 - - + -
1076B MET 2.9 23.5 + - - +
1077B LEU* 3.1 13.4 + - + +
1079B GLN* 1.3 75.4 - - - +
1081B LYS* 1.3 65.1 + - - +
1084B SER* 2.8 31.7 + - - +
1085B THR 3.5 16.6 - - - +
1086B VAL* 4.2 16.8 - - + -
1116B LEU* 4.6 12.1 - - + -
1120B ILE* 3.8 35.2 - - + -
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Residues in contact with LYS1081 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1077B LEU 3.0 14.4 + - - +
1078B GLN* 3.9 6.7 - - - +
1080B ILE* 1.3 78.7 - - - +
1082B ASP* 1.3 62.5 + - - +
1084B SER* 4.8 0.5 + - - -
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Residues in contact with ASP1082 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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915B TYR* 2.5 36.5 + - + +
916B ASN* 4.5 4.4 + - - -
1078B GLN 3.0 17.6 + - - +
1079B GLN 4.1 0.4 - - - +
1081B LYS* 1.3 80.4 - - + +
1083B LYS* 1.3 61.1 + - - +
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Residues in contact with LYS1083 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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915B TYR* 4.3 6.5 - - - +
1079B GLN* 3.0 11.4 + - + +
1082B ASP* 1.3 86.3 - - - +
1084B SER* 1.3 74.0 + - - +
1085B THR* 3.1 22.1 + - + +
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Residues in contact with SER1084 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829B PRO* 3.7 2.6 - - - +
830B VAL* 3.1 36.0 + - - +
1079B GLN 3.3 0.6 + - - -
1080B ILE* 2.8 24.5 + - - +
1081B LYS 4.8 0.5 + - - -
1083B LYS* 1.3 80.0 - - - +
1085B THR* 1.3 61.0 + - - +
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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