Contacts of the helix formed by residues 1054 - 1074 (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 ARG1054 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050A GLN* 3.3 41.1 + - - +
1051A VAL* 3.6 21.6 + - - +
1052A CYS 3.2 1.0 - - - -
1053A GLU* 1.3 77.2 - - + +
1055A ILE* 1.3 66.5 + - - +
1056A PRO 3.5 0.2 - - - -
1057A THR* 3.2 13.4 + - + -
1058A ILE* 3.1 33.8 + - + +
1100A SER* 3.4 18.5 + - - +
1103A GLU* 2.8 28.7 + - - -
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Residues in contact with ILE1055 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025A SER* 3.7 31.6 - - - +
1028A VAL* 4.0 20.9 - - + -
1029A THR* 3.5 15.3 - - - +
1051A VAL 4.2 3.1 - - - +
1052A CYS* 3.2 17.9 + - + +
1054A ARG* 1.3 75.4 - - - +
1056A PRO* 1.4 64.5 - - + +
1058A ILE* 3.1 10.0 + - - +
1059A SER* 3.0 24.6 + - - -
1097A LEU* 4.2 7.2 - - + -
1100A SER* 3.7 29.4 - - - +
1101A VAL* 4.2 8.5 - - + -
1104A THR* 3.4 26.0 - - - +
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Residues in contact with PRO1056 (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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1025A SER* 5.8 1.1 - - - -
1026A ASP* 4.7 7.2 - - - +
1029A THR* 4.0 13.7 - - + +
1033A LYS* 6.0 1.3 - - - +
1052A CYS 3.5 10.3 - - - +
1053A GLU* 3.4 21.5 - - + +
1055A ILE* 1.4 90.5 - - + +
1057A THR* 1.3 55.0 + - - +
1059A SER* 3.4 6.7 + - - -
1060A THR* 2.9 35.1 + - - +
2003A GOL 3.8 22.9 - - - +
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Residues in contact with THR1057 (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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1053A GLU 4.4 6.4 + - - -
1054A ARG* 3.2 16.8 - - + +
1056A PRO* 1.3 76.6 - - - +
1058A ILE* 1.3 67.4 + - + +
1060A THR* 3.4 6.8 + - - -
1061A GLN* 3.2 45.1 + - - +
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Residues in contact with ILE1058 (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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1054A ARG* 3.1 24.1 + - + +
1055A ILE* 3.1 6.3 + - - +
1057A THR* 1.3 79.6 - - + +
1059A SER* 1.3 58.2 + - - +
1061A GLN* 3.4 5.0 + - - +
1062A LEU 3.0 21.5 + - - -
1093A ASN* 3.0 51.5 + - - +
1096A ASN* 3.8 24.2 - - + +
1097A LEU* 3.7 15.9 - - + +
1100A SER* 3.5 28.9 - - - +
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Residues in contact with SER1059 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022A ALA* 3.9 26.3 - - - +
1025A SER* 2.9 26.7 + - - -
1026A ASP* 6.0 0.9 - - - -
1055A ILE 3.0 15.6 + - - -
1056A PRO* 3.9 5.8 - - - -
1058A ILE* 1.3 73.2 - - - +
1060A THR* 1.4 63.9 + - - +
1062A LEU* 3.2 10.6 + - - +
1063A LYS* 3.1 30.1 + - - +
1097A LEU* 3.7 12.0 - - - +
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Residues in contact with THR1060 (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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1056A PRO* 2.9 18.1 + - - +
1057A THR* 3.8 7.2 - - - -
1058A ILE 3.3 0.2 - - - -
1059A SER* 1.4 73.9 - - - +
1061A GLN* 1.3 63.8 + - + +
1063A LYS* 3.2 21.7 + - - +
1064A ILE* 3.2 37.6 + - + +
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Residues in contact with GLN1061 (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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1057A THR* 3.2 31.4 + - - +
1058A ILE* 3.6 5.6 - - - +
1060A THR* 1.3 77.9 - - + +
1062A LEU* 1.4 49.5 + - - +
1064A ILE* 3.3 12.7 + - + +
1065A LEU* 2.8 45.8 + - + +
1093A ASN* 3.4 20.9 + - - +
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Residues in contact with LEU1062 (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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997A MET* 4.1 8.5 - - + -
1000A MET* 4.0 14.4 - - + -
1018A ALA* 4.2 14.6 - - + +
1021A ILE* 3.7 39.9 - - + -
1022A ALA 5.5 0.2 - - - +
1058A ILE 3.0 9.3 + - - +
1059A SER* 3.2 10.7 + - - +
1061A GLN* 1.4 73.3 - - - +
1063A LYS* 1.3 56.8 + - - +
1065A LEU* 3.8 2.5 - - - -
1066A SER* 2.7 37.4 + - - -
1090A LEU* 3.7 26.2 - - + +
1093A ASN* 3.2 27.8 - - + +
1094A ALA 4.7 5.4 - - - +
1097A LEU* 4.0 11.0 - - + -
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Residues in contact with LYS1063 (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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1018A ALA* 3.8 26.9 - - + +
1019A LYS* 4.1 22.7 - - + +
1022A ALA* 3.9 23.8 - - + +
1026A ASP* 5.7 2.2 + - - -
1059A SER 3.1 18.7 + - - +
1060A THR* 3.2 22.9 + - - +
1062A LEU* 1.3 73.9 - - - +
1064A ILE* 1.3 62.7 + - + +
1066A SER* 3.4 2.8 + - - -
1067A THR* 2.9 29.6 + - - -
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Residues in contact with ILE1064 (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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1060A THR* 3.2 30.0 + - + +
1061A GLN* 3.6 12.6 - - + +
1063A LYS* 1.3 77.1 - - + +
1065A LEU* 1.3 66.9 + - + +
1067A THR* 3.3 7.3 + - - -
1068A VAL* 3.1 35.3 + - + +
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Residues in contact with LEU1065 (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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1061A GLN* 2.8 29.5 + - + +
1062A LEU 4.1 0.7 - - - +
1064A ILE* 1.3 77.2 - - + +
1066A SER* 1.4 56.1 + - - +
1068A VAL* 3.5 14.7 + - + +
1069A LYS* 3.1 28.2 + - - +
1086A ALA 5.1 2.7 - - - +
1089A MET* 3.6 59.7 - - + +
1090A LEU* 3.8 20.5 - - + +
1093A ASN* 3.9 20.2 - - + +
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Residues in contact with SER1066 (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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1000A MET* 4.3 5.4 - - - -
1014A LEU* 3.8 24.1 + - - +
1015A ILE* 4.6 4.0 - - - -
1018A ALA* 3.1 25.7 - - - +
1062A LEU* 2.7 25.9 + - - +
1063A LYS 3.6 3.8 - - - -
1064A ILE 3.2 0.2 - - - -
1065A LEU* 1.4 72.4 - - - +
1067A THR* 1.3 54.4 + - - +
1069A LYS* 3.3 2.1 + - - +
1070A ALA* 2.8 37.0 + - - +
1090A LEU* 3.7 16.0 - - - +
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Residues in contact with THR1067 (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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1015A ILE* 4.0 32.0 - - + +
1063A LYS 2.9 16.5 + - - -
1064A ILE* 3.6 7.6 - - - -
1066A SER* 1.3 75.6 - - - +
1068A VAL* 1.3 56.7 + - + +
1070A ALA* 3.7 0.5 - - - +
1071A THR* 2.8 45.1 + - - +
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Residues in contact with VAL1068 (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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1064A ILE* 3.1 26.5 + - + +
1065A LEU* 3.5 16.6 - - + +
1066A SER 3.3 0.2 - - - -
1067A THR* 1.3 78.1 - - + +
1069A LYS* 1.3 60.2 + - - +
1071A THR* 3.5 5.8 + - - -
1072A MET* 3.3 41.1 + - + +
1086A ALA* 4.5 9.6 - - + -
1089A MET* 5.3 9.6 - - + -
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Residues in contact with LYS1069 (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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1004A VAL* 3.4 25.3 + - + +
1014A LEU* 4.0 12.3 - - + -
1065A LEU 3.1 16.5 + - - +
1066A SER 3.8 2.5 - - - +
1068A VAL* 1.3 74.7 - - - +
1070A ALA* 1.3 59.1 + - - +
1072A MET* 3.0 14.1 + - + +
1073A LEU* 2.9 42.1 + - + +
1083A SER* 2.9 33.7 + - - -
1086A ALA* 4.0 17.7 - - + -
1087A THR* 2.9 28.1 + - - +
1090A LEU* 3.7 24.2 - - + -
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Residues in contact with ALA1070 (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 LYS* 3.4 41.0 - - - +
1014A LEU* 4.0 10.9 - - + +
1015A ILE* 3.6 19.5 - - + -
1066A SER 2.8 21.8 + - - +
1067A THR 3.7 2.7 - - - +
1069A LYS* 1.3 70.9 - - - +
1071A THR* 1.4 62.9 + - - +
1073A LEU* 3.2 17.4 + - - +
1074A GLY 3.2 10.0 + - - -
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Residues in contact with THR1071 (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 LYS* 3.7 24.7 + - - +
1015A ILE* 5.6 0.9 - - - +
1067A THR* 2.8 29.5 + - - +
1068A VAL* 3.8 6.5 - - - -
1070A ALA* 1.4 75.0 - - - +
1072A MET* 1.3 60.6 + - + +
1074A GLY* 3.7 2.3 + - - -
1075A ARG* 3.4 53.3 + - - +
1078A ILE* 5.1 0.2 - - - -
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Residues in contact with MET1072 (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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1068A VAL* 3.3 24.2 + - + +
1069A LYS* 3.0 13.8 + - + +
1071A THR* 1.3 77.6 - - + +
1073A LEU* 1.4 64.7 + - - +
1074A GLY 3.2 0.4 - - - -
1075A ARG* 3.2 19.9 + - - +
1078A ILE* 3.8 40.2 - - + +
1082A GLU* 3.5 37.2 - - + +
1083A SER* 4.1 9.4 - - - +
1086A ALA* 3.6 32.8 - - + -
1089A MET* 6.5 0.2 - - + -
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Residues in contact with LEU1073 (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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1003A LEU 3.6 16.4 - - - +
1004A VAL* 3.7 21.3 - - - +
1005A ARG 4.7 0.4 - - - -
1006A GLY* 3.7 15.3 - - - +
1010A THR* 3.5 31.6 - - - +
1011A LYS* 5.1 3.8 - - + +
1014A LEU* 4.1 20.9 - - + -
1069A LYS* 2.9 31.5 + - - +
1070A ALA* 3.2 9.8 + - - +
1072A MET* 1.4 76.6 - - - +
1074A GLY* 1.3 60.4 + - - +
1075A ARG 3.4 7.4 + - - +
1083A SER* 5.8 0.2 - - - +
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Residues in contact with GLY1074 (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 LYS* 4.7 17.4 - - - +
1070A ALA 3.2 12.2 + - - -
1071A THR 4.0 4.3 - - - -
1072A MET 3.2 0.4 - - - -
1073A LEU* 1.3 76.5 - - - +
1075A ARG* 1.4 60.7 + - - +
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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
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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