Contacts of the helix formed by residues 1084 - 1098 (chain A) in PDB entry 1FVR
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 SER1084 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1021A VAL* 4.8 2.5 - - - -
1083A PRO* 1.3 76.6 - - - +
1085A PHE* 1.3 64.1 + - - +
1086A ALA* 3.5 9.3 + - - +
1087A GLN* 2.9 36.2 + - - +
1088A ILE* 3.0 22.2 + - - +
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Residues in contact with PHE1085 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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949A ALA* 3.8 16.3 - - - +
952A MET* 3.6 56.5 - - + -
953A ASP* 3.8 23.1 - - - +
956A SER* 3.8 14.6 - - - +
965A LEU* 4.1 0.9 - - + -
1017A THR* 4.1 10.5 - - - -
1020A ASP* 3.9 8.7 - - + -
1021A VAL* 3.6 36.1 - - + +
1024A TYR* 3.7 27.4 - + + -
1084A SER* 1.3 75.6 - - - +
1086A ALA* 1.3 56.5 + - - +
1088A ILE* 3.4 14.4 + - + +
1089A LEU* 3.0 27.5 + - - +
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Residues in contact with ALA1086 (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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953A ASP* 3.6 25.9 + - - +
957A GLN* 5.9 1.8 - - - +
1084A SER* 3.1 9.5 + - - +
1085A PHE* 1.3 80.9 - - - +
1087A GLN* 1.3 62.2 + - + +
1089A LEU* 3.3 8.4 + - - +
1090A VAL* 3.1 26.8 + - + +
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Residues in contact with GLN1087 (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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1082A ARG 4.7 0.5 - - - +
1083A PRO* 3.3 17.5 - - + +
1084A SER* 2.9 40.8 + - - +
1086A ALA* 1.3 73.2 - - + +
1088A ILE* 1.3 66.0 + - - +
1090A VAL* 3.2 9.5 + - - +
1091A SER* 3.0 27.7 + - - +
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Residues in contact with ILE1088 (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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949A ALA* 3.9 12.3 - - + -
1021A VAL* 4.2 9.2 - - + -
1024A TYR* 3.6 33.0 - - + -
1070A LEU* 4.3 17.0 - - + -
1074A CYS* 3.9 23.3 - - - -
1083A PRO* 3.8 20.0 - - + -
1084A SER 3.0 19.3 + - - +
1085A PHE* 3.5 23.1 - - + +
1087A GLN* 1.3 77.1 - - - +
1089A LEU* 1.3 57.7 + - - +
1091A SER* 3.3 8.0 + - - -
1092A LEU* 2.9 34.9 + - + +
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Residues in contact with LEU1089 (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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946A ALA* 3.6 40.6 - - + +
949A ALA* 4.4 8.5 - - + +
950A ARG* 4.0 39.0 - - + +
953A ASP* 5.6 6.5 - - + +
1085A PHE 3.0 17.2 + - - +
1086A ALA* 3.6 8.5 - - - +
1088A ILE* 1.3 74.5 - - - +
1090A VAL* 1.3 60.0 + - + +
1092A LEU* 3.3 2.8 + - + +
1093A ASN* 2.9 53.8 + - - +
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Residues in contact with VAL1090 (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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1086A ALA 3.1 18.9 + - - +
1087A GLN* 3.2 11.2 + - - +
1089A LEU* 1.3 77.2 - - + +
1091A SER* 1.3 55.6 + - - +
1093A ASN* 3.3 8.6 + - - +
1094A ARG* 2.7 62.4 + - + +
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Residues in contact with SER1091 (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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1066A GLU* 4.9 6.4 - - - +
1070A LEU* 4.2 24.4 - - - +
1073A GLN* 5.4 4.9 + - - -
1087A GLN* 3.0 14.3 + - - +
1088A ILE 3.5 8.3 - - - -
1090A VAL* 1.3 80.6 - - - +
1092A LEU* 1.3 61.3 + - - +
1094A ARG* 3.3 15.5 + - - +
1095A MET* 3.4 22.4 + - - +
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Residues in contact with LEU1092 (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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942A LEU* 4.3 17.8 - - + +
945A ALA* 3.6 13.9 - - + +
946A ALA* 3.5 34.8 - - + +
949A ALA* 4.1 3.8 - - + -
1024A TYR* 3.3 25.6 - - - +
1028A LEU* 4.9 4.9 - - + -
1067A VAL* 6.1 0.7 - - + -
1070A LEU* 3.8 21.5 - - + -
1088A ILE* 2.9 27.2 + - + +
1089A LEU* 3.7 5.2 - - - +
1090A VAL 3.3 0.2 - - - -
1091A SER* 1.3 77.9 - - - +
1093A ASN* 1.3 63.4 + - - +
1095A MET* 3.3 17.2 + - + +
1096A LEU* 3.0 26.5 + - + +
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Residues in contact with ASN1093 (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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946A ALA* 4.6 3.1 - - - +
950A ARG* 4.7 5.6 + - - +
1089A LEU* 2.9 48.6 + - - +
1090A VAL* 3.3 7.1 + - - +
1092A LEU* 1.3 72.7 - - - +
1094A ARG* 1.3 64.8 + - + +
1096A LEU* 3.3 18.5 + - - +
1097A GLU* 2.9 34.6 + - + +
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Residues in contact with ARG1094 (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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1066A GLU* 5.6 3.6 - - - +
1090A VAL* 2.7 46.8 + - - +
1091A SER* 3.7 8.2 - - - +
1092A LEU 3.2 0.2 - - - -
1093A ASN* 1.3 75.5 - - + +
1095A MET* 1.3 64.2 + - + +
1097A GLU* 3.3 15.9 + - - +
1098A GLU* 3.4 21.3 - - - +
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Residues in contact with MET1095 (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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939A GLN* 4.5 1.6 - - - +
942A LEU* 4.2 9.1 - - + +
1066A GLU* 3.9 28.3 - - + +
1067A VAL* 3.8 22.7 - - + -
1070A LEU* 4.0 16.2 - - + -
1091A SER* 3.4 19.5 + - - +
1092A LEU* 3.3 30.1 + - + +
1094A ARG* 1.3 77.3 - - + +
1096A LEU* 1.3 62.1 + - - +
1098A GLU* 3.3 16.0 + - - +
1100A LYS 4.7 0.3 - - - +
1102A TYR* 3.5 65.0 - - + +
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Residues in contact with LEU1096 (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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939A GLN* 3.1 60.1 + - - +
942A LEU* 3.5 33.0 - - + +
943A HIS* 3.5 30.1 - - + +
946A ALA* 4.2 15.9 - - + -
1092A LEU* 3.0 20.2 + - + +
1093A ASN* 3.7 21.1 - - - +
1094A ARG 3.3 0.4 - - - -
1095A MET* 1.3 77.0 - - - +
1097A GLU* 1.3 63.6 + - + +
1098A GLU 3.5 1.7 + - - +
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Residues in contact with GLU1097 (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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1093A ASN* 2.9 26.7 + - + +
1094A ARG* 3.6 10.3 - - - +
1095A MET 3.2 0.4 - - - -
1096A LEU* 1.3 80.3 - - - +
1098A GLU* 1.3 61.7 + - + +
1099A ARG 4.1 0.3 + - - -
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Residues in contact with GLU1098 (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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939A GLN* 4.0 6.6 - - - +
1094A ARG* 3.4 19.1 - - - +
1095A MET* 3.3 12.1 + - - +
1096A LEU 3.3 8.6 - - - +
1097A GLU* 1.3 83.2 - - + +
1099A ARG* 1.3 64.3 + - - +
1100A LYS* 3.2 15.8 + - + +
1102A TYR* 2.4 32.6 + - - +
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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