Contacts of the helix formed by residues 1064 - 1075 (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 ASP1064 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1059A LYS* 4.7 0.4 - - - -
1063A CYS* 1.3 76.8 - - - +
1065A ASP* 1.3 69.0 + - - +
1066A GLU* 3.0 30.3 + - - +
1067A VAL* 3.0 14.8 + - + +
1068A TYR* 3.3 9.0 + - - +
1100A LYS* 3.6 24.7 + - - -
1101A THR 4.7 2.9 - - - +
1102A TYR* 3.0 50.2 + - + +
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Residues in contact with ASP1065 (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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1059A LYS* 2.8 33.2 + - - +
1063A CYS 3.8 0.8 + - - -
1064A ASP* 1.3 77.3 + - - +
1066A GLU* 1.3 57.3 + - - +
1068A TYR* 3.3 3.0 + - - +
1069A ASP* 2.8 41.3 + - - +
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Residues in contact with GLU1066 (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 ASP* 3.0 15.0 + - - +
1065A ASP* 1.3 78.8 - - - +
1067A VAL* 1.3 63.2 + - - +
1069A ASP* 3.4 9.4 + - + +
1070A LEU* 3.2 20.4 + - - +
1091A SER* 4.9 7.4 - - - +
1094A ARG* 5.6 3.3 - - - +
1095A MET* 3.9 25.4 - - + +
1102A TYR* 3.6 25.8 + - + -
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Residues in contact with VAL1067 (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* 4.7 6.1 - - + -
1028A LEU* 4.2 15.0 - - + +
1032A VAL* 3.9 20.2 - - + -
1063A CYS* 3.5 20.6 - - - -
1064A ASP 3.0 4.6 + - - +
1066A GLU* 1.3 76.1 - - - +
1068A TYR* 1.3 63.5 + - - +
1070A LEU* 3.2 9.2 + - - +
1071A MET* 3.2 24.8 + - + +
1092A LEU* 6.1 0.2 - - + -
1095A MET* 3.8 25.8 - - + -
1102A TYR* 3.8 31.2 - - + +
1103A VAL* 4.6 5.4 - - + -
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Residues in contact with TYR1068 (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 ARG 4.8 0.3 + - - -
1057A LEU 2.6 27.7 + - - -
1058A GLU* 3.6 6.2 - - - -
1059A LYS* 3.3 61.9 - - + -
1060A PRO* 4.5 0.2 - - + -
1063A CYS* 3.8 2.4 - - - -
1064A ASP 3.3 3.9 + - - +
1065A ASP* 3.7 7.0 - - - +
1066A GLU 3.3 0.2 - - - -
1067A VAL* 1.3 78.5 - - - +
1069A ASP* 1.3 66.0 + - - +
1071A MET* 2.9 26.3 + - - +
1072A ARG* 2.8 70.4 + - + +
1075A TRP* 4.4 7.0 - + - -
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Residues in contact with ASP1069 (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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1065A ASP* 2.8 30.0 + - - +
1066A GLU* 3.8 9.2 - - + +
1067A VAL 3.3 0.2 - - - -
1068A TYR* 1.3 83.6 - - - +
1070A LEU* 1.3 62.5 + - - +
1072A ARG* 3.2 11.4 + - - +
1073A GLN* 3.0 33.8 + - + +
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Residues in contact with LEU1070 (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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1024A TYR* 5.7 0.2 - - + -
1028A LEU* 4.1 15.0 - - + -
1066A GLU 3.2 12.7 + - - +
1067A VAL* 3.3 10.3 - - - +
1068A TYR 3.1 0.4 - - - -
1069A ASP* 1.3 75.8 - - - +
1071A MET* 1.3 64.6 + - - +
1073A GLN* 3.2 37.6 + - - +
1074A CYS* 3.3 20.0 + - - -
1088A ILE* 4.3 26.9 - - + +
1091A SER* 4.2 21.1 - - - +
1092A LEU* 3.8 34.1 - - + -
1095A MET* 4.0 14.6 - - + -
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Residues in contact with MET1071 (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 GLY* 4.0 10.5 - - - +
1028A LEU* 3.9 16.2 - - + +
1029A TRP* 3.7 40.4 - - + -
1032A VAL* 3.7 32.3 - - + -
1060A PRO* 4.4 1.6 - - + -
1063A CYS* 4.0 19.5 - - - -
1067A VAL* 3.2 14.1 + - + +
1068A TYR* 2.9 20.8 + - + +
1070A LEU* 1.3 80.0 - - - +
1072A ARG* 1.3 61.1 + - - +
1074A CYS* 3.1 19.8 + - - +
1075A TRP* 3.2 38.5 + - + -
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Residues in contact with ARG1072 (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 GLY 5.0 4.4 + - - -
1056A ARG* 4.0 28.8 + - - +
1068A TYR* 2.8 65.3 + - + +
1069A ASP* 3.2 14.1 + - - +
1071A MET* 1.3 72.1 - - - +
1073A GLN* 1.3 67.6 + - - +
1075A TRP* 3.1 27.8 + - - +
1076A ARG* 3.5 13.6 + - - +
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Residues in contact with GLN1073 (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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1069A ASP* 3.0 30.7 + - + +
1070A LEU* 3.2 25.4 + - - +
1072A ARG* 1.3 75.6 - - - +
1074A CYS* 1.3 62.8 + - - +
1075A TRP 3.2 0.7 + - - -
1076A ARG* 3.3 54.3 + - - +
1082A ARG* 3.7 4.2 - - - +
1083A PRO* 3.5 40.2 - - + +
1091A SER* 5.4 4.7 + - - -
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Residues in contact with CYS1074 (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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1021A VAL* 3.3 31.4 - - - +
1022A TRP* 3.2 20.1 - - - +
1024A TYR* 4.2 6.3 - - - -
1025A GLY* 3.8 19.7 - - - -
1028A LEU* 5.9 0.7 - - - -
1070A LEU* 3.3 19.8 + - - -
1071A MET* 3.1 10.2 + - - +
1073A GLN* 1.3 78.9 - - - +
1075A TRP* 1.3 57.3 + - + +
1076A ARG 3.5 0.7 - - - -
1082A ARG* 3.3 14.4 - - - -
1083A PRO* 4.2 4.3 - - - -
1088A ILE* 3.9 27.8 - - - -
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Residues in contact with TRP1075 (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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1022A TRP* 3.1 54.0 + + + -
1025A GLY* 3.4 25.9 - - - -
1026A VAL* 3.5 12.7 - - + +
1029A TRP* 4.3 1.3 - + + -
1039A TYR* 5.8 2.5 - - - -
1056A ARG* 2.8 52.1 + - + +
1057A LEU* 3.8 45.5 - - + -
1068A TYR* 4.4 2.2 - + - -
1071A MET* 3.2 44.8 + - + -
1072A ARG* 3.1 34.5 + - - +
1074A CYS* 1.3 81.1 - - - +
1076A ARG* 1.3 62.6 + - - +
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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