Contacts of the helix formed by residues 1064 - 1075 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1062B ASN 3.9 0.4 + - - -
1063B CYS* 1.3 79.3 - - - +
1065B ASP* 1.3 69.2 + - - +
1066B GLU* 3.0 31.6 + - - +
1067B VAL* 3.2 12.5 + - + -
1068B TYR* 3.2 9.4 + - - +
1100B LYS* 2.9 27.7 + - - -
1101B THR 4.7 2.2 - - - +
1102B TYR* 3.0 42.5 + - + +
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Residues in contact with ASP1065 (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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1059B LYS* 3.4 29.0 + - - +
1063B CYS 3.7 1.0 + - - -
1064B ASP* 1.3 77.8 + - - +
1066B GLU* 1.3 57.4 + - - +
1068B TYR* 3.3 3.4 + - - +
1069B ASP* 2.8 42.5 + - - +
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Residues in contact with GLU1066 (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 ASP* 3.0 12.2 + - - +
1065B ASP* 1.3 78.5 - - - +
1067B VAL* 1.3 61.2 + - - +
1069B ASP* 3.4 10.0 + - + +
1070B LEU* 3.2 20.4 + - - +
1091B SER* 5.0 5.7 - - - +
1094B ARG* 5.5 3.5 - - - +
1095B MET* 3.1 33.7 + - + +
1098B GLU* 4.9 0.5 - - - +
1102B TYR* 3.4 22.5 + - - -
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Residues in contact with VAL1067 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942B LEU* 4.6 9.9 - - + -
1028B LEU* 4.2 16.1 - - + +
1032B VAL* 3.9 20.6 - - + -
1063B CYS* 3.6 20.9 - - - -
1064B ASP 3.2 3.4 + - - +
1066B GLU* 1.3 76.1 - - - +
1068B TYR* 1.3 61.7 + - - +
1070B LEU* 3.3 9.6 + - + +
1071B MET* 3.1 24.7 + - + +
1092B LEU* 6.0 0.7 - - + -
1095B MET* 3.3 26.0 - - + -
1102B TYR* 3.7 31.6 - - + +
1103B VAL* 4.6 2.2 - - + -
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Residues in contact with TYR1068 (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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1057B LEU 2.7 23.4 + - - -
1058B GLU* 3.6 7.7 - - - +
1059B LYS* 3.3 67.2 + - + -
1060B PRO* 4.5 0.4 - - + -
1063B CYS* 3.8 4.4 - - - -
1064B ASP 3.2 3.7 + - - +
1065B ASP* 3.6 7.4 - - - +
1067B VAL* 1.3 78.6 - - - +
1069B ASP* 1.3 65.6 + - - +
1071B MET* 3.1 21.6 + - - +
1072B ARG* 2.9 74.1 + - + +
1075B TRP* 4.5 7.0 - + - -
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Residues in contact with ASP1069 (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 ASP* 2.8 33.0 + - - +
1066B GLU* 3.9 8.2 - - + +
1067B VAL 3.3 0.2 - - - -
1068B TYR* 1.3 79.3 - - - +
1070B LEU* 1.3 64.8 + - - +
1072B ARG* 3.3 11.3 + - - +
1073B GLN* 2.9 36.1 + - + +
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Residues in contact with LEU1070 (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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1028B LEU* 4.0 15.3 - - + -
1066B GLU 3.2 13.2 + - - +
1067B VAL* 3.3 11.4 - - + +
1069B ASP* 1.3 76.9 - - - +
1071B MET* 1.3 62.7 + - - +
1073B GLN* 3.1 38.8 + - - +
1074B CYS* 3.3 16.9 + - - -
1088B ILE* 4.3 28.7 - - + -
1091B SER* 4.3 23.8 - - - +
1092B LEU* 3.7 34.1 - - + -
1095B MET* 5.3 6.7 - - - -
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Residues in contact with MET1071 (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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1025B GLY* 3.9 15.9 - - - +
1028B LEU* 3.9 11.2 - - + +
1029B TRP* 3.7 40.8 - - - +
1032B VAL* 3.8 32.1 - - + -
1060B PRO* 4.3 5.6 - - + -
1063B CYS* 3.8 21.1 - - - -
1067B VAL* 3.1 13.6 + - + +
1068B TYR* 3.1 18.8 + - + +
1070B LEU* 1.3 80.3 - - - +
1072B ARG* 1.3 60.9 + - - +
1074B CYS* 3.1 19.7 + - - +
1075B TRP* 3.2 35.9 + - + -
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Residues in contact with ARG1072 (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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1054B GLY 5.0 4.2 + - - -
1056B ARG* 3.9 31.3 - - - +
1068B TYR* 2.9 64.5 + - + +
1069B ASP* 3.6 14.6 - - - +
1070B LEU 3.2 0.2 - - - -
1071B MET* 1.3 74.0 - - - +
1073B GLN* 1.3 64.7 + - - +
1075B TRP* 3.2 28.5 + - - +
1076B ARG* 3.6 12.4 + - - +
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Residues in contact with GLN1073 (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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1069B ASP* 2.9 31.6 + - + +
1070B LEU* 3.1 26.0 + - - +
1072B ARG* 1.3 75.0 - - - +
1074B CYS* 1.3 62.9 + - - +
1075B TRP 3.3 0.5 + - - -
1076B ARG* 3.3 53.1 + - - +
1082B ARG* 3.6 3.5 - - - +
1083B PRO* 3.5 38.9 - - + +
1091B SER* 5.3 4.2 + - - -
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Residues in contact with CYS1074 (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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1021B VAL* 3.3 39.9 - - - +
1022B TRP* 3.2 13.5 + - - +
1024B TYR* 4.3 4.9 - - - -
1025B GLY* 3.9 20.2 - - - -
1028B LEU* 6.0 0.7 - - - -
1070B LEU* 3.5 18.2 - - - -
1071B MET* 3.1 9.9 + - - +
1073B GLN* 1.3 80.5 - - - +
1075B TRP* 1.3 59.1 + - + +
1076B ARG 3.5 0.4 - - - -
1082B ARG* 3.2 21.5 - - - -
1083B PRO* 4.2 4.7 - - - -
1088B ILE* 3.9 18.4 - - - -
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Residues in contact with TRP1075 (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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1022B TRP* 3.1 54.7 + + + -
1025B GLY* 3.5 25.0 - - - -
1026B VAL* 3.5 12.2 - - + +
1029B TRP* 4.4 0.7 - + + -
1039B TYR* 5.6 3.1 - - - -
1056B ARG* 2.8 53.6 + - + +
1057B LEU* 3.8 45.3 - - + -
1068B TYR* 4.5 2.7 - + - -
1071B MET* 3.2 44.2 - - + -
1072B ARG* 3.2 31.6 + - - +
1073B GLN 3.2 1.2 - - - -
1074B CYS* 1.3 82.6 - - + +
1076B ARG* 1.3 60.0 + - - +
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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
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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