Contacts of the helix formed by residues 1112 - 1123 (chain B) in PDB entry 1VDV
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 SER1112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1111B GLY* 1.3 73.7 - - - -
1113B TRP* 1.3 65.0 + - - +
1114B GLU* 3.5 19.0 + - - +
1115B ASP* 2.9 41.8 + - - -
1116B TRP* 3.0 20.2 + - - -
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Residues in contact with TRP1113 (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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1023B VAL* 4.0 21.1 - - + -
1027B GLY* 2.9 34.0 + - - -
1029B VAL* 4.1 6.5 - - + -
1054B LEU* 4.2 29.8 - - + -
1056B ILE* 3.7 41.4 - - + +
1060B LYS* 4.3 14.4 - - + +
1097B ILE* 4.3 5.2 - - + -
1098B LEU* 4.6 9.2 - - + -
1101B LEU* 3.4 31.4 - - + -
1112B SER* 1.3 74.4 - - - +
1114B GLU* 1.3 78.4 + - - +
1116B TRP* 3.4 29.3 + + + +
1117B VAL* 3.0 40.4 + - + +
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Residues in contact with GLU1114 (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 THR 5.1 2.7 - - - +
1026B ASP 3.7 24.0 - - - +
1027B GLY* 4.8 2.5 - - - -
1060B LYS* 2.7 39.5 + - - +
1112B SER* 3.5 19.8 + - - +
1113B TRP* 1.3 90.4 + - + +
1115B ASP* 1.3 64.2 + - - +
1117B VAL* 3.4 5.0 + - - +
1118B MET* 3.0 25.3 + - - +
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Residues in contact with ASP1115 (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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1108B ASN* 4.1 16.7 + - - +
1111B GLY* 3.6 6.6 - - - -
1112B SER* 2.9 36.9 + - - +
1114B GLU* 1.3 78.0 - - - +
1116B TRP* 1.3 59.4 + - + +
1118B MET* 3.8 3.9 - - - +
1119B ALA* 2.9 30.9 + - - +
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Residues in contact with TRP1116 (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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1101B LEU* 4.0 18.5 - - + +
1104B PHE* 3.6 27.6 - - + +
1105B LYS* 3.7 48.1 - - + +
1108B ASN* 2.9 29.8 + - + -
1109B PRO 3.9 14.6 - - - -
1111B GLY* 3.4 22.2 - - - -
1112B SER* 3.0 10.5 + - - -
1113B TRP* 3.7 36.8 - + + +
1115B ASP* 1.3 76.8 - - - +
1117B VAL* 1.3 57.8 + - - +
1119B ALA* 3.3 6.8 + - + +
1120B ALA* 2.9 31.0 + - - +
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Residues in contact with VAL1117 (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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1023B VAL* 3.9 10.1 - - + -
1024B TYR 3.5 25.4 - - - +
1025B THR* 4.4 6.7 - - - +
1027B GLY* 4.3 6.3 - - - +
1101B LEU* 4.3 16.8 - - + -
1113B TRP* 3.0 52.9 + - + +
1114B GLU* 3.8 5.8 - - - +
1116B TRP* 1.3 76.1 - - - +
1118B MET* 1.3 58.6 + - - +
1120B ALA* 3.3 3.5 + - - +
1121B TYR* 3.0 26.5 + - - +
1127B LEU* 3.8 18.8 - - + +
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Residues in contact with MET1118 (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 THR* 3.7 31.2 + - - +
1114B GLU 3.0 17.9 + - - +
1115B ASP* 3.9 4.7 - - - +
1117B VAL* 1.3 76.5 - - - +
1119B ALA* 1.3 61.3 + - - +
1121B TYR* 3.2 23.6 + - + +
1122B GLN* 2.9 55.1 + - - +
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Residues in contact with ALA1119 (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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1104B PHE* 3.5 20.8 - - + -
1115B ASP 2.9 17.3 + - - +
1116B TRP* 3.6 7.0 - - - +
1118B MET* 1.3 77.5 - - - +
1120B ALA* 1.3 58.3 + - - +
1122B GLN* 3.5 6.3 + - - +
1123B ASP* 3.0 30.1 + - - +
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Residues in contact with ALA1120 (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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1101B LEU* 3.8 20.6 - - + -
1104B PHE* 3.6 25.7 - - + -
1116B TRP 2.9 17.0 + - - +
1117B VAL 3.6 4.7 - - - +
1119B ALA* 1.3 75.3 - - - +
1121B TYR* 1.3 64.7 + - - +
1123B ASP 3.1 6.6 + - - -
1124B ARG 3.2 0.2 + - - -
1125B VAL* 2.9 35.6 + - + +
1127B LEU* 4.3 7.9 - - + -
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Residues in contact with TYR1121 (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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770A MET* 3.7 21.5 - - + +
771A LYS* 5.1 1.6 + - - -
1013A PHE* 3.9 21.5 - + - -
1014A LEU* 3.7 24.1 - - - +
1016A GLN* 3.1 45.1 + - - -
1073A ASN* 3.7 31.7 + - + -
1075A SER* 4.6 2.8 + - - -
1025B THR* 3.7 24.9 - - + -
1117B VAL 3.0 13.4 + - - +
1118B MET* 3.2 22.6 + - + +
1120B ALA* 1.3 77.3 - - - +
1122B GLN* 1.3 61.9 + - + +
1124B ARG* 2.8 17.7 + - - -
1125B VAL 4.4 7.4 - - - -
1127B LEU* 4.2 11.6 - - + +
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Residues in contact with GLN1122 (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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1013A PHE* 3.1 56.3 - - + +
1118B MET* 2.9 44.6 + - - +
1119B ALA* 3.8 5.8 - - - +
1121B TYR* 1.3 86.8 - - + +
1123B ASP* 1.3 56.5 + - - +
1124B ARG* 3.1 3.3 + - - +
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Residues in contact with ASP1123 (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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1134A ARG* 2.7 38.5 + - - -
1104B PHE* 3.4 31.6 - - + -
1107B LYS* 5.3 5.4 + - - -
1119B ALA 3.0 17.0 + - - +
1120B ALA 3.7 0.7 - - - +
1121B TYR 3.1 0.6 - - - -
1122B GLN* 1.3 76.4 - - - +
1124B ARG* 1.3 57.6 + - - +
1125B VAL* 3.4 5.1 + - + +
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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