Contacts of the strand formed by residues 1029 - 1033 (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 VAL1029 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785A ASN* 3.1 8.7 + - - -
1021B ILE* 3.5 24.0 - - + -
1022B HIS 3.3 10.8 - - - +
1023B VAL* 4.2 8.7 - - + -
1027B GLY 3.7 10.3 - - - +
1028B SER* 1.3 78.2 - - - +
1030B LEU* 1.3 61.7 + - - +
1031B VAL* 4.0 12.8 - - + -
1054B LEU* 4.4 11.7 - - + -
1056B ILE* 4.1 21.1 - - + -
1060B LYS 2.8 17.0 + - - +
1061B ILE* 4.2 7.4 - - + -
1062B TYR 3.0 26.3 + - - -
1113B TRP* 4.1 12.1 - - + -
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Residues in contact with LEU1030 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785A ASN* 3.9 9.9 - - + +
1069A ASN* 4.0 19.5 - - + +
5011A GOL 2.9 32.1 - - - +
1020B LEU 3.9 1.0 - - - +
1021B ILE* 3.5 4.0 - - - +
1022B HIS* 2.8 42.6 + - + +
1024B TYR* 3.4 33.2 - - + +
1028B SER 4.2 0.4 + - - -
1029B VAL* 1.3 73.4 - - - +
1031B VAL* 1.3 67.6 + - - +
1032B SER* 5.5 4.2 - - - -
1062B TYR* 3.6 23.8 - - + +
1064B SER* 4.4 10.5 - - - +
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Residues in contact with VAL1031 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020B LEU 3.8 2.5 - - - -
1021B ILE* 4.0 23.3 - - + -
1029B VAL* 4.0 8.7 - - + -
1030B LEU* 1.3 80.2 - - - +
1032B SER* 1.3 70.4 + - - +
1033B HIS* 4.7 1.3 - - + -
1046B MET* 5.2 1.3 - - + +
1050B ALA* 4.3 9.6 - - + -
1054B LEU* 6.2 0.2 - - + -
1061B ILE* 3.8 24.7 - - + -
1062B TYR 2.9 9.5 + - - +
1063B ILE* 3.6 46.2 - - + +
1064B SER 4.6 1.0 + - - -
1065B GLU 5.2 0.7 - - - +
1090B VAL* 4.1 27.6 - - + -
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Residues in contact with SER1032 (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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1019B ALA* 3.3 5.0 - - - +
1020B LEU* 2.7 48.7 + - - +
1022B HIS* 6.5 0.7 - - - -
1030B LEU* 5.5 4.3 - - - -
1031B VAL* 1.3 76.1 - - - +
1033B HIS* 1.3 67.0 + - - +
1063B ILE* 5.2 0.4 - - - -
1065B GLU 4.2 15.5 + - - -
1067B SER 5.2 0.3 + - - -
1070B THR* 3.1 32.1 + - - +
1071B VAL* 4.0 3.0 - - - +
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Residues in contact with HIS1033 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1018B GLY 3.5 15.5 - - - +
1019B ALA* 4.2 7.6 - - + -
1031B VAL* 4.7 3.4 - - + -
1032B SER* 1.3 81.9 + - - +
1034B GLY* 1.3 61.3 + - - +
1035B GLY* 2.9 51.8 + - - +
1042B LEU* 3.8 16.2 - - + -
1043B HIS* 2.9 29.6 + + - -
1046B MET* 3.7 22.1 - - + +
1063B ILE* 4.1 14.3 - - + +
1065B GLU 5.0 1.2 + - - +
1066B THR* 3.7 13.7 + - - +
1067B SER 5.3 0.3 + - - -
1071B VAL* 3.8 9.7 - - - +
1086B TYR* 3.7 18.4 - + + -
1090B VAL* 4.5 4.7 - - + -
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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
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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