Contacts of the strand formed by residues 728 - 736 (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 ASN 728 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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726B ALA* 3.6 1.0 - - - +
727B ASP* 1.3 96.3 - - - +
729B VAL* 1.3 70.0 + - - +
730B VAL* 5.6 0.2 - - + -
849B GLY* 3.3 0.3 - - - -
850B PHE* 2.8 64.6 + - + -
852B LYS* 4.0 19.0 - - - +
933B THR* 4.6 12.8 + - + +
934B CYS* 4.8 2.4 - - - +
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Residues in contact with VAL 729 (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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723B PHE* 4.3 18.2 - - + +
726B ALA* 4.4 10.1 - - + +
727B ASP 5.6 0.2 - - - -
728B ASN* 1.3 83.4 - - - +
730B VAL* 1.3 67.8 + - - +
731B SER* 4.3 4.0 + - - +
847B LYS* 3.8 38.1 - - + -
848B VAL 3.2 6.7 - - - +
849B GLY* 4.1 9.4 - - - -
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Residues in contact with VAL 730 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728B ASN* 5.6 0.4 - - + -
729B VAL* 1.3 75.9 - - - +
731B SER* 1.3 72.4 + - - +
846B TYR* 4.4 5.0 - - + +
847B LYS* 3.1 1.9 + - - -
848B VAL* 2.7 49.3 + - + +
850B PHE* 3.6 26.2 - - + -
929B GLU* 3.7 28.5 - - + +
933B THR* 4.0 18.8 - - + +
1293B LEU* 4.0 19.1 - - + -
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Residues in contact with SER 731 (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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729B VAL* 4.2 4.6 + - - +
730B VAL* 1.3 82.5 - - - +
732B GLY* 1.3 58.9 + - - +
846B TYR* 3.3 8.7 + - - -
847B LYS* 3.3 28.1 - - - +
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Residues in contact with GLY 732 (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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731B SER* 1.3 75.1 - - - +
733B GLU* 1.3 60.3 + - - +
845B ARG* 3.4 6.1 - - - +
846B TYR* 2.9 51.4 + - - +
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Residues in contact with GLU 733 (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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732B GLY* 1.3 75.0 - - - +
734B LEU* 1.3 67.1 + - - +
843B LEU* 3.8 21.8 - - + +
844B ALA 3.1 13.5 - - - +
845B ARG* 3.1 33.6 + - + +
846B TYR* 3.5 7.0 + - - -
925B ASN* 5.4 0.2 + - - -
1295B ARG* 3.3 48.3 + - - +
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Residues in contact with LEU 734 (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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733B GLU* 1.3 77.8 - - - +
735B TYR* 1.3 62.5 + - - +
842B PHE 4.1 0.2 - - - +
843B LEU* 3.4 5.5 - - - +
844B ALA* 2.8 40.8 + - + +
846B TYR* 4.4 5.6 - - + -
921B PHE* 3.6 28.7 - - + -
922B ILE* 3.9 17.5 - - + -
925B ASN* 3.5 47.8 - - + +
1295B ARG* 3.8 7.2 - - + +
1296B LEU 3.7 21.3 - - - +
1297B ASP* 3.5 19.5 - - - +
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Residues in contact with TYR 735 (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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698B ILE* 4.6 9.4 - - + -
699B GLU* 5.5 5.4 - - - -
734B LEU* 1.3 82.0 - - - +
736B ILE* 1.3 68.7 + - - +
737B GLY* 3.5 22.6 - - - -
841B PRO* 3.6 23.9 - - + +
842B PHE 3.4 19.1 - - - -
843B LEU* 4.3 13.7 - - + -
921B PHE* 4.4 0.2 - - - -
1295B ARG* 3.7 8.1 - - - +
1297B ASP* 2.9 28.7 + - + +
1298B SER* 3.0 27.2 + - - -
1304B LYS* 6.4 0.4 - - - -
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Residues in contact with ILE 736 (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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735B TYR* 1.3 77.1 - - - +
737B GLY* 1.3 73.4 + - - +
839B ARG* 5.8 0.2 - - - -
841B PRO* 3.4 2.3 - - - +
842B PHE* 2.9 53.7 + - + +
918B GLN* 4.0 25.6 - - + +
921B PHE* 4.0 21.1 - - + -
922B ILE* 5.7 3.1 - - + -
1205B LEU* 4.5 12.8 - - + -
1206B PHE* 3.5 32.1 - - + -
1298B SER* 3.5 19.3 - - - +
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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