Contacts of the strand formed by residues 677 - 681 (chain B) in PDB entry 2VKZ
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 TYR 677 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675B ASP* 3.6 22.5 + - - -
676B LYS* 1.3 71.0 - - - +
678B VAL* 1.3 61.3 + - - +
702B LYS* 3.3 49.4 + - + +
763B TRP* 3.5 45.5 - + + -
764B ASP 3.5 20.4 - - - +
765B LEU* 3.7 9.8 - - + -
766B ASP* 2.7 34.3 + - - +
767B ALA 3.1 5.9 + - - -
818B ARG* 3.3 24.0 - - - -
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Residues in contact with VAL 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676B LYS* 4.0 26.5 - - + +
677B TYR* 1.3 79.9 - - - +
679B LEU* 1.3 72.5 + - - +
680B ILE* 4.1 1.8 - - + +
696B LEU* 3.6 35.0 - - + -
701B ALA* 4.8 3.4 - - + -
702B LYS 3.0 7.8 + - - +
703B VAL* 3.4 9.8 - - + +
704B VAL* 2.9 29.3 + - - +
763B TRP* 5.4 0.4 - - - -
765B LEU* 4.2 5.1 - - - +
767B ALA* 3.4 22.4 - - + +
769B ILE* 4.0 15.5 - - + -
909B LEU* 5.5 0.4 - - + -
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Residues in contact with LEU 679 (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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678B VAL* 1.3 75.5 - - - +
680B ILE* 1.3 65.2 + - - +
681B THR* 4.5 2.7 - - + -
704B VAL* 3.8 20.4 - - + +
706B THR* 4.2 12.8 - - + -
748B LEU* 4.0 24.0 - - + -
749B ILE* 4.1 20.6 - - + -
752B ILE* 4.4 5.6 - - + -
765B LEU* 3.4 33.3 - - + +
767B ALA 2.9 9.0 + - - +
768B ILE* 3.4 6.2 - - + -
769B ILE 2.9 25.1 + - - -
802B MET* 3.8 29.8 - - + -
806B VAL* 5.7 0.2 - - + -
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Residues in contact with ILE 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678B VAL* 4.6 2.5 - - + -
679B LEU* 1.3 76.6 - - - +
681B THR* 1.3 67.0 + - - +
683B ALA* 4.2 14.3 - - + +
689B GLY* 4.1 17.7 - - - +
692B VAL* 3.7 30.1 - - + -
693B LEU* 4.7 6.7 - - + +
696B LEU* 5.1 1.8 - - + -
703B VAL* 4.1 16.2 - - + -
704B VAL 3.1 16.6 + - - +
705B VAL* 3.7 14.4 - - + +
706B THR* 3.3 21.5 + - - +
769B ILE* 3.5 35.4 - - + +
771B PHE* 5.5 2.0 - - + -
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Residues in contact with THR 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B LEU* 4.5 5.6 - - + -
680B ILE* 1.3 77.9 - - - +
682B GLY* 1.3 60.8 + - - +
683B ALA 3.5 0.4 - - - -
706B THR* 3.0 29.2 - - + +
737B PHE* 4.2 7.6 - - + -
739B GLN* 3.0 27.4 + - - +
769B ILE 3.0 5.0 + - - +
770B PRO* 3.1 18.0 - - - +
771B PHE* 2.9 24.6 + - - +
772B ALA* 3.2 8.6 + - - -
802B MET* 4.2 17.7 - - + -
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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
------------------------------------------------------------
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