Contacts of the helix formed by residues 608 - 617 (chain B) in PDB entry 2VF8
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 LEU 608 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602B MET* 6.1 0.2 - - + -
603B ALA* 3.6 21.1 - - + +
606B THR* 2.7 32.5 + - + +
607B GLY* 1.3 77.5 - - - +
609B PHE* 1.3 66.1 + - - +
611B GLN* 3.3 13.0 + - - +
612B VAL* 3.4 24.8 + - + +
706B ALA 4.6 7.9 - - - +
707B ILE* 3.8 28.6 - - + +
710B ALA* 4.3 19.5 - - + -
711B LEU* 4.6 18.8 - - + -
714B LEU* 4.7 5.6 - - + -
724B LEU* 4.7 15.9 - - + -
746B ARG* 5.4 3.8 - - - +
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Residues in contact with PHE 609 (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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603B ALA* 3.2 35.6 + - + +
604B THR* 3.9 17.7 - - - +
607B GLY 3.0 1.8 + - - -
608B LEU* 1.3 76.3 - - + +
610B ASP* 1.3 70.2 + - - +
612B VAL* 2.7 44.9 + - + +
613B ARG* 2.9 46.0 + - + +
632B PHE 3.7 17.7 - - - -
633B SER* 4.5 1.3 - - - -
634B PHE* 3.7 18.2 - + - -
672B TYR* 3.9 7.4 - - - -
686B ILE* 4.4 9.9 - - + -
689B VAL* 5.4 1.3 - - + -
690B LEU* 4.0 26.5 - - + -
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Residues in contact with ASP 610 (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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607B GLY* 3.2 24.9 + - - +
609B PHE* 1.3 76.4 - - - +
611B GLN* 1.3 74.1 + - - +
613B ARG* 2.7 40.2 + - - +
614B LYS* 3.0 26.5 + - - +
629B ALA* 4.9 0.5 - - - +
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Residues in contact with GLN 611 (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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607B GLY 4.7 2.8 + - - -
608B LEU* 3.3 6.9 + - - +
609B PHE 2.9 2.4 + - - -
610B ASP* 1.3 91.3 - - - +
612B VAL* 1.3 65.5 + - - +
614B LYS* 3.9 19.6 - - + +
615B LEU* 3.3 25.9 + - + +
706B ALA* 3.4 27.0 - - + +
707B ILE* 3.5 23.5 - - + +
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Residues in contact with VAL 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B LEU* 3.4 34.1 - - + +
609B PHE* 2.7 34.6 + - + +
611B GLN* 1.3 67.6 - - - +
613B ARG* 1.3 56.7 + - - +
615B LEU* 2.6 38.3 + - - +
616B PHE* 3.2 26.5 + - + -
686B ILE* 4.5 1.3 - - + -
689B VAL* 4.3 18.6 - - + -
701B PHE* 4.6 13.7 - - + -
707B ILE* 4.0 12.6 - - + -
724B LEU* 5.9 1.3 - - + -
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Residues in contact with ARG 613 (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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609B PHE* 2.9 39.6 + - + +
610B ASP* 2.7 51.1 + - - +
612B VAL* 1.3 75.0 - - - +
614B LYS* 1.3 62.3 + - - +
615B LEU 3.2 0.3 + - - -
616B PHE* 3.2 9.4 + - - +
617B ALA* 3.2 16.5 + - - +
629B ALA* 3.4 42.0 + - + +
630B GLY 4.5 1.1 - - - +
632B PHE* 3.9 18.6 - - + +
633B SER* 3.6 38.2 - - - +
686B ILE* 5.6 0.7 - - - -
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Residues in contact with LYS 614 (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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610B ASP 3.0 18.0 + - - +
611B GLN* 4.0 20.4 - - + +
613B ARG* 1.3 72.1 - - - +
615B LEU* 1.3 62.5 + - + +
617B ALA* 3.2 20.5 + - + +
618B ALA* 3.7 7.3 + - - +
629B ALA* 3.7 11.1 - - + +
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Residues in contact with LEU 615 (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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611B GLN 3.3 16.5 + - - +
612B VAL* 2.6 21.2 + - - +
614B LYS* 1.3 69.8 - - + +
616B PHE* 1.3 63.7 + - + +
617B ALA 3.0 5.0 + - - -
618B ALA* 3.0 18.7 + - - +
619B THR* 4.0 6.2 + - - +
681B TYR* 3.4 45.8 - - + +
701B PHE* 3.5 30.1 - - + -
704B GLU* 3.3 26.7 - - + +
707B ILE* 5.2 3.4 - - + -
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Residues in contact with PHE 616 (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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612B VAL* 3.2 25.5 + - + -
613B ARG 3.2 6.8 + - - +
615B LEU* 1.3 80.1 - - + +
617B ALA* 1.3 55.8 - - - +
618B ALA 3.3 0.2 - - - -
619B THR* 3.0 18.3 + - - -
622B ALA* 3.0 19.4 - - - +
632B PHE* 3.4 32.9 - + + -
679B VAL* 4.0 13.7 - - + -
680B GLU 4.5 0.2 - - - -
681B TYR* 3.7 34.8 - + + -
684B LYS* 3.7 7.4 - - + -
685B ASN 3.0 37.0 - - - -
686B ILE* 3.6 34.1 - - + -
689B VAL* 3.8 8.5 - - + -
700B PHE* 6.3 0.7 - + - -
701B PHE* 5.7 1.1 - + - -
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Residues in contact with ALA 617 (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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613B ARG 3.2 10.5 + - - +
614B LYS* 3.2 17.5 - - + +
615B LEU 3.0 1.0 - - - -
616B PHE* 1.3 77.5 - - - +
618B ALA* 1.3 56.1 + - - +
622B ALA* 3.3 21.9 - - - +
623B LYS* 3.6 10.0 + - - -
627B TYR 4.2 5.1 - - - +
628B ASN* 4.3 6.3 - - - -
629B ALA* 3.9 22.0 - - + +
632B PHE* 4.3 2.7 - - - -
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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