Contacts of the helix formed by residues 704 - 717 (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 GLU 704 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615B LEU* 3.3 23.1 - - + +
681B TYR* 2.7 26.0 + - - +
682B ARG* 4.4 0.4 - - - +
701B PHE* 3.0 44.6 + - + +
703B ASP* 1.3 96.7 + - - +
705B SER* 1.3 64.8 + - - +
706B ALA 3.4 2.2 - - - -
707B ILE* 3.3 13.3 + - + -
708B PHE* 3.2 14.6 + - - +
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Residues in contact with SER 705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B ALA 5.2 0.2 - - - -
703B ASP 2.8 12.1 + - - -
704B GLU* 1.3 72.8 - - - +
706B ALA* 1.3 61.8 + - - +
707B ILE 3.1 1.4 + - - -
708B PHE* 4.1 5.2 - - - +
709B ARG* 3.2 36.1 + - - +
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Residues in contact with ALA 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B LEU* 4.6 6.1 - - - +
611B GLN* 3.4 41.5 - - + +
704B GLU 3.4 0.6 - - - -
705B SER* 1.3 76.7 - - - +
707B ILE* 1.3 61.6 + - + +
709B ARG* 4.4 3.8 - - - -
710B ALA* 4.4 2.9 - - - +
746B ARG* 3.7 25.4 + - - +
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Residues in contact with ILE 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B LEU* 3.8 34.7 - - + +
611B GLN* 3.5 37.7 - - + +
612B VAL* 4.0 9.2 - - + +
615B LEU* 5.2 3.1 - - + -
697B ALA* 5.8 0.2 - - + -
701B PHE* 3.8 27.6 - - + -
704B GLU* 3.3 22.1 + - + +
705B SER 3.1 0.4 - - - -
706B ALA* 1.3 79.8 - - + +
708B PHE* 1.3 51.6 + - - +
709B ARG 2.8 15.2 + - - -
710B ALA* 3.0 5.5 + - - +
711B LEU* 2.8 49.5 + - + +
724B LEU* 5.9 0.4 - - + -
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Residues in contact with PHE 708 (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 HIS* 3.2 70.7 - + - -
701B PHE 3.6 5.1 + - - +
702B ALA* 3.5 35.2 - - + +
704B GLU 3.2 15.1 + - - +
705B SER* 4.1 4.9 - - - +
707B ILE* 1.3 78.1 - - - +
709B ARG* 1.3 54.8 + - - +
711B LEU* 3.5 9.1 - - - +
712B ASP* 2.7 49.1 + - - +
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Residues in contact with ARG 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705B SER* 3.2 26.8 + - - +
706B ALA* 4.5 2.0 - - - +
707B ILE 2.8 5.3 + - - -
708B PHE* 1.3 74.1 - - - +
710B ALA* 1.3 63.2 - - - +
712B ASP* 3.2 22.1 + - - +
713B THR* 3.5 12.5 + - + +
746B ARG* 4.2 26.3 - - + +
747B ARG* 3.7 26.5 - - - +
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Residues in contact with ALA 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B THR* 4.2 22.8 - - - +
608B LEU* 4.3 11.2 - - + -
706B ALA 4.4 1.3 + - - +
707B ILE 3.0 6.6 + - - +
709B ARG* 1.3 79.3 - - - +
711B LEU* 1.3 61.5 + - - +
713B THR* 2.8 24.7 + - - -
714B LEU* 3.3 14.0 + - - +
746B ARG* 3.7 32.5 - - + +
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Residues in contact with LEU 711 (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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608B LEU* 4.6 8.7 - - + -
694B VAL* 4.1 25.4 - - + +
697B ALA* 3.6 46.9 - - + +
698B HIS* 3.7 11.4 - - + +
701B PHE* 4.6 0.7 - - + -
707B ILE* 2.8 42.6 + - + +
708B PHE* 3.5 11.2 - - - +
710B ALA* 1.3 76.2 - - - +
712B ASP* 1.3 65.5 + - - +
714B LEU* 3.1 13.8 + - + +
715B ARG* 2.9 26.9 + - + +
724B LEU* 4.1 9.9 - - + -
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Residues in contact with ASP 712 (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 HIS* 2.8 33.8 + - - -
708B PHE* 2.7 29.4 + - - +
709B ARG* 3.2 13.5 + - - +
711B LEU* 1.3 73.3 - - - +
713B THR* 1.3 59.4 + - + +
715B ARG* 2.8 25.0 + - - +
716B GLU* 3.0 20.9 + - + +
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Residues in contact with THR 713 (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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709B ARG* 3.6 7.0 - - + +
710B ALA* 2.8 21.5 + - - -
712B ASP* 1.3 75.8 - - + +
714B LEU* 1.3 60.4 + - - +
716B GLU* 3.5 20.5 - - - +
717B VAL* 3.2 25.8 + - - +
742B ALA* 3.0 31.4 + - - +
743B THR* 5.1 0.2 - - - -
745B LEU* 4.4 8.2 - - + +
746B ARG* 3.5 36.5 - - + +
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Residues in contact with LEU 714 (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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602B MET* 4.3 28.3 - - + -
606B THR* 4.2 22.0 - - + -
608B LEU* 4.7 4.3 - - + -
694B VAL* 4.0 24.7 - - + -
710B ALA 3.3 14.8 + - - +
711B LEU* 3.1 18.8 + - + +
712B ASP 3.1 0.2 - - - -
713B THR* 1.3 82.5 + - - +
715B ARG* 1.3 65.3 + - - +
717B VAL* 3.0 20.8 - - - +
719B LEU* 3.3 20.7 + - + +
724B LEU* 6.0 0.2 - - + -
739B ILE* 4.3 20.6 - - + -
742B ALA* 3.8 17.7 - - + -
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Residues in contact with ARG 715 (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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694B VAL* 3.8 20.8 + - + +
695B ASP* 3.2 37.4 + - - +
698B HIS* 3.0 59.6 + - - +
711B LEU 2.9 15.5 - - - +
712B ASP* 2.8 17.1 + - - +
714B LEU* 1.3 71.6 - - - +
716B GLU* 1.3 56.7 + - - +
718B GLY* 2.9 22.0 + - - -
720B GLY* 4.6 4.4 + - - +
771B ARG* 3.2 9.1 + - - -
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Residues in contact with GLU 716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712B ASP* 3.0 20.1 + - - +
713B THR* 3.5 21.4 + - - +
715B ARG* 1.3 75.9 - - - +
717B VAL* 1.3 57.9 + - - +
718B GLY 3.1 1.1 - - - -
745B LEU* 3.3 15.7 - - + +
771B ARG* 2.8 24.0 + - - +
775B GLN* 3.2 33.9 + - - +
778B LYS* 2.9 28.9 + - - -
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Residues in contact with VAL 717 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713B THR 3.2 19.2 + - - +
714B LEU* 3.0 23.1 - - - +
715B ARG 3.1 1.8 - - - -
716B GLU* 1.3 75.5 - - + +
718B GLY* 1.3 56.0 + - - +
719B LEU* 3.7 15.5 + - + -
738B ARG* 3.4 50.0 - - + +
741B LEU* 3.8 28.0 - - + -
742B ALA* 4.0 6.1 - - + +
745B LEU* 5.4 3.4 - - + -
771B ARG* 4.0 5.8 - - - +
772B LEU* 4.8 6.3 - - + +
775B GLN* 4.4 10.8 - - + -
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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