Contacts of the helix formed by residues 693 - 701 (chain C) in PDB entry 2VF7
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 THR 693 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691C ALA 3.7 0.2 + - - -
692C LEU* 1.3 75.5 - - - +
694C VAL* 1.3 54.6 + - - +
695C ASP* 3.0 8.1 + - - +
696C GLU* 3.0 37.1 + - - +
697C ALA* 2.8 31.7 + - - +
720C GLY 3.4 13.2 + - - -
721C TYR* 3.8 15.7 - - - +
722C LEU 3.3 7.9 - - - -
723C ARG* 4.0 26.2 - - + +
724C LEU* 3.8 0.4 - - - -
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Residues in contact with VAL 694 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602C MET* 3.4 32.3 - - + -
693C THR* 1.3 71.1 - - - +
695C ASP* 1.3 55.9 + - - +
696C GLU 3.5 0.2 - - - -
697C ALA* 4.0 1.7 - - - +
698C HIS* 3.2 24.6 + - - +
711C LEU* 3.8 21.0 - - + +
714C LEU* 4.0 21.8 - - + -
715C ARG* 3.6 26.2 - - + -
719C LEU 3.6 19.1 - - - +
720C GLY* 3.4 6.5 + - - +
722C LEU 2.9 9.4 + - - +
724C LEU* 3.7 14.0 - - + +
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Residues in contact with ASP 695 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693C THR* 3.0 8.6 - - - +
694C VAL* 1.3 75.2 - - - +
696C GLU* 1.3 65.0 + - + +
698C HIS* 3.5 14.9 - - - +
699C ASP* 3.6 16.6 - - - +
715C ARG* 3.3 25.9 + - - +
720C GLY* 3.3 31.6 + - - +
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Residues in contact with GLU 696 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459C GLU* 5.6 4.3 - - - +
691C ALA 4.4 3.1 - - - +
692C LEU* 3.8 24.4 - - + +
693C THR* 3.0 40.7 + - - +
695C ASP* 1.3 73.3 - - + +
697C ALA* 1.3 66.0 + - - +
698C HIS 3.2 0.2 - - - -
699C ASP* 3.3 10.3 + - - +
700C PHE* 3.0 21.8 + - - +
723C ARG* 5.6 1.0 + - - -
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Residues in contact with ALA 697 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692C LEU* 4.0 16.5 - - + +
693C THR 2.8 15.9 + - - +
694C VAL 4.1 1.3 - - - +
696C GLU* 1.3 76.6 - - - +
698C HIS* 1.3 53.8 + - - +
700C PHE* 4.1 1.6 - - - -
701C PHE* 2.8 45.7 + - + +
711C LEU* 3.7 11.9 - - + -
724C LEU* 3.6 33.7 - - + -
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Residues in contact with HIS 698 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694C VAL 3.2 20.6 + - - +
695C ASP* 3.5 9.2 - - - +
697C ALA* 1.3 76.7 - - - +
699C ASP* 1.3 68.2 + - - +
700C PHE 3.5 0.5 + - - -
701C PHE 3.9 0.2 - - - -
702C ALA* 3.6 14.4 + - - +
708C PHE* 3.3 56.7 - + - -
711C LEU* 3.7 12.2 - - + +
712C ASP* 2.9 24.2 + - - -
715C ARG* 3.5 42.1 + - - +
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Residues in contact with ASP 699 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695C ASP 3.6 15.0 - - - +
696C GLU* 3.3 9.6 + - - +
698C HIS* 1.3 85.0 + - - +
700C PHE* 1.3 60.1 + - - +
701C PHE 3.6 0.2 - - - -
702C ALA* 4.1 13.9 - - - +
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Residues in contact with PHE 700 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681C TYR* 3.8 27.4 + + - -
682C ARG* 3.5 58.1 + - + -
684C LYS* 3.5 38.6 - - + -
689C VAL* 4.4 5.8 - - + -
692C LEU* 4.3 7.6 - - + -
696C GLU 3.0 16.5 + - - +
697C ALA* 3.1 7.4 + - - +
699C ASP* 1.3 78.8 - - - +
701C PHE* 1.3 83.2 + + - +
702C ALA 3.4 4.0 + - - -
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Residues in contact with PHE 701 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612C VAL* 4.3 15.0 - - + -
615C LEU* 4.0 20.2 - - + -
616C PHE* 6.2 0.4 - + - -
681C TYR* 4.2 6.5 - + - -
682C ARG* 6.3 0.2 - - - +
689C VAL* 4.0 28.9 - - + -
692C LEU* 4.8 1.1 - - + -
697C ALA* 2.8 42.9 + - + +
698C HIS 3.9 4.3 - - - -
700C PHE* 1.3 99.7 - + - +
702C ALA* 1.3 59.7 + - - +
703C ASP 3.3 3.1 - - - -
704C GLU* 3.2 33.8 + - + +
707C ILE* 3.7 40.4 - - + -
708C PHE* 3.5 8.8 - - - +
711C LEU* 4.4 3.6 - - + -
724C LEU* 4.5 6.1 - - + -
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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