Contacts of the helix formed by residues 704 - 717 (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 GLU 704 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614C LYS* 4.9 6.8 + - - -
615C LEU* 3.7 41.3 - - + +
681C TYR* 4.1 14.2 + - - +
682C ARG* 5.2 2.3 + - - +
701C PHE* 3.2 20.9 + - + +
702C ALA 3.4 0.4 - - - -
703C ASP* 1.3 93.7 - - + +
705C SER* 1.3 54.9 + - - +
706C ALA 3.5 1.8 - - - -
707C ILE* 3.3 19.1 + - + +
708C PHE* 2.8 34.5 + - - +
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Residues in contact with SER 705 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702C ALA 5.6 1.1 - - - -
703C ASP 3.9 4.3 + - - -
704C GLU* 1.3 72.2 + - - +
706C ALA* 1.3 61.3 + - - +
708C PHE* 3.3 6.3 + - - +
709C ARG* 2.9 40.5 + - - +
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Residues in contact with ALA 706 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611C GLN* 4.6 24.5 + - + +
704C GLU 3.5 0.6 - - - -
705C SER* 1.3 78.4 + - - +
707C ILE* 1.3 64.6 + - + +
709C ARG* 3.8 3.6 + - - +
710C ALA* 3.4 22.9 + - - +
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Residues in contact with ILE 707 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608C LEU* 4.3 22.2 - - + +
611C GLN* 3.8 31.9 - - + +
612C VAL* 4.2 9.9 - - + +
614C LYS* 5.0 2.2 - - - +
615C LEU* 4.2 12.6 - - + -
701C PHE* 3.7 52.0 - - + -
704C GLU* 3.3 17.9 + - + +
706C ALA* 1.3 74.5 - - + +
708C PHE* 1.3 69.0 + - - +
710C ALA* 3.4 5.6 + - - +
711C LEU* 3.3 29.0 + - + +
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Residues in contact with PHE 708 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698C HIS* 3.3 51.3 - + - -
701C PHE 3.5 8.7 - - - +
702C ALA* 3.7 32.5 - - + +
704C GLU 2.8 22.8 + - - +
705C SER* 3.5 8.3 - - - +
707C ILE* 1.3 76.0 - - - +
709C ARG* 1.3 71.1 + - + +
711C LEU* 3.2 9.2 + - - +
712C ASP* 3.1 38.7 + - - +
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Residues in contact with ARG 709 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705C SER* 2.9 24.7 + - - +
706C ALA* 4.3 4.3 - - - +
708C PHE* 1.3 86.1 - - + +
710C ALA* 1.3 59.7 + - - +
712C ASP* 3.2 38.3 + - - +
713C THR* 3.4 2.4 + - - +
746C ARG* 2.6 69.4 + - - +
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Residues in contact with ALA 710 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606C THR* 5.2 8.3 - - - +
608C LEU* 4.5 21.8 - - + -
611C GLN* 6.1 1.1 - - - +
706C ALA 3.4 16.6 + - - +
707C ILE 3.9 4.3 - - - +
708C PHE 3.3 0.6 - - - -
709C ARG* 1.3 77.0 - - - +
711C LEU* 1.3 59.7 + - - +
713C THR* 2.3 31.8 + - - +
714C LEU* 3.5 11.8 + - + +
746C ARG* 4.9 0.7 - - - +
747C ARG* 5.9 5.6 - - - +
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Residues in contact with LEU 711 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608C LEU* 3.8 23.8 - - + -
694C VAL* 3.8 17.3 - - + +
697C ALA* 3.7 13.2 - - + +
698C HIS* 3.7 35.4 - - + +
701C PHE* 4.4 2.5 - - + -
707C ILE* 3.3 31.2 - - + +
708C PHE* 3.2 9.7 + - - +
710C ALA* 1.3 73.9 - - - +
712C ASP* 1.3 60.3 + - - +
713C THR 3.3 0.7 - - - -
714C LEU* 3.4 10.5 + - + +
715C ARG* 3.0 34.7 + - - +
724C LEU* 4.2 23.1 - - + -
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Residues in contact with ASP 712 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698C HIS* 2.9 26.6 + - - -
708C PHE* 3.1 29.4 + - - -
709C ARG* 3.2 42.5 + - - +
711C LEU* 1.3 77.4 - - - +
713C THR* 1.3 57.0 + - - +
715C ARG* 3.4 14.6 + - - +
716C GLU* 2.8 34.6 + - - +
746C ARG* 4.2 2.2 - - - +
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Residues in contact with THR 713 (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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709C ARG 3.4 2.0 + - - +
710C ALA* 2.3 31.2 + - - -
712C ASP* 1.3 77.4 - - - +
714C LEU* 1.3 59.1 + - - +
716C GLU* 3.6 9.9 - - - +
717C VAL* 3.3 24.8 + - - +
742C ALA* 3.4 35.6 + - - +
745C LEU* 4.0 12.9 - - + +
746C ARG* 3.5 36.8 - - - +
747C ARG* 4.3 8.7 + - - +
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Residues in contact with LEU 714 (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* 4.0 33.7 - - + -
606C THR* 4.8 10.8 - - + -
608C LEU* 4.6 11.2 - - + -
694C VAL* 4.0 28.9 - - + -
710C ALA* 3.5 14.1 + - + +
711C LEU* 3.4 18.5 + - + +
712C ASP 3.3 0.6 - - - -
713C THR* 1.3 76.9 + - - +
715C ARG* 1.3 66.3 + - - +
717C VAL* 3.3 7.0 + - - +
718C GLY 3.2 5.4 + - - -
719C LEU* 3.1 28.7 + - + +
739C ILE* 4.3 17.3 - - + -
742C ALA* 4.2 15.9 - - + -
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Residues in contact with ARG 715 (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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694C VAL* 3.6 10.8 - - + -
695C ASP* 3.3 28.1 + - - +
698C HIS* 3.5 49.4 + - - +
711C LEU 3.0 17.8 + - - +
712C ASP* 3.5 20.9 + - - +
714C LEU* 1.3 74.4 - - - +
716C GLU* 1.3 54.6 + - - +
718C GLY* 2.8 26.7 + - - -
719C LEU 4.5 3.6 - - - +
720C GLY* 4.6 4.3 - - - +
771C ARG* 3.4 8.3 + - - -
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Residues in contact with GLU 716 (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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712C ASP* 2.8 20.1 + - - +
713C THR* 3.6 7.5 - - - +
714C LEU 3.3 0.2 - - - -
715C ARG* 1.3 71.7 - - - +
717C VAL* 1.3 58.2 + - - +
745C LEU* 4.0 11.5 - - + +
746C ARG* 3.9 20.1 + - - -
771C ARG* 2.9 30.2 + - - +
775C GLN* 3.3 34.6 - - - +
778C LYS* 2.8 27.4 + - - +
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Residues in contact with VAL 717 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713C THR 3.3 13.4 + - - +
714C LEU* 3.3 11.0 + - + +
715C ARG 3.1 0.6 - - - -
716C GLU* 1.3 77.7 - - - +
718C GLY* 1.3 54.8 + - - +
719C LEU* 3.8 10.5 - - + -
738C ARG* 3.2 68.1 + - + +
741C LEU* 4.0 25.4 - - + -
742C ALA* 4.0 10.5 - - + +
745C LEU* 4.1 12.1 - - + -
771C ARG* 3.7 8.9 - - - +
772C LEU* 5.9 0.7 - - + -
775C GLN* 4.8 7.6 - - + -
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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