Contacts of the helix formed by residues 685 - 695 (chain C) in PDB entry 5VOT
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 685 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650C LEU* 3.9 7.0 - - - -
683C VAL* 3.2 13.0 - - - +
684C ARG* 1.3 86.2 - - + +
686C THR* 1.3 65.1 + - - +
687C ALA* 4.0 6.0 + - - +
688C GLU* 3.1 40.7 + - - +
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Residues in contact with THR 686 (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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402C GLU* 4.6 16.9 + - - +
450C TYR* 5.6 1.0 + - - -
650C LEU* 3.9 18.4 - - - +
685C THR* 1.3 71.0 - - - +
687C ALA* 1.3 62.4 + - - +
689C GLY* 2.8 20.1 + - - -
690C VAL* 2.9 18.9 + - + +
702C TYR* 4.1 25.2 + - + +
704C LEU* 5.0 11.4 - - + -
708C MET* 5.3 11.0 - - + +
712C ILE* 6.0 3.8 - - + -
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Residues in contact with ALA 687 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685C THR* 3.4 6.8 + - - +
686C THR* 1.3 78.7 - - - +
688C GLU* 1.3 56.3 + - - +
690C VAL* 3.3 15.1 - - + +
691C ALA* 2.9 32.4 + - - +
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Residues in contact with GLU 688 (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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682C PHE 5.1 0.5 - - - +
683C VAL* 3.4 23.0 - - + +
684C ARG* 2.6 33.4 + - - +
685C THR* 3.1 30.1 + - - +
686C THR 3.1 0.4 - - - -
687C ALA* 1.3 76.3 - - - +
689C GLY* 1.3 54.5 + - - +
691C ALA* 4.2 2.7 - - - +
692C ARG* 2.9 32.1 + - + +
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Residues in contact with GLY 689 (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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503C MET* 6.0 0.4 - - - -
683C VAL* 4.1 6.6 - - - +
685C THR 3.4 4.2 + - - -
686C THR 2.8 12.2 + - - -
688C GLU* 1.3 73.7 - - - +
690C VAL* 1.3 65.4 + - - +
692C ARG* 3.9 7.0 - - - -
693C VAL* 2.9 32.0 + - - +
702C TYR* 4.0 28.9 - - - -
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Residues in contact with VAL 690 (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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503C MET* 5.2 14.8 - - + -
686C THR* 2.9 27.8 + - + +
687C ALA* 3.0 16.8 + - + +
689C GLY* 1.3 78.6 - - - +
691C ALA* 1.3 60.1 + - + +
693C VAL* 3.2 3.0 + - - +
694C ARG* 2.9 69.5 + - + +
702C TYR* 6.3 1.1 - - + -
712C ILE* 4.7 23.8 - - + -
720C THR* 5.3 4.3 - - + +
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Residues in contact with ALA 691 (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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687C ALA 2.9 16.0 + - - +
688C GLU* 4.4 3.1 - - - +
690C VAL* 1.3 74.7 - - + +
692C ARG* 1.3 57.4 + - - +
694C ARG* 3.7 13.8 - - - +
695C LYS* 2.9 33.3 + - - +
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Residues in contact with ARG 692 (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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646C ALA* 5.4 1.8 - - - +
679C PRO* 5.2 6.9 + - - +
680C SER 3.5 19.1 + - - -
681C VAL* 3.1 33.1 + - - +
682C PHE 3.8 1.4 + - - -
683C VAL* 3.4 26.3 - - - +
688C GLU* 2.9 22.9 + - + +
689C GLY* 3.5 5.4 - - - +
690C VAL 3.1 0.2 - - - -
691C ALA* 1.3 79.4 - - - +
693C VAL* 1.3 54.3 + - - +
695C LYS* 3.4 3.0 + - - +
696C SER* 2.2 39.0 + - - +
700C TYR* 3.2 49.9 + - + +
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Residues in contact with VAL 693 (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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503C MET* 4.8 8.3 - - + +
504C ILE* 4.1 29.6 - - - +
505C LYS* 4.2 10.8 - - + +
689C GLY 2.9 20.7 + - - +
690C VAL* 3.9 3.4 - - - +
692C ARG* 1.3 72.1 - - - +
694C ARG* 1.3 67.8 + - + +
696C SER* 3.1 18.7 + - - -
697C LYS 4.2 2.3 + - - -
698C GLY* 4.5 5.0 + - - -
700C TYR* 3.3 38.4 - - + +
702C TYR* 3.6 23.6 - - + +
720C THR* 5.4 5.6 - - + -
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Residues in contact with ARG 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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505C LYS* 5.9 3.4 - - - -
690C VAL* 2.9 45.4 + - - +
691C ALA* 3.7 10.4 - - - +
693C VAL* 1.3 78.3 - - - +
695C LYS* 1.3 57.9 + - + +
696C SER 3.6 0.3 + - - -
697C LYS* 4.3 5.4 + - - -
712C ILE* 4.4 14.6 + - - +
715C ARG 5.7 0.4 + - - -
716C LYS 3.7 7.7 + - - -
717C PRO* 3.5 32.1 - - - +
719C ASP* 3.2 33.1 + - - +
720C THR* 4.3 11.2 - - + +
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Residues in contact with LYS 695 (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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691C ALA 2.9 18.0 + - - +
692C ARG* 3.6 4.5 - - - +
694C ARG* 1.3 74.1 - - + +
696C SER* 1.3 60.8 + - - +
697C LYS* 3.3 11.2 + - - +
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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