Contacts of the helix formed by residues 653 - 662 (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 GLY 653 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450C TYR* 3.6 16.4 - - - -
451C GLY 5.7 0.7 - - - -
452C ALA* 5.4 0.2 - - - +
485C ARG* 4.4 1.3 - - - -
650C LEU* 4.0 9.9 + - - -
651C ASP 3.1 6.3 - - - -
652C SER* 1.3 80.9 - - - +
654C SER* 1.3 66.2 + - - -
655C THR* 3.1 6.2 + - - -
656C LYS* 3.2 15.6 + - - +
657C GLU* 3.4 8.1 + - - +
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Residues in contact with SER 654 (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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450C TYR* 3.9 5.9 - - - -
480C THR* 3.1 34.9 + - - +
482C THR* 4.2 12.4 - - - +
485C ARG* 3.3 33.4 + - - +
653C GLY* 1.3 68.9 - - - -
655C THR* 1.3 61.9 + - - +
657C GLU* 3.2 11.3 + - - +
658C PHE* 2.9 28.1 + - - +
705C GLU* 4.4 3.3 + - - -
730C LYS* 5.2 3.4 + - - +
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Residues in contact with THR 655 (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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450C TYR* 5.8 3.3 - - - -
500C ILE* 5.4 12.3 - - + +
649C THR* 3.7 22.4 - - + -
650C LEU* 5.4 2.5 - - - -
653C GLY* 3.1 3.3 - - - -
654C SER* 1.3 80.1 + - - +
656C LYS* 1.3 64.1 + - - +
658C PHE* 3.0 8.7 + - - +
659C PHE* 3.0 51.9 + - + -
703C LEU* 5.1 8.7 - - + +
704C LEU* 5.4 5.6 - - - +
705C GLU* 4.9 13.9 + - - +
730C LYS* 6.0 0.4 - - - +
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Residues in contact with LYS 656 (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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649C THR* 4.3 8.0 + - - +
650C LEU 4.2 12.2 + - - +
651C ASP* 2.9 30.7 + - - +
652C SER 5.0 3.1 - - - +
653C GLY 3.2 11.2 + - - +
655C THR* 1.3 79.6 - - - +
657C GLU* 1.3 57.2 + - - +
659C PHE* 3.4 3.3 + - - +
660C ARG* 2.9 41.2 + - - +
671C TRP* 3.7 28.5 - - + -
682C PHE* 3.5 34.7 - - + -
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Residues in contact with GLU 657 (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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482C THR* 5.7 5.8 - - + +
484C VAL* 4.7 28.6 - - + +
653C GLY 3.4 4.3 + - - +
654C SER* 3.2 19.0 + - - +
655C THR 3.2 0.4 - - - -
656C LYS* 1.3 78.7 - - - +
658C PHE* 1.3 64.0 + - - +
660C ARG* 2.3 36.8 + - - +
661C ARG* 2.9 58.9 + - + +
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Residues in contact with PHE 658 (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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754B ASN 6.1 0.2 - - - -
755B GLU* 4.7 19.7 - - + -
500C ILE* 3.5 25.4 - - + -
654C SER 2.9 15.0 + - - +
655C THR* 3.0 11.2 + - - +
657C GLU* 1.3 73.9 - - - +
659C PHE* 1.3 72.8 + + - +
661C ARG* 3.2 4.8 + - - +
662C SER* 2.8 36.1 + - - -
667C PHE* 4.4 28.7 - + - -
727C LEU* 5.3 1.6 - - + -
728C ASP* 3.3 24.9 - - + -
730C LYS* 3.5 24.9 - - - +
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Residues in contact with PHE 659 (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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500C ILE* 4.6 14.1 - - + -
649C THR* 4.2 6.1 - - + -
655C THR* 3.0 50.6 + - + +
656C LYS* 3.9 3.1 - - - +
658C PHE* 1.3 93.0 - + - +
660C ARG* 1.3 62.8 + - - +
662C SER* 3.1 20.0 + - - +
667C PHE* 4.5 28.1 - + + +
668C ASP* 5.7 0.7 - - - -
670C MET* 4.4 17.3 - - + -
671C TRP* 3.7 31.9 - - + +
674C MET* 3.8 21.1 - - + -
703C LEU* 3.5 29.2 - - + -
727C LEU* 5.0 4.7 - - + -
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Residues in contact with ARG 660 (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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656C LYS* 2.9 42.6 + - - +
657C GLU* 2.3 38.6 + - - +
659C PHE* 1.3 77.7 - - - +
661C ARG* 1.3 84.6 + - - +
662C SER 4.4 2.8 - - - +
671C TRP* 3.6 39.8 + - + +
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Residues in contact with ARG 661 (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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755B GLU* 6.1 1.1 - - - +
657C GLU* 2.9 47.0 + - + +
658C PHE* 3.5 4.9 - - - +
660C ARG* 1.3 113.4 - - - +
662C SER* 1.3 65.4 + - - +
663C LYS* 3.6 7.1 + - - +
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Residues in contact with SER 662 (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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658C PHE* 2.8 24.2 + - - -
659C PHE* 3.1 17.6 + - - +
660C ARG 4.4 3.3 - - - +
661C ARG* 1.3 79.6 - - - +
663C LYS* 1.3 62.8 + - - +
664C ILE* 3.2 7.0 + - - +
667C PHE* 3.2 41.7 - - - +
668C ASP* 5.0 9.8 - - - +
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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