Contacts of the helix formed by residues 659 - 664 (chain C) in PDB entry 2C11
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 ASP 659 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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623C ARG* 2.6 54.1 + - - +
626C SER* 3.2 16.0 + - - -
656C PRO* 4.2 16.0 + - + +
657C THR 4.2 1.0 - - - -
658C VAL* 1.3 69.9 - - - +
660C PHE* 1.3 62.0 + - - +
661C SER 3.5 4.8 + - - -
662C ASP* 2.9 37.5 + - - +
663C PHE* 3.8 10.1 - - - -
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Residues in contact with PHE 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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525C HIS* 3.6 20.4 - + - -
626C SER* 2.9 17.1 + - - +
627C TRP* 3.3 29.4 - - + +
630C TYR* 3.8 26.2 - + + -
633C ALA* 4.6 6.5 - - + -
635C THR* 5.6 0.7 - - + -
644C SER* 3.6 27.4 - - - +
658C VAL 3.6 4.2 + - - -
659C ASP* 1.3 67.8 - - - +
661C SER* 1.3 63.8 + - - +
662C ASP 3.1 2.7 - - - -
663C PHE* 3.1 55.3 + + + +
664C ILE* 4.1 7.7 + - + +
677C TRP* 3.7 36.6 - + + -
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Residues in contact with SER 661 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623C ARG* 3.9 30.0 + - - -
626C SER* 3.1 23.7 + - - -
629C ARG* 3.8 17.3 + - - -
630C TYR* 4.1 14.9 + - - -
659C ASP* 3.4 2.5 + - - -
660C PHE* 1.3 76.2 - - - +
662C ASP* 1.3 60.7 - - - +
664C ILE* 3.3 26.3 + - - +
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Residues in contact with ASP 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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623C ARG* 3.4 9.9 + - - -
641C GLU* 3.9 1.7 - - - +
659C ASP* 2.9 40.7 - - - +
660C PHE 3.1 0.8 - - - -
661C SER* 1.3 74.3 - - - +
663C PHE* 1.3 59.3 + - + +
664C ILE 3.0 7.9 + - - -
665C ASN* 2.9 25.1 + - - +
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Residues in contact with PHE 663 (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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572C GLU* 2.8 22.3 - - - +
635C THR* 3.5 12.4 - - + +
640C GLU 5.0 1.8 - - - -
641C GLU* 3.1 60.0 - - + +
642C PRO* 5.1 0.4 - - + -
643C SER 2.9 33.9 - - - -
658C VAL* 4.2 12.3 - - + -
659C ASP 3.8 18.4 - - - -
660C PHE* 3.1 39.4 + + + +
662C ASP* 1.3 78.4 - - + +
664C ILE* 1.3 54.5 + - + +
665C ASN* 3.7 1.3 - - - -
677C TRP* 4.0 14.8 - + - -
1739C CA 2.9 10.2 - - - -
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Residues in contact with ILE 664 (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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572C GLU* 3.5 21.5 - - + +
573C GLU* 3.2 28.9 - - - +
576C ALA* 4.0 18.8 - - + -
630C TYR* 3.2 46.0 - - + +
633C ALA* 4.4 7.9 - - + -
635C THR* 4.6 9.6 - - + -
660C PHE* 4.2 11.9 - - + +
661C SER 3.3 15.8 + - - +
662C ASP* 3.0 2.9 - - - +
663C PHE* 1.3 82.4 - - + +
665C ASN* 1.3 58.4 + - - +
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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