Contacts of the strand formed by residues 633 - 637 (chain C) in PDB entry 7C97
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 LEU 633 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631C GLU* 3.1 25.3 - - + +
632C ASP* 1.3 111.9 - - - +
634C VAL* 1.3 62.2 + - - +
644C LEU* 3.5 30.2 - - + +
645C PHE 3.1 15.7 - - - +
646C SER* 5.1 0.4 - - - -
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Residues in contact with VAL 634 (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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617C ALA* 5.1 2.7 - - + -
621C SER* 4.4 16.6 - - - +
629C PHE* 3.5 39.9 - - + -
631C GLU* 4.4 6.7 - - + +
633C LEU* 1.3 78.6 - - - +
635C THR* 1.3 64.7 + - - +
636C CYS* 3.8 5.1 - - - -
644C LEU* 3.0 22.0 - - - +
645C PHE 3.2 24.2 + - - +
646C SER 4.3 5.6 - - - +
647C ARG* 4.8 0.2 - - - -
650C VAL* 3.7 31.4 - - + -
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Residues in contact with THR 635 (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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617C ALA* 3.4 16.8 - - - +
618C GLN* 3.6 22.1 + - + +
621C SER* 5.1 4.3 + - - -
634C VAL* 1.3 75.1 - - - +
636C CYS* 1.3 69.1 + - - +
642C SER* 5.3 1.1 - - - -
643C SER 3.7 12.3 - - - +
644C LEU* 4.5 11.2 - - + +
768D ASN* 6.2 1.8 - - - +
770D LEU* 4.3 22.9 - - + -
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Residues in contact with CYS 636 (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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615C VAL* 3.8 5.2 - - + -
616C ILE 3.0 16.2 - - - +
617C ALA* 4.2 2.5 - - - +
618C GLN* 5.3 2.5 - - - -
634C VAL* 3.8 11.9 - - - -
635C THR* 1.3 82.1 - - - +
637C ARG* 1.3 63.1 + - - +
638C SER 4.3 0.2 - - - -
642C SER* 3.4 8.0 - - - -
643C SER* 3.3 26.6 + - - -
645C PHE* 3.3 35.4 - - + -
650C VAL* 3.4 33.2 - - - -
770D LEU* 4.3 5.8 - - - +
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Residues in contact with ARG 637 (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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552C PRO 6.0 1.5 + - - -
555C TYR* 3.3 39.9 - - - +
591C TYR* 2.5 40.4 + - - -
611C GLU* 4.2 18.6 + - - +
614C TYR 4.1 1.9 - - - +
616C ILE* 3.0 35.3 + - + +
617C ALA 4.3 0.8 + - - -
618C GLN* 3.8 11.7 + - - +
636C CYS* 1.3 77.4 - - - +
638C SER* 1.3 62.1 + - - +
640C GLY* 4.9 6.3 - - - +
641C GLU 3.0 17.7 - - - +
642C SER* 4.7 1.3 - - - -
654C ASP* 3.2 23.6 + - - -
770D LEU* 4.9 17.7 - - + -
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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