Contacts of the strand formed by residues 628 - 633 (chain C) in PDB entry 4YZ9
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 TYR 628 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613C VAL* 3.6 24.2 - - + +
616C LEU* 5.3 9.2 - - + -
617C ARG* 3.4 44.9 + - + -
621C GLU* 4.0 14.8 + - - +
626C ILE 3.4 3.2 + - - +
627C ARG* 1.3 75.9 + - - +
629C PHE* 1.3 70.3 + - - +
630C CYS* 3.6 10.1 - - - -
631C THR* 2.7 39.1 + - - -
640C ILE* 3.5 26.0 - - + -
641C ALA 4.2 2.5 - - - -
642C ILE* 4.7 3.1 - - - -
1001C 4K7 4.0 22.4 - + + -
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Residues in contact with PHE 629 (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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591C PHE* 4.0 28.6 - + + -
594C ARG* 3.8 30.7 - - - -
596C VAL* 4.0 17.0 - - + -
617C ARG* 4.9 3.3 + - - -
627C ARG* 3.4 51.1 - - - -
628C TYR* 1.3 83.5 - - - +
630C CYS* 1.3 64.7 + - - +
641C ALA* 3.1 15.0 + - + +
642C ILE 3.8 17.7 - - - -
643C GLU* 3.6 30.7 - - + -
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Residues in contact with CYS 630 (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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568C LYS* 4.0 23.1 - - - -
569C ILE* 4.0 13.2 - - + -
591C PHE* 3.2 38.8 - - + -
628C TYR* 3.6 7.9 - - - -
629C PHE* 1.3 81.8 - - - +
631C THR* 1.3 87.7 + - - +
632C GLU* 4.4 0.9 - - - -
640C ILE* 3.3 7.3 - - - +
641C ALA* 2.7 29.4 + - + +
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Residues in contact with THR 631 (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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568C LYS* 4.8 1.7 + - - -
569C ILE* 4.3 0.4 - - - -
610C ASP* 5.9 1.6 - - - +
613C VAL* 4.6 3.8 - - - +
628C TYR* 2.7 36.1 + - - -
630C CYS* 1.3 85.9 + - - +
632C GLU* 1.3 81.3 + - - +
633C LYS* 5.7 1.3 - - + -
638C GLN* 4.7 13.9 - - + +
639C TYR 3.3 9.2 - - - +
640C ILE* 3.7 19.0 - - + +
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Residues in contact with GLU 632 (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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566C VAL* 3.8 22.1 - - + +
567C GLY* 2.7 31.3 + - - +
568C LYS* 3.3 25.1 + - - -
569C ILE* 3.7 22.9 - - + -
630C CYS* 4.4 0.9 - - - -
631C THR* 1.3 86.0 - - - +
633C LYS* 1.3 66.8 + - - +
638C GLN* 3.2 4.2 - - - +
639C TYR* 2.4 49.5 + - + +
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Residues in contact with LYS 633 (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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566C VAL* 4.4 8.8 - - - +
606C PHE* 4.1 15.1 - - - -
631C THR* 5.7 1.6 - - + -
632C GLU* 1.3 82.6 + - - +
634C ASP* 1.3 91.0 + - - +
635C ARG* 2.9 20.0 + - - +
637C PHE 3.4 13.2 + - - +
638C GLN* 3.7 22.7 - - + +
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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