Contacts of the strand formed by residues 628 - 633 (chain B) in PDB entry 4YZC
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592A ASP* 2.3 33.0 + - - -
627A ARG* 3.0 23.5 + - - -
629A PHE* 5.7 1.9 - - - -
613B VAL* 4.1 6.1 - - + -
616B LEU* 4.1 23.3 - - + -
617B ARG* 3.5 43.8 + - + -
620B ASP* 3.2 15.9 + - + +
626B ILE 3.8 0.8 + - - -
627B ARG* 1.3 75.2 - - - +
629B PHE* 1.3 72.9 + - - +
630B CYS 3.8 9.2 - - - -
631B THR* 3.2 35.1 + - + +
640B ILE* 3.8 21.8 - - + -
641B ALA 4.0 3.6 - - - -
642B ILE* 4.2 3.6 - - + -
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Residues in contact with PHE 629 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A PHE* 3.9 15.8 - - - -
592A ASP* 3.9 2.9 - - - +
628A TYR 5.7 0.9 - - - -
629A PHE* 5.3 9.4 - - - +
591B PHE* 3.7 26.5 - + + -
594B ARG* 3.4 45.5 - - - -
595B ASP 5.2 0.4 - - - -
596B VAL* 3.7 22.7 - - + -
627B ARG* 3.6 34.1 - - + -
628B TYR* 1.3 89.1 - - - +
630B CYS* 1.3 63.6 + - - +
641B ALA* 2.9 13.1 + - + +
642B ILE* 3.6 18.6 - - - -
643B GLU* 3.5 32.1 - - + -
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Residues in contact with CYS 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A LYS* 3.7 28.0 - - - -
591A PHE* 3.9 14.6 - - - -
592A ASP* 3.4 13.2 - - - -
569B ILE* 4.7 3.6 - - + -
591B PHE* 3.6 28.7 - - + -
628B TYR* 3.5 8.3 - - - -
629B PHE* 1.3 81.0 - - - +
631B THR* 1.3 77.8 + - - +
632B GLU* 4.5 4.0 - - - -
639B TYR 3.9 0.2 - - - +
640B ILE* 3.5 2.3 - - - -
641B ALA* 2.6 37.6 + - + +
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Residues in contact with THR 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568A LYS* 4.4 2.6 - - - -
592A ASP* 2.9 24.0 + - - +
593A ASN* 5.4 1.2 + - - -
569B ILE* 4.6 0.2 - - - -
613B VAL* 3.8 18.6 - - + -
617B ARG* 5.3 1.2 + - - -
628B TYR* 3.2 28.9 + - + +
630B CYS* 1.3 86.5 - - - +
632B GLU* 1.3 67.8 + - - +
638B GLN* 5.4 9.4 - - - +
639B TYR 3.2 4.3 - - - -
640B ILE* 4.1 16.6 - - + -
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Residues in contact with GLU 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568A LYS* 2.4 46.4 + - - +
566B VAL* 3.4 32.2 - - + +
567B GLY* 3.7 9.0 - - - -
568B LYS* 3.0 24.6 + - - +
569B ILE* 3.8 19.1 + - + +
630B CYS* 4.5 3.3 - - - -
631B THR* 1.3 76.0 - - - +
633B LYS* 1.3 65.4 + - - +
638B GLN* 3.3 6.0 - - - +
639B TYR* 2.6 42.3 + - + +
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Residues in contact with LYS 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566B VAL* 3.9 9.8 - - - +
632B GLU* 1.3 81.3 + - - +
634B ASP* 1.3 64.2 + - - +
637B PHE 3.7 7.4 - - - +
638B GLN* 4.6 12.3 - - + +
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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