Contacts of the strand formed by residues 638 - 643 (chain B) 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 GLN 638 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599B LYS 3.8 0.2 - - - +
600B ARG* 3.7 2.4 - - - +
601B ILE* 3.0 49.9 + - + +
606B PHE* 3.3 37.0 - - + +
609B ALA* 4.6 1.7 - - - +
610B ASP* 3.4 25.4 + - - +
631B THR* 3.9 17.6 - - + +
632B GLU 3.5 15.0 - - - +
633B LYS* 3.3 37.4 - - + +
637B PHE* 1.3 74.9 - - - +
639B TYR* 1.3 64.1 + - - +
640B ILE* 5.1 1.1 - - + +
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Residues in contact with TYR 639 (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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564B VAL* 5.0 3.6 - - - +
566B VAL* 3.8 26.1 - - + +
569B ILE* 4.0 13.4 - - + +
571B PHE* 3.5 36.5 - + - -
598B VAL* 4.2 16.6 - - + -
599B LYS 3.4 3.8 - - - +
600B ARG* 3.7 29.8 + - + -
631B THR* 3.2 7.4 - - - +
632B GLU* 2.7 44.6 + - + +
634B ASP* 3.0 39.2 + - - -
637B PHE* 3.9 22.4 - - + +
638B GLN* 1.3 74.2 - - - +
640B ILE* 1.3 63.9 + - - +
641B ALA 4.3 0.2 - - - -
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Residues in contact with ILE 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B ILE* 4.6 1.1 - - - -
597B ALA 3.7 1.0 - - - +
598B VAL* 3.6 1.7 - - - -
599B LYS* 2.7 51.8 + - - +
601B ILE* 4.5 14.4 - - + -
609B ALA* 4.3 13.9 - - + -
610B ASP* 6.2 0.2 - - - +
613B VAL* 4.9 3.8 - - + -
628B TYR* 3.6 29.4 - - + -
630B CYS 3.4 2.7 - - - -
631B THR* 3.6 19.5 - - + +
638B GLN* 5.1 0.9 - - - +
639B TYR* 1.3 80.5 - - - +
641B ALA* 1.3 61.0 + - - +
642B ILE* 3.9 13.9 + - + +
1001B 4K7 4.0 37.5 - - + +
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Residues in contact with ALA 641 (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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569B ILE* 4.0 20.9 - - + +
591B PHE* 4.2 12.8 - - + -
596B VAL* 3.9 21.5 - - + -
597B ALA 3.4 5.2 - - - -
598B VAL* 4.5 1.3 - - + +
628B TYR* 4.0 0.2 - - - -
629B PHE* 3.0 28.7 + - + -
630B CYS 2.8 21.7 + - - +
640B ILE* 1.3 73.5 - - - +
642B ILE* 1.3 64.6 + - - +
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Residues in contact with ILE 642 (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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596B VAL* 3.3 5.4 - - - +
597B ALA* 2.8 48.9 + - + +
599B LYS* 3.9 23.3 - - + +
626B ILE* 4.0 10.8 - - + -
627B ARG 3.2 15.7 - - - +
628B TYR* 4.1 2.0 - - - -
629B PHE* 3.8 7.9 - - - -
640B ILE* 3.9 19.7 - - + +
641B ALA* 1.3 80.8 - - - +
643B GLU* 1.3 62.4 + - - +
710B SER* 5.0 0.4 - - - +
712B PHE* 3.2 38.6 - - + -
1001B 4K7 4.0 20.9 - - + -
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Residues in contact with GLU 643 (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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597B ALA* 4.0 6.8 - - - +
626B ILE* 3.4 28.0 - - + +
627B ARG* 2.9 60.0 + - + +
629B PHE* 3.7 11.3 - - + -
642B ILE* 1.3 74.1 - - - +
644B LEU* 1.3 72.4 + - - +
645B CYS* 3.8 2.4 + - - -
697B SER* 4.4 8.8 - - - -
698B MET* 5.2 2.1 + - - +
706B LYS* 4.7 7.1 + - - -
708B MET* 3.4 34.6 - - + +
712B PHE* 4.9 1.4 - - - -
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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