Contacts of the strand formed by residues 595 - 599 (chain B) in PDB entry 3A8P
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 VAL 595 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515B PRO* 4.0 0.3 - - - +
516B LEU* 2.7 44.7 + - + -
517B VAL* 2.7 41.8 + - + +
587B CYS* 3.2 34.3 - - - -
588B LEU 3.4 3.8 - - - +
589B SER* 4.2 2.2 - - - -
594B ASP* 1.3 80.3 - - - +
596B TYR* 1.3 58.2 + - - +
731B SER* 3.8 28.7 - - - +
732B SER* 4.6 2.7 - - - +
735B ALA* 3.9 14.4 - - + -
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Residues in contact with TYR 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B PHE* 3.3 42.2 - + + -
514B LYS 4.0 3.6 - - - -
515B PRO* 3.8 17.0 - - + -
516B LEU 4.0 0.2 - - - +
517B VAL 5.6 0.7 - - - -
566B LEU* 3.8 28.4 - - + +
587B CYS* 3.3 7.4 - - - -
588B LEU* 2.9 47.0 + - + +
590B ASN* 3.2 27.7 + - - -
594B ASP* 3.5 30.4 + - + +
595B VAL* 1.3 75.7 - - - +
597B LEU* 1.3 64.2 + - - +
598B PHE* 4.0 10.1 - - + -
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Residues in contact with LEU 597 (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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513B PHE* 3.6 4.7 - - - -
514B LYS* 2.9 69.6 + - + +
516B LEU* 4.0 25.1 - - + -
533B TRP* 3.7 20.4 - - + -
576B VAL* 4.6 10.8 - - + -
579B HIS* 4.7 12.6 - - + +
585B VAL* 5.1 6.5 - - + -
586B PHE 3.5 4.0 - - - +
587B CYS* 3.9 28.5 - - + -
596B TYR* 1.3 75.7 - - - +
598B PHE* 1.3 65.7 + - - +
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Residues in contact with PHE 598 (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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511B LEU* 3.9 25.4 - - + -
512B PHE 3.1 14.6 - - - -
513B PHE* 3.7 27.4 - + + -
533B TRP* 3.6 3.7 - - - -
538B VAL* 5.3 0.9 - - + -
545B LEU* 4.0 23.6 - - + -
547B PHE* 3.8 18.8 - + - -
566B LEU* 4.2 4.3 - - + -
585B VAL* 3.0 10.4 - - - +
586B PHE* 2.8 68.7 + + + +
588B LEU* 3.9 25.8 - - + -
596B TYR* 4.0 14.1 - - + -
597B LEU* 1.3 76.3 - - - +
599B GLN* 1.3 61.9 - - - +
613B ILE* 6.0 0.2 - - + -
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Residues in contact with GLN 599 (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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510B TRP 4.5 0.2 - - - +
511B LEU* 3.5 11.4 - - - +
512B PHE* 3.0 56.4 + - + +
533B TRP* 4.0 7.2 - - + -
582B LYS* 3.1 49.0 + - - +
583B GLU 3.3 24.8 + - - +
584B HIS* 3.5 3.6 + - - -
585B VAL* 4.0 2.7 - - + +
598B PHE* 1.3 75.1 - - - +
600B ALA* 1.3 74.3 + - - +
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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