Contacts of the strand formed by residues 462 - 465 (chain A) in PDB entry 2A8B
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 PHE 462 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451A TYR* 3.5 5.2 - - - +
452A ILE* 2.7 48.4 + - + +
453A ARG 4.8 0.2 - - - -
454A GLY* 4.8 0.7 - - - -
460A LYS 4.2 0.9 - - - -
461A ALA* 1.3 97.7 - - + +
463A ILE* 1.3 60.2 + - - +
571A VAL* 5.5 1.1 - - + -
575A ARG* 4.0 24.2 - - - -
583A PRO* 3.5 8.0 - - - +
584A VAL* 3.2 28.7 - - + +
586A VAL* 3.8 13.5 - - + -
598A PHE* 4.2 20.4 - + - -
599A ILE* 3.7 35.7 - - + -
602A SER* 3.8 22.9 - - - -
603A ILE* 4.2 16.2 - - + -
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Residues in contact with ILE 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A VAL* 3.9 12.1 - - + -
449A ALA* 4.0 7.6 - - + -
450A ASN 3.2 9.4 - - - +
451A TYR* 3.8 17.0 - - + -
452A ILE* 4.3 0.7 - - - -
462A PHE* 1.3 81.2 - - - +
464A ALA* 1.3 67.9 + - - +
465A THR* 4.3 1.6 - - - -
479A MET* 3.9 31.9 - - + -
483A GLU* 3.8 26.5 - - + -
583A PRO* 3.8 20.6 - - + +
584A VAL 2.9 6.5 + - - +
585A VAL* 4.2 17.2 - - + +
586A VAL* 2.8 34.7 + - - +
599A ILE* 4.9 0.4 - - - -
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Residues in contact with ALA 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A ALA* 3.2 2.3 - - - -
450A ASN 3.0 30.5 + - - -
452A ILE* 3.6 19.3 - - + +
463A ILE* 1.3 71.2 - - - +
465A THR* 1.3 60.4 + - - +
586A VAL 3.4 5.4 - - - -
591A GLY 3.7 1.6 - - - +
595A THR* 3.6 22.0 - - + -
599A ILE* 4.2 1.3 - - + -
627A ARG* 3.5 27.8 + - - -
630A MET* 3.9 6.5 - - + -
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Residues in contact with THR 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A ILE* 4.4 7.8 - - - +
448A ASN 2.6 23.0 + - - -
449A ALA* 3.4 13.8 - - - +
463A ILE* 4.3 2.2 - - + -
464A ALA* 1.3 76.4 - - - +
466A GLN* 1.3 70.4 + - - +
476A PHE* 4.1 12.1 - - + -
479A MET* 4.1 3.8 - - + +
585A VAL* 3.9 24.9 - - + -
586A VAL 3.1 3.0 + - - -
587A HIS* 2.9 34.6 - - + +
591A GLY* 3.0 19.2 + - - -
627A ARG* 4.2 2.2 - - - +
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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