Contacts of the strand formed by residues 493 - 498 (chain A) in PDB entry 2A2N
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 SER 493 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491A SER* 3.1 7.9 + - - -
492A ASP* 1.3 87.7 + - - +
494A ALA* 1.3 65.7 + - - +
505A THR 3.2 14.1 - - - -
506A LYS* 4.6 2.0 - - - -
507A LEU* 4.2 5.1 - - - +
645A VAL* 3.9 3.3 - - - +
646A LYS* 3.0 47.4 + - - +
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Residues in contact with ALA 494 (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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493A SER* 1.3 80.4 - - - +
495A ILE* 1.3 67.8 + - - +
496A ILE* 5.6 0.2 - - + -
504A HIS* 3.6 0.7 - - - +
505A THR* 2.8 42.7 + - - +
507A LEU* 4.2 5.2 - - + -
519A PHE* 4.1 22.7 - - + -
643A ILE* 4.2 8.5 - - + -
644A THR 3.2 13.2 - - - +
645A VAL* 4.3 7.2 - - + -
646A LYS* 4.5 1.1 - - - +
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Residues in contact with ILE 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A ALA* 1.3 77.4 - - - +
496A ILE* 1.3 64.0 + - - +
497A HIS* 3.4 38.2 + - + +
502A ASP* 3.8 22.7 - - + +
503A ILE 3.4 6.5 - - - +
504A HIS* 3.4 34.8 - - + +
643A ILE* 3.3 5.3 - - - -
644A THR* 2.8 43.1 + - + +
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Residues in contact with ILE 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A ILE* 1.3 73.0 - - - +
497A HIS* 1.3 61.8 + - - +
498A THR* 3.5 20.7 + - + +
501A GLY 3.8 0.5 - - - +
502A ASP* 3.5 0.2 - - - -
503A ILE* 2.8 49.1 + - + +
505A THR* 4.0 24.9 - - + +
519A PHE* 4.4 9.9 - - + -
533A PHE* 5.0 2.9 - - + -
578A LEU* 5.2 1.6 - - + -
592A PHE* 4.1 24.7 - - + -
594A ILE* 4.3 14.4 - - + -
640A ILE* 4.0 24.7 - - + -
642A ASN 4.1 2.0 - - - -
643A ILE* 4.0 25.8 - - + -
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Residues in contact with HIS 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A ILE* 3.4 30.3 - - + +
496A ILE* 1.3 70.7 - - - +
498A THR* 1.3 55.7 + - - +
502A ASP* 2.8 32.1 + - - +
640A ILE* 3.7 1.6 - - - -
641A ILE* 2.7 40.8 + - + +
642A ASN* 2.9 45.8 + - - +
644A THR* 2.8 33.9 + - - -
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Residues in contact with THR 498 (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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496A ILE* 3.9 14.8 - - + +
497A HIS* 1.3 77.6 - - - +
499A SER* 1.3 60.0 + - - +
500A MET* 3.0 19.9 + - - -
501A GLY* 2.7 37.9 + - - +
502A ASP* 5.1 0.3 - - - +
503A ILE* 3.7 27.6 - - + -
533A PHE* 3.9 19.1 - - + -
618A VAL* 3.9 0.3 - - - +
622A ILE* 3.9 10.3 - - + +
638A VAL* 4.9 0.7 - - - -
639A SER 3.1 13.2 - - - +
640A ILE* 4.9 0.4 - - - -
641A ILE* 3.8 12.2 - - - +
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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