Contacts of the strand formed by residues 577 - 580 (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 THR 577 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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571A ARG 4.0 4.1 + - - +
572A HIS* 4.0 16.1 - - + -
574A ARG 3.0 15.6 + - - -
576A TYR* 1.3 78.2 - - - +
578A LEU* 1.3 62.4 + - - +
579A SER* 3.6 13.3 + - - +
593A PHE 3.6 1.2 - - - +
594A ILE* 3.3 5.2 - - - -
595A THR* 3.0 35.6 + - - +
608A VAL* 3.6 29.8 - - + -
610A GLY 3.8 5.6 - - - +
611A ARG* 2.8 26.5 + - - +
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Residues in contact with LEU 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A ILE* 5.2 0.7 - - + -
505A THR* 4.0 24.0 - - + +
507A LEU* 3.8 20.4 - - + -
519A PHE* 4.7 7.0 - - + -
576A TYR 3.9 0.6 + - - +
577A THR* 1.3 71.4 - - - +
579A SER* 1.3 63.6 + - - +
592A PHE* 3.3 35.7 - - + -
593A PHE 3.4 10.3 - - - +
594A ILE* 3.9 14.1 - - + -
608A VAL* 3.7 0.7 - - - -
609A PHE* 2.9 57.0 + - + -
610A GLY* 2.9 22.1 + - - +
611A ARG* 4.2 2.2 - - - +
612A VAL* 5.6 0.9 - - + +
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Residues in contact with SER 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A HIS* 2.8 27.5 + - - -
577A THR* 3.6 4.4 + - - +
578A LEU* 1.3 78.3 + - - +
580A MET* 1.3 61.0 + - - +
592A PHE* 3.2 5.5 - - - +
593A PHE* 2.8 59.3 + - - -
606A HIS* 4.3 2.5 - - - -
607A THR 3.1 12.8 - - - -
608A VAL* 3.6 8.5 - - - -
609A PHE* 3.5 7.6 - - - -
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Residues in contact with MET 580 (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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515A THR* 3.5 28.9 - - + +
518A ASN* 4.1 10.1 - - - +
519A PHE* 6.0 2.0 - - - -
528A TYR* 5.5 0.9 - - - +
562A PHE* 4.2 2.5 - - + -
579A SER* 1.3 72.3 - - - +
581A ALA* 1.3 61.4 + - - +
582A ASN* 4.2 0.8 + - - +
588A ASN* 3.0 33.0 - - + +
589A GLY 3.7 37.7 - - - +
590A SER 4.2 4.3 - - - +
591A GLN 3.4 21.1 - - - +
592A PHE* 4.2 3.6 - - - -
593A PHE* 3.2 5.6 - - - -
606A HIS* 3.0 26.3 + - - +
607A THR* 2.9 20.5 + - - +
609A PHE* 3.5 22.0 - - + -
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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