Contacts of the strand formed by residues 592 - 595 (chain C) 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 PHE 592 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496C ILE* 4.1 18.2 - - + -
519C PHE* 3.9 20.2 - + - -
528C TYR* 3.8 31.6 - + - -
533C PHE* 5.5 0.7 - + - -
543C GLN* 3.5 3.6 - - - +
544C THR* 3.0 56.9 + - + +
545C GLY* 4.4 0.4 - - - -
578C LEU* 3.3 27.1 - - + -
579C SER 3.2 15.9 - - - +
580C MET* 4.2 2.7 - - - -
581C ALA* 3.8 2.9 - - - +
590C SER 3.5 13.5 - - - -
591C GLN* 1.3 75.7 - - - +
593C PHE* 1.3 66.4 + - - +
594C ILE* 4.8 6.7 - - + -
609C PHE* 4.0 16.8 - + + -
640C ILE* 4.0 11.7 - - + -
643C ILE* 4.4 1.6 - - + -
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Residues in contact with PHE 593 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A PRO* 3.7 35.0 - - + -
541C MET* 3.7 28.5 - - + -
542C ILE 3.1 15.3 - - - +
543C GLN* 3.9 4.5 - - + -
544C THR* 5.7 0.2 - - - -
572C HIS* 4.2 1.1 - - - -
577C THR 3.5 1.1 - - - +
578C LEU* 3.4 6.4 - - - +
579C SER* 2.9 58.0 + - - -
580C MET 3.3 21.8 - - - -
581C ALA* 3.9 9.4 - - + -
592C PHE* 1.3 78.2 - - - +
594C ILE* 1.3 68.0 + - - +
595C THR* 3.6 24.5 - - + -
602C LEU* 3.8 17.7 - - + -
606C HIS* 3.8 11.9 - + + -
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Residues in contact with ILE 594 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496C ILE* 4.3 16.2 - - + -
503C ILE* 4.1 36.6 - - + -
505C THR* 5.0 0.9 - - + -
533C PHE* 5.2 3.8 - - + -
541C MET* 3.3 3.3 - - - -
542C ILE* 2.9 45.2 + - + +
576C TYR* 3.9 6.3 - - - +
577C THR 3.1 9.2 - - - +
578C LEU* 3.7 19.5 - - + -
592C PHE* 4.8 5.8 - - + -
593C PHE* 1.3 78.0 - - - +
595C THR* 1.3 72.6 + - - +
596C VAL* 4.7 0.2 - - - +
612C VAL* 3.7 24.2 - - + -
619C VAL* 4.0 12.5 - - + +
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Residues in contact with THR 595 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540C PHE 3.4 10.3 - - - +
541C MET* 3.8 2.5 - - + -
572C HIS* 4.5 6.5 - - + +
574C ARG 3.9 1.2 + - - -
575C PRO 3.8 0.5 - - - -
576C TYR* 2.8 32.4 + - - -
577C THR* 3.0 30.9 + - - +
593C PHE* 3.6 26.7 - - + -
594C ILE* 1.3 77.6 - - - +
596C VAL* 1.3 61.1 + - - +
597C VAL 3.4 16.7 + - - -
599C THR* 3.4 27.6 - - + +
602C LEU* 4.8 0.4 - - + -
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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