Contacts of the strand formed by residues 582 - 587 (chain A) in PDB entry 2XT6
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 ALA 582 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546A LEU* 3.7 29.6 - - + -
550A VAL* 4.2 12.3 - - + -
552A LYS* 4.4 11.4 - - + +
581A GLY* 1.3 76.8 - - - +
583A THR* 1.4 65.6 + - - +
598A SER* 3.3 4.3 - - - -
599A LEU* 2.9 33.3 + - + +
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Residues in contact with THR 583 (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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532A GLU* 5.3 3.6 - - - +
550A VAL* 3.8 4.3 - - - -
552A LYS* 3.3 27.0 + - - +
582A ALA* 1.4 77.2 + - - +
584A GLY* 1.3 61.5 + - - +
596A GLU* 3.9 19.1 - - + +
597A VAL 3.5 7.6 - - - +
598A SER* 4.0 10.6 - - - -
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Residues in contact with GLY 584 (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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550A VAL* 3.5 20.0 - - - +
552A LYS* 4.8 2.7 - - - -
583A THR* 1.3 74.5 - - - +
585A THR* 1.3 62.7 + - - -
596A GLU* 3.0 15.6 - - - +
597A VAL* 2.7 33.3 + - - +
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Residues in contact with THR 585 (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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549A ILE 5.4 0.2 - - - +
550A VAL 4.0 9.9 + - - +
551A GLY* 5.3 2.9 - - - -
584A GLY* 1.3 76.1 + - - -
586A TYR* 1.3 69.5 + - - +
587A ILE* 4.1 17.7 + - + +
594A ASP* 4.3 20.9 - - + +
595A ILE 3.5 8.5 - - - +
596A GLU* 3.0 27.1 + - - +
597A VAL* 4.8 1.1 - - - -
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Residues in contact with TYR 586 (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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481A TYR* 3.5 9.2 + - - -
485A LYS* 5.8 0.7 - - - -
519A ASP* 3.2 42.5 + - - -
522A ILE* 3.5 20.2 - - + -
523A ASP* 3.4 35.8 + - + +
526A ALA* 4.9 2.5 - - + -
548A ASN 5.8 1.8 - - - -
549A ILE* 4.3 17.0 - - + +
585A THR* 1.3 73.6 - - - +
587A ILE* 1.3 80.0 + - - +
588A GLN* 4.1 8.8 - - + -
589A MET 5.1 1.4 + - - -
594A ASP* 3.1 7.2 - - - +
595A ILE* 2.7 45.4 + - + +
597A VAL* 3.5 20.8 - - + +
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Residues in contact with ILE 587 (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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481A TYR* 5.7 0.3 + - - -
585A THR* 4.3 19.5 - - + +
586A TYR* 1.3 92.4 - - - +
588A GLN* 1.3 75.6 + - - +
589A MET* 3.7 1.4 + - - +
592A ASP 6.5 0.4 - - - -
593A ASN 4.0 6.3 - - - +
594A ASP* 4.3 11.7 - - + +
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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