Contacts of the strand formed by residues 537 - 542 (chain A) in PDB entry 2HAZ
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 HIS 537 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527A GLU* 3.1 4.5 - - - -
528A TRP* 2.7 88.0 + + + +
529A ARG* 4.2 4.3 - - - -
530A ALA* 5.1 2.7 + - - +
533A GLU* 4.8 10.5 + - - -
535A VAL* 3.9 28.4 + - + +
536A TRP* 1.3 75.0 + - - +
538A SER* 1.3 62.4 + - - +
563A TYR* 5.2 4.8 - + - -
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Residues in contact with SER 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A LYS* 3.7 27.5 - - - -
526A ALA 3.1 12.1 - - - -
527A GLU* 3.9 8.7 - - - -
528A TRP* 4.1 5.4 - - - -
536A TRP* 4.3 2.4 + - - -
537A HIS* 1.3 77.9 - - - +
539A LYS* 1.3 63.3 + - - +
540A TRP* 5.9 0.5 + - - -
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Residues in contact with LYS 539 (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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525A LYS* 3.5 4.5 - - - -
526A ALA 3.0 30.3 + - - -
528A TRP* 3.9 10.3 - - + -
538A SER* 1.3 76.1 - - - +
540A TRP* 1.3 77.7 + - - +
541A TYR* 3.2 37.7 - - + +
553A THR 5.1 2.6 + - - -
555A VAL* 4.9 23.8 - - + +
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Residues in contact with TRP 540 (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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523A LYS* 4.0 29.4 - - + -
524A TYR 3.4 20.2 - - - -
525A LYS* 3.7 39.2 - - + +
538A SER* 5.9 0.2 + - - -
539A LYS* 1.3 91.1 - - - +
541A TYR* 1.3 67.5 + - - +
570A LEU* 3.9 27.1 - - + -
575A LEU* 3.9 26.7 - - + -
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Residues in contact with TYR 541 (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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523A LYS* 3.2 8.7 - - - +
524A TYR* 2.7 48.2 + - + +
526A ALA* 3.6 20.6 - - + -
528A TRP* 4.2 0.9 - - - -
539A LYS* 3.2 53.2 - - + +
540A TRP* 1.3 76.9 - - - +
542A ASP* 1.3 64.3 + - - +
546A ALA* 4.9 0.9 - - + -
552A VAL* 3.6 40.2 - - + -
553A THR* 2.8 34.0 + - - -
554A ILE* 3.7 12.5 - - - +
567A LEU* 5.6 0.2 - - + -
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Residues in contact with ASP 542 (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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522A LEU 4.5 4.5 - - - -
523A LYS* 3.8 19.5 + - - +
541A TYR* 1.3 74.2 - - - +
543A ALA* 1.3 64.3 + - - +
544A LYS* 4.4 2.0 - - + +
545A GLU* 3.3 27.8 - - + +
546A ALA* 3.3 22.3 + - - +
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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