Contacts of the strand formed by residues 562 - 571 (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 THR 562 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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530A ALA* 3.5 5.5 - - - -
531A VAL* 2.9 42.7 + - + +
561A THR* 1.3 76.2 - - - +
563A TYR* 1.3 61.5 + - - +
583A GLU* 4.8 7.2 - - + -
584A PHE 3.2 20.2 - - - +
585A LYS* 3.6 25.6 - - + +
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Residues in contact with TYR 563 (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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528A TRP* 4.0 12.1 - + + -
529A ARG* 3.3 8.7 - - - +
530A ALA* 3.4 30.7 - - + -
531A VAL* 3.9 5.8 - - - -
537A HIS* 5.2 4.7 - + - -
556A GLY 5.0 0.2 + - - -
557A LEU* 3.6 28.2 - - + -
558A LYS* 2.9 47.8 + - - +
561A THR* 3.3 42.4 - - + -
562A THR* 1.3 74.1 - - - +
564A ALA* 1.3 61.7 + - - +
582A SER 3.8 0.2 - - - +
583A GLU* 3.2 6.2 - - - +
584A PHE* 2.7 68.5 + + + +
586A THR* 4.2 1.8 - - + -
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Residues in contact with ALA 564 (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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528A TRP* 3.1 5.9 - - - +
529A ARG* 2.8 49.5 + - + +
531A VAL* 4.0 6.8 - - + +
536A TRP* 3.9 14.7 - - + -
563A TYR* 1.3 73.9 - - - +
565A VAL* 1.3 59.4 + - - +
581A ALA* 4.5 9.2 - - + -
582A SER 3.5 4.7 - - - -
583A GLU* 3.9 22.4 - - + +
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Residues in contact with VAL 565 (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* 3.5 17.2 - - + +
499A VAL* 4.0 15.3 - - + -
508A VAL* 4.3 13.7 - - + -
526A ALA* 4.7 5.2 - - + -
527A GLU 3.3 13.0 - - - +
528A TRP* 4.2 9.6 - - + -
536A TRP* 4.8 0.4 - - - -
554A ILE* 4.3 16.4 - - + -
564A ALA* 1.3 75.0 - - - +
566A ARG* 1.3 72.7 + - - +
567A LEU* 5.5 0.4 - - + -
581A ALA* 3.3 4.3 - - - -
582A SER 2.8 42.6 + - - +
584A PHE* 3.7 22.2 - - + -
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Residues in contact with ARG 566 (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 2.0 - - - -
525A LYS 3.9 0.2 - - - +
526A ALA* 3.5 4.2 - - - -
527A GLU* 3.0 74.0 + - + +
536A TRP* 3.5 44.8 - - - +
565A VAL* 1.3 78.9 - - - +
567A LEU* 1.3 62.8 + - - +
578A ILE* 3.5 37.7 - - + +
579A SER* 3.5 25.6 - - - +
581A ALA* 4.4 10.1 - - - -
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Residues in contact with LEU 567 (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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494A PRO* 3.4 19.6 - - + +
496A ILE* 4.4 13.5 - - + -
508A VAL* 4.5 7.6 - - + -
510A PHE* 3.4 50.5 - - + -
524A TYR* 4.9 11.4 - - + -
525A LYS 3.3 15.0 - - - +
526A ALA* 3.7 22.9 - - + +
552A VAL* 3.8 16.6 - - + -
565A VAL* 5.5 0.4 - - + -
566A ARG* 1.3 74.7 - - - +
568A ALA* 1.3 60.4 + - - +
578A ILE* 4.4 2.5 - - - -
579A SER* 2.8 40.9 + - - +
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Residues in contact with ALA 568 (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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494A PRO* 4.0 9.4 - - - -
524A TYR* 3.4 5.5 - - - -
525A LYS* 2.8 38.6 + - + +
527A GLU* 5.6 2.9 - - - +
567A LEU* 1.3 75.1 - - - +
569A ALA* 1.3 59.5 + - - +
575A LEU* 3.8 31.0 - - + -
576A GLY 3.9 13.9 - - - +
577A GLU 4.1 2.9 - - - +
578A ILE* 4.3 11.4 - - + -
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Residues in contact with ALA 569 (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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491A PRO* 3.8 14.1 - - + +
492A SER 4.8 0.6 + - - +
494A PRO* 3.9 5.3 - - - +
513A PRO* 3.7 29.8 - - + -
521A ILE* 3.8 19.3 - - + -
523A LYS 3.6 4.7 - - - -
524A TYR* 3.8 8.1 - - + -
568A ALA* 1.3 72.7 - - - +
570A LEU* 1.3 58.2 + - - +
575A LEU* 3.7 2.8 - - - -
576A GLY* 2.8 33.2 + - - +
577A GLU 4.8 1.0 + - - -
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Residues in contact with LEU 570 (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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491A PRO* 4.4 1.8 - - - -
521A ILE* 3.6 2.6 - - - -
522A LEU* 2.7 44.1 + - + -
523A LYS* 2.8 38.0 + - + +
540A TRP* 3.9 24.7 - - + -
568A ALA 4.1 0.2 + - - -
569A ALA* 1.3 73.2 - - - +
571A ASN* 1.3 59.9 + - - +
574A GLY* 3.4 29.6 - - - -
575A LEU* 3.6 20.8 - - + +
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Residues in contact with ASN 571 (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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489A ASP 3.1 17.6 + - - -
490A THR* 3.6 0.2 - - - -
491A PRO* 3.5 16.2 - - + +
516A THR 2.8 26.9 + - - -
519A VAL* 3.1 21.5 + - + +
520A PRO 3.2 23.6 - - - +
522A LEU* 3.8 9.2 - - - +
570A LEU* 1.3 82.0 - - - +
572A GLY* 1.3 59.2 + - - +
573A LYS* 3.0 18.2 + - - +
574A GLY* 3.0 35.0 + - - +
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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