Contacts of the helix formed by residues 522 - 533 (chain A) in PDB entry 3ZRH
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 GLU 522 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481A TRP* 4.8 4.7 + - - -
484A TRP* 5.9 2.4 - - - -
510A ILE* 2.8 30.6 - - + +
513A LEU* 4.0 15.3 - - + -
520A SER 5.1 0.2 - - - +
521A LEU* 1.3 76.5 - - - +
523A GLN* 1.3 82.7 + - - +
524A THR* 3.0 15.3 + - - -
525A HIS* 2.3 50.8 + - - +
526A ILE* 3.3 12.6 + - - +
558A PHE* 4.0 11.9 - - + -
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Residues in contact with GLN 523 (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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484A TRP* 2.8 46.7 - - + +
522A GLU* 1.3 91.5 - - - +
524A THR* 1.3 63.2 + - - +
526A ILE* 3.1 8.7 + - - +
527A PHE 2.9 18.7 + - - -
557A ARG* 3.3 29.2 + - - +
558A PHE* 3.5 28.7 - - + -
562A TYR* 3.4 30.6 - - + +
631A PHE* 3.3 11.4 - - + -
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Residues in contact with THR 524 (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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470A LEU* 4.3 14.4 - - + -
477A PHE* 4.6 7.9 - - + +
481A TRP* 3.4 25.8 - - + -
484A TRP* 5.7 0.3 - - - -
507A TRP* 3.9 19.5 - - + -
510A ILE* 3.5 15.7 - - + +
522A GLU* 3.0 21.1 + - - -
523A GLN* 1.3 76.3 - - - +
525A HIS* 1.3 56.5 + - - +
527A PHE* 3.2 5.3 + - + +
528A VAL* 3.0 29.4 + - + +
631A PHE* 3.4 19.6 - - + -
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Residues in contact with HIS 525 (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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444A LEU* 4.1 6.5 - - + -
466A LEU* 3.7 32.5 - - + +
470A LEU* 3.4 25.5 - - + +
510A ILE* 3.5 30.9 + - + -
513A LEU* 3.9 13.5 - - + -
514A ALA* 3.6 17.0 + - + +
521A LEU* 3.9 22.4 - - + +
522A GLU* 2.3 42.9 + - - +
524A THR* 1.3 75.6 - - - +
526A ILE* 1.3 65.0 + - - +
528A VAL* 3.5 1.0 + - - -
529A LEU* 3.0 28.4 + - - +
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Residues in contact with ILE 526 (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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444A LEU* 4.3 17.9 - - + -
522A GLU 3.6 8.3 - - - +
523A GLN* 3.1 9.1 + - - +
525A HIS* 1.3 75.7 - - - +
527A PHE* 1.3 64.2 + - - +
529A LEU* 3.1 9.7 + - + +
530A ALA* 3.0 19.6 + - - +
537A ILE* 3.6 26.3 - - + +
539A VAL* 4.3 6.5 - - + -
558A PHE* 4.1 15.3 - - + -
562A TYR* 3.7 38.1 - - + -
579A LEU* 5.0 3.6 - - + -
586A PHE* 3.5 34.5 - - + -
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Residues in contact with PHE 527 (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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477A PHE* 3.8 28.5 - + - -
480A ARG* 4.0 18.6 - - + -
523A GLN 2.9 12.0 + - - +
524A THR* 3.2 11.7 - - + +
525A HIS 3.2 0.2 - - - -
526A ILE* 1.3 76.6 - - - +
528A VAL* 1.3 61.9 + - - +
530A ALA* 3.2 12.0 + - - +
531A HIS* 3.0 35.6 + + - -
562A TYR* 3.9 9.1 - + + -
563A LEU 3.0 33.4 - - - -
565A LEU* 4.2 21.3 - - + -
566A LEU* 4.7 2.9 - - + -
630A HIS 4.4 2.9 - - - -
631A PHE* 3.4 52.9 - + + -
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Residues in contact with VAL 528 (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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372A CYS* 4.9 1.3 - - - -
466A LEU* 3.5 28.0 - - + +
469A SER* 3.9 26.0 - - - -
470A LEU* 3.9 17.5 - - + +
477A PHE* 3.6 41.7 - - + -
524A THR* 3.0 19.4 + - + +
525A HIS 3.9 0.2 - - - +
526A ILE 3.4 0.2 - - - -
527A PHE* 1.3 75.7 - - - +
529A LEU* 1.3 57.5 + - - +
531A HIS* 3.0 11.3 + - - +
532A ILE* 2.9 27.9 + - + +
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Residues in contact with LEU 529 (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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444A LEU* 3.4 42.4 - - + -
445A LEU* 4.3 12.8 - - + -
448A VAL* 4.1 19.1 - - + -
462A LEU* 4.1 24.9 - - + -
466A LEU* 4.3 15.3 - - + -
525A HIS 3.0 13.2 + - - +
526A ILE* 3.1 9.6 + - - +
528A VAL* 1.3 72.5 - - - +
530A ALA* 1.3 61.1 + - - +
532A ILE* 3.0 22.0 + - + +
533A LEU* 2.9 34.2 + - + +
537A ILE* 3.9 9.9 - - + -
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Residues in contact with ALA 530 (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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526A ILE 3.0 9.9 + - - +
527A PHE 3.5 10.8 - - - +
529A LEU* 1.3 74.1 - - - +
531A HIS* 1.3 63.7 + - - +
533A LEU* 4.6 1.6 - - - +
534A ARG 3.1 16.1 + - - -
535A ARG 3.3 28.8 + - - +
537A ILE* 3.4 16.2 - - + +
562A TYR 3.5 23.6 - - - +
563A LEU 4.4 0.2 - - - -
564A PRO* 3.4 14.8 - - - +
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Residues in contact with HIS 531 (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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370A PHE* 4.4 4.9 - + - -
372A CYS* 3.9 14.8 - - - -
373A TYR 4.2 2.2 - - - +
477A PHE* 4.1 11.9 - + - -
527A PHE* 3.0 52.2 + + - -
528A VAL* 3.0 8.9 + - - +
530A ALA* 1.3 80.4 - - - +
532A ILE* 1.3 64.5 + - - +
534A ARG* 3.0 10.2 + - - +
564A PRO* 3.1 25.1 - - + +
565A LEU 3.6 4.0 - - - -
566A LEU* 2.8 43.4 + - + +
567A TRP* 2.9 36.9 + + - +
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Residues in contact with ILE 532 (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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363A LEU* 4.0 26.0 - - + -
372A CYS* 4.4 2.9 - - - -
373A TYR* 3.6 21.1 - - + +
374A PHE* 3.4 2.5 - - - +
375A LEU* 2.9 38.7 + - + +
462A LEU* 4.1 11.2 - - + -
465A ALA* 4.1 5.4 - - + -
466A LEU* 3.8 32.1 - - - +
469A SER* 3.9 15.3 - - - +
528A VAL* 2.9 22.3 + - + +
529A LEU* 3.0 21.5 + - + +
531A HIS* 1.3 76.3 - - - +
533A LEU* 1.3 59.9 + - + +
534A ARG* 3.5 0.5 + - - +
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Residues in contact with LEU 533 (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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375A LEU* 3.5 28.2 - - + +
377A ASP 5.3 0.9 - - - +
378A LEU* 5.0 0.2 - - - +
448A VAL* 3.7 33.4 - - + -
449A LEU* 6.2 1.1 - - + -
452A THR* 4.8 13.7 - - + +
462A LEU* 5.3 5.4 - - + -
529A LEU* 2.9 20.4 + - + +
530A ALA 4.3 1.6 - - - +
532A ILE* 1.3 77.5 - - + +
534A ARG* 1.3 71.7 + - - +
535A ARG* 3.1 27.4 + - + +
537A ILE* 4.2 13.9 - - + -
573A TRP* 3.7 13.3 - - - -
577A ILE* 3.7 20.9 - - + -
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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