Contacts of the helix formed by residues 525 - 535 (chain A) in PDB entry 2I91
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 GLY 525 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ARG* 3.5 22.2 + - - +
362A LYS* 3.9 17.5 - - - -
523A ASP* 2.8 10.7 + - - -
524A SER* 1.3 78.2 + - - +
526A ALA* 1.3 65.8 + - - +
527A LEU 3.1 3.6 - - - -
528A ASP* 3.0 19.7 + - - +
529A VAL* 3.2 10.4 + - - +
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Residues in contact with ALA 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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361A PHE* 5.6 0.9 - - + -
399A MET* 3.6 27.1 - - + -
519A ILE* 4.6 9.4 - - + -
520A CYS 4.2 7.2 - - - +
523A ASP* 2.7 28.3 + - + +
524A SER 3.4 0.2 - - - -
525A GLY* 1.3 75.4 - - - +
527A LEU* 1.3 64.6 + - + +
529A VAL* 3.0 14.5 - - - +
530A ILE* 3.0 29.3 + - + +
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Residues in contact with LEU 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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361A PHE* 4.2 6.3 - - + -
362A LYS 3.4 25.8 - - - +
363A LEU* 4.1 14.6 - - + -
364A VAL* 4.1 20.2 - - + +
399A MET* 6.0 1.1 - - + -
402A LEU* 3.4 50.0 - - + +
403A VAL* 4.1 25.1 - - + -
406A THR* 4.5 11.7 - - + +
524A SER 4.8 1.7 + - - +
525A GLY 3.0 1.3 + - - -
526A ALA* 1.3 80.8 - - + +
528A ASP* 1.3 60.7 + - - +
530A ILE* 3.5 7.6 + - + +
531A ARG* 3.1 23.0 + - - +
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Residues in contact with ASP 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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362A LYS* 4.8 7.5 + - + +
364A VAL* 2.9 30.2 - - + +
525A GLY* 3.0 13.3 + - - +
527A LEU* 1.3 75.6 - - - +
529A VAL* 1.3 62.0 + - + +
531A ARG* 3.2 6.8 + - - +
532A ASN* 2.8 40.1 + - - +
109B GLN* 2.6 34.3 + - - +
113B ARG* 5.2 4.0 + - - -
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Residues in contact with VAL 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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34A ARG* 6.2 2.2 - - - +
85A ARG* 4.3 11.0 - - - +
517A LEU* 4.3 7.8 - - + +
519A ILE* 4.6 22.4 - - + -
523A ASP* 4.6 3.1 - - - +
525A GLY 3.2 14.4 - - - +
526A ALA* 3.0 22.4 - - - +
528A ASP* 1.3 72.3 - - + +
530A ILE* 1.3 62.9 - - - +
532A ASN* 3.4 10.2 + - + +
533A PHE* 3.1 24.6 + - - +
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Residues in contact with ILE 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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371A PHE* 4.5 9.9 - - + -
399A MET* 5.7 3.4 - - + -
403A VAL* 4.0 19.5 - - + -
465A ILE* 3.8 29.2 - - + -
467A PHE* 5.8 2.2 - - + -
497A ILE* 3.5 27.0 - - + +
517A LEU* 5.4 0.4 - - - -
519A ILE* 3.6 29.4 - - + -
526A ALA* 3.0 22.0 + - + +
527A LEU* 3.9 7.9 - - + +
529A VAL* 1.3 76.6 - - - +
531A ARG* 1.3 57.6 + - - +
533A PHE* 3.5 1.9 + - - +
534A THR* 2.9 38.6 + - - +
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Residues in contact with ARG 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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364A VAL* 3.8 19.0 - - + +
365A GLU* 3.1 42.7 + - - +
366A PRO 5.0 1.2 + - - -
367A THR* 3.9 17.4 - - + +
407A GLU* 5.6 0.9 - - - +
527A LEU 3.1 17.5 + - - +
528A ASP* 3.5 9.5 + - - +
529A VAL 3.1 0.2 - - - -
530A ILE* 1.3 76.2 - - - +
532A ASN* 1.3 78.1 + - - +
534A THR* 2.9 8.3 + - - -
535A LEU* 2.9 45.9 + - + +
537A LEU* 5.5 2.0 - - - +
109B GLN* 4.6 12.5 - - - +
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Residues in contact with ASN 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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528A ASP* 2.8 34.4 + - - +
529A VAL* 3.8 9.7 - - + +
531A ARG* 1.3 80.2 + - - +
533A PHE* 1.3 60.2 - - - +
536A ASP 3.5 1.2 + - - -
537A LEU* 2.8 59.3 + - + +
106B LYS* 3.7 27.2 - - - +
109B GLN* 3.5 26.5 + - - +
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Residues in contact with PHE 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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463A ILE* 5.2 0.4 - - + -
495A LYS* 3.8 30.0 + - + -
497A ILE* 4.0 16.8 - - + -
514A ARG 3.3 26.5 - - - -
515A GLY* 3.7 24.2 - - - -
516A MET 3.9 2.0 - - - -
517A LEU* 3.5 51.4 - - + -
529A VAL 3.1 16.5 + - - +
530A ILE 3.7 3.8 - - - +
531A ARG 3.0 0.8 - - - -
532A ASN* 1.3 76.2 - - - +
534A THR* 1.3 68.2 + - - +
536A ASP* 3.0 13.9 + - - +
537A LEU 4.6 4.5 - - - +
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Residues in contact with THR 534 (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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367A THR* 3.9 18.4 - - - +
369A LYS* 3.6 38.9 - - + +
371A PHE* 3.8 13.3 - - + -
463A ILE* 3.6 32.0 - - + +
495A LYS* 3.0 22.0 + - - -
497A ILE* 4.9 0.5 - - - +
530A ILE* 2.9 22.3 + - - +
531A ARG* 2.9 8.8 + - - -
533A PHE* 1.3 75.1 - - - +
535A LEU* 1.3 58.7 + - - +
536A ASP* 3.2 0.7 + - - -
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Residues in contact with LEU 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A THR* 4.0 25.8 - - + -
369A LYS* 4.6 15.3 - - - +
531A ARG* 2.9 56.3 + - + +
533A PHE 3.2 0.2 - - - -
534A THR* 1.3 76.1 - - - +
536A ASP* 1.3 70.0 + - - +
537A LEU* 3.3 29.2 - - + +
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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