Contacts of the helix formed by residues 524 - 535 (chain A) in PDB entry 2Q8J
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 TYR 524 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A VAL* 5.3 3.2 - - + +
377A THR* 4.5 10.9 + - - -
398A TYR* 4.5 4.6 + - - -
459A THR 3.7 8.1 - - - -
460A ALA* 3.8 18.2 - - + -
463A ARG* 3.1 27.2 + - - -
493A PRO* 3.9 7.9 - - + -
517A PRO* 3.2 28.2 + - + -
518A ASN* 3.3 46.3 - - - +
519A SER* 3.5 13.8 - - - -
521A GLU* 3.3 19.5 + - + +
522A LYS 3.4 1.1 - - - +
523A TYR* 1.4 75.5 - - - +
525A GLY* 1.3 70.8 + - - +
527A THR* 4.6 0.9 + - - -
528A GLY* 3.2 11.6 + - - -
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Residues in contact with GLY 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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459A THR* 2.9 28.1 + - - +
463A ARG* 3.9 16.2 - - - -
524A TYR* 1.3 80.8 - - - +
526A TYR* 1.3 67.3 + - - -
527A THR 3.2 3.1 - - - -
528A GLY 3.1 1.0 + - - -
529A ALA* 2.8 26.0 + - - +
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Residues in contact with TYR 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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433A TYR* 2.7 13.8 + + - -
459A THR* 4.0 15.1 - - + +
463A ARG* 3.5 19.2 - - - +
465A ALA* 4.8 0.2 - - + -
525A GLY* 1.3 70.4 - - - +
527A THR* 1.3 62.4 + - - +
529A ALA 3.6 0.2 + - - -
530A PHE* 3.1 18.4 + - - +
543A VAL* 3.6 7.5 - - - +
544A LYS* 3.7 48.2 - - + -
547A THR* 3.5 28.9 - - + +
595A HIS* 2.9 9.1 + + - -
638A ASN* 4.5 12.8 - - + +
642A ASN* 3.6 26.0 - - - -
801A FE 1.7 32.4 - - - -
802A CO3 3.0 18.6 - - - -
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Residues in contact with THR 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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524A TYR 5.2 0.7 - - - -
525A GLY 3.2 0.8 - - - -
526A TYR* 1.3 74.6 - - - +
528A GLY* 1.3 66.1 + - - +
530A PHE* 3.4 1.5 + - - -
531A ARG* 2.9 23.4 + - - +
547A THR* 4.6 5.8 - - - +
551A ASN* 4.1 12.8 + - - +
560A TRP* 3.3 31.3 - - + +
636A THR* 3.3 27.9 + - + +
637A LYS* 4.8 4.6 - - - -
638A ASN* 3.8 14.0 + - - +
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Residues in contact with GLY 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A LYS 3.7 7.9 - - - -
523A TYR* 3.3 25.9 - - - -
524A TYR 3.2 20.3 + - - -
525A GLY 3.1 2.6 + - - -
527A THR* 1.3 76.0 - - - +
529A ALA* 1.3 61.0 + - - +
531A ARG* 3.1 8.6 + - - +
532A CYS* 2.9 21.3 + - - +
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Residues in contact with ALA 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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457A CYS* 3.5 13.5 - - + +
458A HIS 3.9 25.4 - - - -
459A THR* 4.1 2.5 - - - +
523A TYR 3.7 6.1 + - - -
525A GLY 2.8 18.4 + - - +
528A GLY* 1.3 71.3 - - - -
530A PHE* 1.3 64.2 + - - +
532A CYS* 3.2 17.6 + - - +
533A LEU 3.4 6.6 + - - -
541A ALA* 3.5 12.8 - - + +
542A PHE 4.3 0.2 - - - +
543A VAL* 3.7 20.2 - - + -
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Residues in contact with PHE 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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438A VAL* 4.4 5.6 - - + -
526A TYR 3.1 18.1 + - - +
527A THR* 4.0 2.9 - - - +
529A ALA* 1.3 77.1 - - - +
531A ARG* 1.3 62.5 + - - +
533A LEU* 2.9 13.9 + - + +
534A ALA* 2.8 20.2 + - + +
541A ALA* 4.5 2.9 - - + -
543A VAL* 4.1 12.5 - - + +
547A THR* 3.8 17.0 - - + -
548A VAL* 4.2 27.4 - - + -
551A ASN* 4.2 12.1 - - + -
552A THR* 4.0 14.4 - - + -
560A TRP* 3.7 17.3 - + + -
564A LEU* 3.7 24.0 - - + -
569A PHE* 3.4 46.0 - + - -
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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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522A LYS* 3.4 42.8 + - - +
523A TYR* 4.0 11.9 - - + -
527A THR 2.9 14.6 + - - +
528A GLY* 3.3 9.6 - - - +
530A PHE* 1.3 74.2 - - - +
532A CYS* 1.3 56.3 + - - +
533A LEU 2.9 0.7 + - - -
534A ALA* 4.1 0.9 - - - -
535A GLU* 2.8 63.2 + - + +
559A ASP* 5.7 3.2 + - - -
560A TRP* 3.7 57.1 - - + +
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Residues in contact with CYS 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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456A SER 4.8 0.7 - - - -
457A CYS* 2.0 48.0 - - + -
491A CYS* 4.5 9.2 - - - -
504A LEU* 5.1 0.7 - - - -
523A TYR* 3.6 33.0 - - + -
528A GLY 2.9 12.7 + - - +
529A ALA* 3.4 7.4 - - - +
530A PHE 3.1 0.6 + - - -
531A ARG* 1.3 75.7 - - - +
533A LEU* 1.3 51.4 + - - +
537A VAL* 3.0 33.1 + - - +
538A GLY 2.8 29.3 + - - -
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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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438A VAL* 3.6 29.6 - - + +
439A VAL* 4.2 3.4 - - - +
440A LYS* 3.8 24.6 + - + +
457A CYS* 4.5 2.9 - - - -
529A ALA 3.4 1.4 + - - -
530A PHE* 2.9 10.9 + - + +
531A ARG 2.9 0.2 - - - -
532A CYS* 1.3 79.0 - - - +
534A ALA* 1.3 65.1 + - - +
535A GLU 3.2 1.1 - - - -
536A ASP* 2.8 16.6 + - - +
538A GLY 3.5 10.1 - - - +
539A ASP* 3.2 37.0 - - - +
540A VAL* 3.8 1.6 - - - +
541A ALA* 3.8 21.3 - - + -
569A PHE* 4.1 23.1 - - + -
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Residues in contact with ALA 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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440A LYS* 3.2 28.4 + - - +
530A PHE* 2.8 15.7 + - + +
531A ARG 3.7 5.2 - - - +
533A LEU* 1.3 79.1 - - - +
535A GLU* 1.3 57.8 + - + +
536A ASP* 3.2 1.9 + - - +
560A TRP* 4.0 15.0 - - + +
564A LEU* 3.6 40.6 - - + +
569A PHE* 4.8 3.1 - - - -
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Residues in contact with GLU 535 (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 LYS* 3.9 7.2 + - - -
523A TYR* 2.8 29.6 + - - -
531A ARG* 2.8 55.0 + - + +
534A ALA* 1.3 73.3 - - + +
536A ASP* 1.3 70.2 + - - +
537A VAL* 3.2 11.2 + - + +
560A TRP* 4.0 12.7 - - + +
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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