Contacts of the helix formed by residues 487 - 501 (chain A) in PDB entry 3O8C
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 ASP 487 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433A THR* 5.8 0.4 - - - +
434A GLN 3.8 13.7 - - - +
435A THR* 3.1 27.6 - - + +
436A VAL* 2.9 26.6 + - - +
486A PHE* 1.3 81.9 - - - +
488A SER* 1.3 61.9 + - - +
489A SER* 2.8 23.1 + - - +
490A VAL* 2.9 30.8 + - + +
491A LEU 3.9 0.2 + - - -
525A CYS* 3.6 2.3 - - - -
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Residues in contact with SER 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A VAL* 3.6 17.1 - - - +
438A PHE* 4.2 0.6 - - - -
487A ASP* 1.3 76.0 + - - +
489A SER* 1.3 62.1 + - - +
491A LEU* 2.9 17.5 + - - +
492A CYS 3.1 8.3 + - - -
525A CYS* 3.6 16.2 - - - -
526A GLN* 5.2 2.8 - - - +
528A HIS* 2.6 40.1 + - - +
532A TRP* 2.8 27.9 + - - -
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Residues in contact with SER 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A GLN* 3.1 28.8 + - - +
435A THR* 4.0 4.7 - - - -
436A VAL* 3.8 17.5 - - - +
446A ILE* 4.2 17.9 - - - -
487A ASP* 2.8 17.4 + - - +
488A SER* 1.3 78.3 - - - +
490A VAL* 1.3 62.6 + - - +
492A CYS* 3.3 11.2 + - - +
493A GLU* 3.0 30.4 + - - +
557A PHE* 4.0 3.5 - - - -
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Residues in contact with VAL 490 (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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295A THR* 3.5 26.7 - - - +
296A ASP* 5.8 0.2 - - - -
297A SER* 4.0 16.4 - - - +
300A ILE* 3.6 21.1 - - + -
434A GLN 5.7 0.9 - - - +
486A PHE* 3.6 13.9 - - + -
487A ASP* 2.9 22.1 + - + +
489A SER* 1.3 81.0 + - - +
491A LEU* 1.3 65.8 + - - +
493A GLU* 3.2 15.3 + - - +
494A CYS* 2.9 22.8 + - - -
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Residues in contact with LEU 491 (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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300A ILE* 5.3 1.6 - - + -
486A PHE* 4.0 20.6 - - + -
488A SER* 2.9 13.0 + - - +
490A VAL* 1.3 77.1 - - - +
492A CYS* 1.3 64.6 + - - +
494A CYS* 3.0 17.0 + - - +
495A TYR* 3.1 26.0 + - + -
513A LEU* 4.4 14.4 - - + -
517A LEU* 5.1 8.7 - - + -
525A CYS* 3.8 14.1 - - + -
526A GLN 3.5 25.4 - - - +
527A ASP* 5.1 0.4 - - - -
528A HIS* 4.0 21.3 - - + +
529A LEU* 4.2 22.0 - - + -
532A TRP* 3.7 9.4 - - + -
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Residues in contact with CYS 492 (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 PHE* 4.9 0.2 - - - -
446A ILE* 4.9 3.8 - - + -
488A SER 3.1 2.2 + - - -
489A SER* 3.3 12.3 - - - +
491A LEU* 1.3 78.3 - - - +
493A GLU* 1.3 62.8 + - - +
495A TYR* 3.1 3.0 + - - -
496A ASP* 3.0 21.3 + - - +
532A TRP* 3.4 55.7 - - + +
536A PHE* 3.6 10.6 - - - -
557A PHE* 3.7 11.4 - - + -
560A LEU* 3.7 28.7 - - - -
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Residues in contact with GLU 493 (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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296A ASP* 5.8 0.5 - - - -
297A SER* 3.7 23.5 + - - +
434A GLN* 3.7 22.0 + - - -
489A SER* 3.0 11.6 + - - +
490A VAL* 3.2 26.4 + - - +
492A CYS* 1.3 76.6 - - - +
494A CYS* 1.3 56.2 + - - +
496A ASP* 3.3 9.0 + - - +
497A ALA* 2.9 31.4 + - - +
556A ASN* 3.8 20.6 + - - +
557A PHE* 3.4 28.6 + - + +
4C 5BU 5.8 0.7 + - - -
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Residues in contact with CYS 494 (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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297A SER* 3.5 32.1 - - - -
300A ILE* 4.0 11.0 - - - -
301A LEU* 3.8 16.9 - - + +
490A VAL* 2.9 21.5 + - - -
491A LEU* 3.0 10.3 + - - +
493A GLU* 1.3 76.0 - - - +
495A TYR* 1.3 56.6 + - - +
497A ALA* 3.3 2.4 + - - -
498A GLY* 2.8 26.3 + - - -
509A THR* 4.0 4.4 - - + +
513A LEU* 3.8 36.3 - - + -
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Residues in contact with TYR 495 (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 LEU* 3.1 26.8 + - + -
492A CYS 3.1 0.6 + - - +
494A CYS* 1.3 74.6 - - - +
496A ASP* 1.3 56.4 + - - +
498A GLY* 3.3 1.3 + - - +
499A CYS* 2.9 35.7 + - - -
506A PRO* 3.4 24.9 - - + -
509A THR* 3.7 19.4 + - + -
510A SER* 2.7 32.4 + - - -
513A LEU* 3.5 20.6 - - + -
529A LEU* 3.2 35.6 + - + +
532A TRP* 3.6 23.8 - + + -
533A GLU* 3.8 14.8 - - - -
536A PHE* 3.5 29.4 - + + -
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Residues in contact with ASP 496 (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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492A CYS 3.0 12.8 + - - +
493A GLU* 3.3 14.6 - - - +
495A TYR* 1.3 77.5 - - - +
497A ALA* 1.3 50.9 + - - +
499A CYS* 3.3 2.1 + - - -
500A ALA* 2.8 37.2 + - - +
536A PHE* 3.6 12.5 - - + -
557A PHE* 3.4 19.4 - - + -
558A PRO* 3.1 16.9 - - - +
559A TYR* 2.9 27.3 + - - +
560A LEU* 2.9 35.0 + - - +
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Residues in contact with ALA 497 (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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297A SER* 4.9 9.6 - - - +
298A THR* 5.8 3.6 - - - +
301A LEU* 4.8 3.1 - - + -
493A GLU 2.9 16.1 + - - +
494A CYS* 3.9 4.9 - - - +
496A ASP* 1.3 74.7 - - - +
498A GLY* 1.3 61.5 + - - +
500A ALA* 4.3 0.7 - - - +
501A TRP* 2.8 41.1 + - + +
502A TYR* 3.4 27.9 + - + -
558A PRO* 6.0 0.4 - - - -
7C U 6.2 0.7 - - + -
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Residues in contact with GLY 498 (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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301A LEU* 4.4 1.3 - - - +
494A CYS 2.8 15.8 + - - -
495A TYR 3.6 4.0 - - - -
497A ALA* 1.3 77.5 - - - +
499A CYS* 1.3 56.7 + - - +
502A TYR* 4.3 4.2 - - - -
503A GLU 3.2 12.1 + - - -
504A LEU* 2.9 51.9 + - - -
509A THR* 4.0 6.7 - - - -
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Residues in contact with CYS 499 (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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495A TYR 2.9 20.4 + - - +
496A ASP 3.8 1.6 - - - +
498A GLY* 1.3 74.7 - - - +
500A ALA* 1.3 63.2 + - - +
503A GLU* 4.8 6.2 + - - +
504A LEU 4.0 14.8 - - - +
506A PRO* 4.3 21.8 - - - -
536A PHE* 4.0 19.7 - - - -
547A LEU* 4.8 3.6 - - - +
559A TYR* 3.6 36.7 - - + -
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Residues in contact with ALA 500 (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 ASP 2.8 22.1 + - - +
499A CYS* 1.3 76.3 - - - +
501A TRP* 1.3 75.1 + - + +
547A LEU* 4.1 24.0 - - + +
551A LYS* 3.1 32.2 + - + +
558A PRO* 4.2 11.4 - - + -
559A TYR* 4.2 8.3 - - + -
8C U 4.5 0.5 - - - +
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Residues in contact with TRP 501 (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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275A ALA* 5.7 0.7 - - - -
497A ALA* 2.8 30.4 + - + +
500A ALA* 1.3 84.1 - - + +
502A TYR* 1.3 80.9 + - + +
503A GLU* 3.6 6.4 + - - +
551A LYS* 3.5 62.7 - - + +
552A GLN* 5.5 1.1 - - - -
558A PRO* 4.3 12.4 - - + +
7C U 3.2 79.4 + + + +
8C U 3.6 49.6 - + + +
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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