Contacts of the helix formed by residues 490 - 501 (chain B) in PDB entry 1YOJ
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 PRO 490 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362B LEU* 3.6 30.5 - - + -
485B CYS* 4.2 0.3 - - - -
488B GLU 3.6 7.1 - - - +
489B CYS* 1.3 91.4 - - - +
491B GLU* 1.3 65.7 + - - +
492B SER* 3.8 0.4 - - - +
493B LEU* 3.0 14.9 + - + +
494B HIS 3.2 8.0 + - - -
521B TYR* 3.2 26.0 - - - +
526B GLU* 3.8 22.4 - - + +
529B TYR* 5.4 5.2 - - + -
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Residues in contact with GLU 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485B CYS* 3.6 28.2 - - - +
489B CYS 3.4 2.8 + - - +
490B PRO* 1.3 70.8 - - - +
492B SER* 1.3 51.0 + - - +
494B HIS* 3.0 16.2 + - - +
495B ASP* 2.6 48.2 + - - +
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Residues in contact with SER 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490B PRO* 3.8 0.4 - - - +
491B GLU* 1.3 78.3 - - - +
493B LEU* 1.3 57.5 + - - +
495B ASP* 3.5 13.3 + - - +
496B LEU 3.2 17.2 + - - -
499B GLN* 5.7 0.2 + - - -
517B PHE* 3.8 15.5 - - - -
521B TYR* 2.9 17.5 + - - -
525B THR* 3.6 21.6 - - - +
526B GLU* 2.4 30.7 + - - -
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Residues in contact with LEU 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B LEU* 3.9 20.0 - - + -
366B VAL* 4.1 12.1 - - + -
454B LEU* 4.5 11.7 - - + -
458B THR* 3.8 26.5 - - + -
489B CYS* 3.7 9.9 - - - -
490B PRO* 3.0 9.9 + - + +
492B SER* 1.3 80.2 + - - +
494B HIS* 1.3 63.7 + - - +
496B LEU* 3.1 23.6 + - + +
497B MET* 3.1 22.9 + - + +
517B PHE* 4.5 0.7 - - + -
518B LEU* 3.8 27.6 - - + -
521B TYR* 3.7 22.0 + - + +
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Residues in contact with HIS 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ARG* 6.2 0.2 - - + -
483B MET 2.8 25.7 + - - -
484B PRO* 3.4 8.1 - - + -
485B CYS* 3.6 47.4 - - + +
489B CYS* 4.3 1.2 - - - -
490B PRO 3.2 4.9 + - - -
491B GLU* 3.0 20.8 + - - +
493B LEU* 1.3 76.8 - - - +
495B ASP* 1.3 67.5 + - - +
497B MET* 3.5 24.2 + - + +
498B CYS* 3.1 44.7 + - - -
501B TRP* 4.4 2.1 - + - -
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Residues in contact with ASP 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491B GLU* 2.6 36.6 + - - +
492B SER* 3.6 11.8 - - - +
493B LEU 3.1 0.2 - - - -
494B HIS* 1.3 78.7 + - - +
496B LEU* 1.3 61.3 + - - +
498B CYS* 3.3 9.8 + - - +
499B GLN* 3.1 35.8 + - - +
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Residues in contact with LEU 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B LEU* 3.9 20.2 - - + -
492B SER 3.2 12.1 + - - +
493B LEU* 3.1 12.6 + - + +
495B ASP* 1.3 73.4 - - - +
497B MET* 1.3 65.6 + - - +
499B GLN* 3.2 29.1 + - - +
500B CYS* 3.1 23.9 + - - -
509B PRO* 5.2 0.4 - - + -
513B TYR* 4.6 5.6 - - + -
514B LEU* 3.6 31.6 - - + -
517B PHE* 3.7 46.7 - - + -
518B LEU* 4.0 18.6 - - + -
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Residues in contact with MET 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451B GLY* 3.9 15.3 - - - +
454B LEU* 4.0 24.7 - - + +
455B THR* 3.8 20.0 - - - +
458B THR* 3.8 22.4 - - + +
484B PRO 5.5 0.2 - - - +
486B PRO* 4.2 7.2 - - + -
489B CYS* 3.9 22.7 - - - -
493B LEU* 3.1 19.7 + - + +
494B HIS* 3.6 25.6 - - + +
496B LEU* 1.3 75.0 - - - +
498B CYS* 1.3 57.7 + - - +
500B CYS* 2.9 26.6 + - - +
501B TRP* 3.0 34.2 + - + -
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Residues in contact with CYS 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482B ARG* 5.2 9.1 - - + +
483B MET 5.2 0.4 - - - -
494B HIS* 3.1 45.1 + - - -
495B ASP* 3.5 13.7 - - - +
496B LEU 3.3 0.2 - - - -
497B MET* 1.3 78.5 - - - +
499B GLN* 1.3 61.0 + - + +
501B TRP* 3.1 25.6 + - - +
502B ARG* 3.2 14.4 + - - +
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Residues in contact with GLN 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492B SER 5.7 0.2 + - - -
495B ASP* 3.1 24.4 + - - +
496B LEU* 3.2 24.3 + - - +
498B CYS* 1.3 73.5 - - - +
500B CYS* 1.3 63.1 + - - +
501B TRP 3.3 0.5 + - - -
502B ARG* 3.4 55.2 + - - +
508B ARG* 3.5 4.5 - - - +
509B PRO* 3.3 23.0 - - + +
513B TYR* 3.7 27.5 + - - -
517B PHE* 5.7 4.6 - - - -
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Residues in contact with CYS 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447B VAL* 3.6 37.0 - - - +
448B TRP* 3.4 12.6 - - - -
450B PHE* 4.4 3.1 - - - -
451B GLY* 3.7 21.5 - - - -
454B LEU* 4.8 1.8 - - - -
496B LEU 3.1 18.5 + - - -
497B MET* 2.9 12.6 + - - +
499B GLN* 1.3 77.1 - - - +
501B TRP* 1.3 57.6 + - + +
502B ARG 3.4 0.2 - - - -
508B ARG* 3.1 21.8 + - - -
509B PRO* 4.2 1.8 - - - -
514B LEU* 3.8 29.4 - - - -
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Residues in contact with TRP 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B TRP* 3.3 38.7 + + + -
451B GLY 3.4 22.6 - - - -
452B ILE* 3.3 37.1 - - + +
455B THR* 3.7 21.3 - - + -
465B TYR* 5.7 1.1 - - - -
482B ARG* 2.9 58.8 + - + +
483B MET* 3.8 36.8 - - + -
484B PRO 5.8 0.2 - - - -
494B HIS* 4.4 5.2 - + - -
497B MET* 3.0 38.2 + - + +
498B CYS* 3.1 13.0 + - - +
499B GLN 3.1 0.6 - - - -
500B CYS* 1.3 82.3 - - + +
502B ARG* 1.3 59.8 + - - +
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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