Contacts of the helix formed by residues 494 - 512 (chain B) in PDB entry 5OC9
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 THR 494 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B THR* 4.0 39.5 - - + +
208B ILE* 4.7 6.1 - - + -
211B TYR* 4.3 13.2 - - + -
401B ILE* 6.0 1.6 - - - +
491B TYR* 3.5 22.2 - - + +
493B GLY* 1.3 70.1 - - - -
495B PHE* 1.4 64.8 + - - +
496B ASP 3.6 0.7 - - - -
497B ASP* 3.3 5.0 + - - +
498B TYR* 2.9 48.3 + - + -
555B TRP* 5.2 1.4 + - - -
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Residues in contact with PHE 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B ARG* 3.8 25.4 - - - +
397B GLN* 6.2 0.4 - - - +
401B ILE* 3.8 44.6 - - + +
404B VAL* 3.6 26.2 - - + -
405B LEU* 4.0 10.1 - - + -
408B ASN* 3.5 23.6 - - - -
493B GLY* 3.2 4.4 - - - +
494B THR* 1.4 77.6 + - - +
496B ASP* 1.4 62.6 + - - +
499B LEU* 2.9 47.7 + - + +
555B TRP* 3.5 34.8 - + - +
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Residues in contact with ASP 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B ARG* 2.9 41.2 + - - -
448B GLU* 5.4 1.1 - - - +
492B LEU* 4.6 15.9 - - - +
493B GLY 4.3 7.9 + - - +
494B THR 3.6 0.4 - - - -
495B PHE* 1.4 79.1 - - - +
497B ASP* 1.4 64.7 + - - +
499B LEU* 3.8 10.3 - - - +
500B GLU* 3.4 29.5 + - - +
536B LYS* 5.5 4.0 - - - +
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Residues in contact with ASP 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B TYR* 3.6 36.8 + - + -
491B TYR* 2.7 28.4 + - - +
493B GLY 3.6 7.8 - - - +
494B THR 3.5 6.7 - - - +
495B PHE 3.2 0.4 - - - -
496B ASP* 1.4 75.2 - - - +
498B TYR* 1.4 62.5 + - - +
500B GLU* 3.4 17.4 - - - +
501B LEU* 3.8 5.5 - - - +
533B ASP* 3.1 10.9 - - - +
536B LYS* 2.8 31.8 + - - +
702B CA 2.9 19.4 - - - -
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Residues in contact with TYR 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B THR* 4.4 3.2 + - + -
210B LEU* 3.6 5.5 - - - +
211B TYR* 3.3 41.8 + + + -
214B PHE* 3.9 29.8 - + + -
494B THR* 2.9 49.0 + - + +
497B ASP* 1.4 73.2 - - - +
499B LEU* 1.4 54.7 + - - +
501B LEU* 3.1 8.8 + - + +
502B PHE* 2.8 32.1 + - - +
552B ILE* 3.3 38.2 - - + +
555B TRP* 3.5 46.2 - + + -
559B PHE* 4.5 3.6 - + - -
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Residues in contact with LEU 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B ARG* 5.5 0.7 - - - +
405B LEU* 3.8 26.9 - - + -
408B ASN* 3.5 37.9 - - + +
495B PHE* 2.9 28.9 + - + +
496B ASP* 3.8 11.4 - - - +
497B ASP 3.4 0.2 - - - -
498B TYR* 1.4 74.3 - - - +
500B GLU* 1.4 53.3 + - - +
502B PHE* 3.1 4.2 + - + +
503B LEU* 2.9 67.1 + - + +
555B TRP* 3.7 10.0 - - + -
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Residues in contact with GLU 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B GLN* 5.2 3.1 - - - +
444B ASN* 3.1 28.2 + - - +
448B GLU* 2.9 26.9 - - - +
496B ASP* 3.4 14.1 + - - +
497B ASP 3.4 9.0 - - - +
498B TYR 3.2 0.2 - - - -
499B LEU* 1.4 77.7 - - + +
501B LEU* 1.4 61.9 + - + +
503B LEU* 3.6 9.3 + - + +
504B GLN* 3.0 33.3 + - - +
525B ASN* 4.5 4.9 + - - +
529B GLU* 3.0 15.9 - - - +
701B CA 2.6 18.9 - - - -
702B CA 3.1 3.1 - - - -
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Residues in contact with LEU 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B TYR* 3.7 26.7 - - + +
214B PHE* 3.9 23.8 - - + -
215B LEU* 3.7 28.3 - - + -
218B PHE* 3.3 27.5 - - + -
497B ASP 3.8 10.8 - - - +
498B TYR* 3.1 8.4 + - - +
500B GLU* 1.4 76.7 - - + +
502B PHE* 1.4 59.2 + - - +
504B GLN* 3.9 10.5 - - - +
505B PHE* 2.9 24.6 + - - +
526B ASN* 3.5 24.5 - - - +
529B GLU* 5.1 3.6 - - + -
559B PHE* 3.8 9.0 - - + -
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Residues in contact with PHE 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B LEU* 3.7 23.6 - - + -
409B PHE* 4.1 15.9 - + + -
498B TYR 2.8 13.6 + - - +
499B LEU* 3.1 13.2 + - + +
501B LEU* 1.4 75.5 - - - +
503B LEU* 1.4 65.6 + - + +
505B PHE* 3.3 4.9 + + - +
506B GLY* 2.9 23.4 + - - -
555B TRP* 3.7 15.0 - + + -
558B ALA* 3.3 36.1 - - + -
559B PHE* 3.6 30.7 - + + -
562B MET* 3.5 33.2 - - + +
712B 79M 3.7 22.2 - - + -
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Residues in contact with LEU 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ASN* 4.7 6.1 - - + +
409B PHE* 4.7 3.6 - - - -
412B CYS* 3.7 20.2 - - + -
413B PHE* 3.6 25.9 - - + -
499B LEU* 2.9 49.7 + - + +
500B GLU* 3.9 7.9 - - - +
502B PHE* 1.4 78.5 - - + +
504B GLN* 1.4 64.3 + - - +
506B GLY* 3.1 2.5 + - - +
507B TYR* 3.0 50.1 + - + +
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Residues in contact with GLN 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B PHE* 3.6 12.5 - - + -
437B LEU* 5.2 2.0 - - + -
441B GLN* 2.9 29.7 + - - +
500B GLU* 3.0 20.5 + - - +
501B LEU* 3.4 13.9 - - - +
503B LEU* 1.4 74.7 - - - +
505B PHE* 1.4 61.5 + - - +
506B GLY 3.2 0.7 + - - -
507B TYR* 3.2 16.9 + - + +
508B VAL* 3.1 30.4 + - - +
522B ALA* 3.7 26.2 + - + +
525B ASN* 3.1 9.7 - - - +
526B ASN* 2.8 43.0 + - - +
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Residues in contact with PHE 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B PHE* 3.5 26.4 - + + -
253B TRP* 3.8 28.7 - + - -
254B SER* 4.0 17.0 - - - -
257B ILE* 3.8 15.0 - - + -
258B LEU* 4.0 17.5 - - + -
501B LEU 2.9 17.6 + - - +
502B PHE* 3.5 5.4 - + - +
504B GLN* 1.4 73.8 - - - +
506B GLY* 1.3 53.2 + - - +
508B VAL* 4.6 4.3 - - - -
509B SER* 2.7 42.3 + - - -
559B PHE* 3.2 46.4 - + + -
562B MET* 3.7 21.5 - - + -
563B SER* 4.1 7.0 - - - -
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Residues in contact with GLY 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B PHE* 3.6 18.6 - - - -
502B PHE 2.9 9.6 + - - -
503B LEU 3.1 5.7 + - - -
505B PHE* 1.3 76.6 - - - +
507B TYR* 1.4 57.9 - - - +
510B LEU* 3.1 34.5 + - - +
562B MET* 3.7 23.3 - - - +
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Residues in contact with TYR 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B CYS* 3.4 22.8 - - - -
413B PHE* 3.7 23.6 - + - -
416B LEU* 4.0 3.4 - - + -
433B LEU* 3.8 28.9 - - + +
436B LEU* 3.5 43.7 + - + +
437B LEU* 3.8 34.5 - - + -
441B GLN* 6.2 2.0 - - - -
503B LEU* 3.0 35.7 + - + +
504B GLN* 3.2 9.4 + - + +
506B GLY* 1.4 73.9 - - - +
508B VAL* 1.4 61.7 + - - +
511B PHE* 3.3 29.4 + - - +
518B ALA* 4.0 6.0 - - + +
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Residues in contact with VAL 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LEU* 3.8 17.9 - - + -
225B MET* 3.9 16.6 - - + -
250B ASN* 3.6 1.4 + - - -
253B TRP* 3.7 25.4 - - + -
437B LEU* 5.6 0.9 - - + -
504B GLN 3.1 18.2 + - - +
505B PHE* 4.1 3.6 - - - +
507B TYR* 1.4 75.5 - - + +
509B SER* 1.3 65.6 + - - +
510B LEU 3.4 0.3 + - - -
512B SER* 2.7 33.0 + - - +
518B ALA* 3.8 10.5 - - + +
519B ALA* 3.7 34.3 - - + +
522B ALA* 4.2 4.3 - - + -
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Residues in contact with SER 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ASN* 3.1 17.3 + - - +
253B TRP* 4.3 7.6 - - - -
254B SER* 3.7 21.8 - - - -
505B PHE* 2.7 34.3 + - - -
508B VAL* 1.3 73.7 - - - +
510B LEU* 1.3 71.8 + - - +
562B MET* 3.9 9.1 + - - +
563B SER* 5.2 0.2 - - - -
566B SER* 3.4 13.2 - - - -
570B ASN* 3.0 25.1 + - - -
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Residues in contact with LEU 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B PHE* 5.4 0.2 - - + -
413B PHE* 3.9 9.9 - - + -
417B PHE* 3.7 33.4 - - + -
506B GLY 3.1 14.8 + - - +
509B SER* 1.3 95.9 + - - +
511B PHE* 1.3 78.1 + - + +
512B SER 3.6 3.3 + - - -
562B MET* 3.6 36.1 - - - +
565B ILE* 4.2 3.1 - - + -
566B SER* 3.7 11.9 - - - +
569B THR* 3.5 33.8 - - + +
570B ASN* 3.8 13.5 + - - +
573B LEU* 3.9 5.9 - - - +
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Residues in contact with PHE 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B PHE* 4.1 13.9 - + - -
416B LEU* 4.1 27.1 - - + -
417B PHE* 4.5 11.7 - + - -
420B ALA* 4.0 21.3 - - + -
421B PHE* 4.3 4.0 - + - -
429B LEU* 3.8 16.4 - - + -
433B LEU* 3.8 33.7 - - + -
507B TYR* 3.3 19.4 + - - +
510B LEU* 1.3 100.4 - - + +
512B SER* 1.3 57.7 + - - +
513B CYS 3.3 3.4 - - - +
514B VAL* 3.5 6.2 + - + +
515B TYR* 3.0 28.1 + - - +
569B THR* 3.9 15.3 - - + -
573B LEU* 4.1 16.8 - - + -
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Residues in contact with SER 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B MET* 3.4 12.5 - - - +
246B PHE* 3.3 32.1 - - - -
250B ASN* 3.7 17.0 - - - +
507B TYR 4.7 0.2 - - - -
508B VAL* 2.7 30.7 + - - +
510B LEU 3.6 3.0 + - - -
511B PHE* 1.3 75.2 - - - +
513B CYS* 1.3 63.9 + - - +
514B VAL 3.3 0.2 - - - -
515B TYR 3.5 6.3 + - - -
516B PRO* 3.3 20.4 + - - +
518B ALA* 4.2 6.4 - - - +
519B ALA* 5.0 2.3 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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