Contacts of the helix formed by residues 494 - 512 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A THR* 3.9 39.7 - - + +
208A ILE* 4.7 5.8 - - + -
211A TYR* 4.3 13.0 - - + -
401A ILE* 6.0 1.6 - - - +
491A TYR* 3.5 22.7 - - + +
493A GLY* 1.3 69.0 - - - -
495A PHE* 1.4 63.7 + - - +
496A ASP 3.6 0.4 - - - -
497A ASP* 3.3 5.4 + - - +
498A TYR* 2.9 47.5 + - + -
555A TRP* 5.2 1.4 + - - -
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Residues in contact with PHE 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ARG* 3.8 24.7 - - - +
397A GLN* 6.2 0.2 - - - +
401A ILE* 3.8 44.4 - - + +
404A VAL* 3.6 20.6 - - + -
405A LEU* 4.0 9.9 - - + -
408A ASN* 3.4 30.1 - - - -
493A GLY* 3.2 4.6 - - - +
494A THR* 1.4 76.9 + - - +
496A ASP* 1.4 64.3 + - - +
498A TYR 3.3 0.2 + - - -
499A LEU* 2.9 47.0 + - + +
555A TRP* 3.5 34.2 - + - +
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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
----------------------------------------------------------
378A ARG* 2.9 41.4 + - - -
448A GLU* 5.6 0.7 - - - +
492A LEU* 4.6 15.9 - - - +
493A GLY 4.3 8.5 + - - +
494A THR 3.6 0.2 - - - -
495A PHE* 1.4 79.4 - - - +
497A ASP* 1.3 64.7 + - - +
499A LEU* 3.8 10.2 + - - +
500A GLU* 3.4 29.4 + - - +
536A LYS* 5.5 3.8 - - - +
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Residues in contact with ASP 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A TYR* 3.4 35.7 + - + -
491A TYR* 2.7 29.3 + - - +
493A GLY 3.6 6.8 - - - +
494A THR* 3.5 7.4 - - - +
495A PHE 3.2 0.4 - - - -
496A ASP* 1.3 75.7 - - - +
498A TYR* 1.4 62.5 + - - +
500A GLU* 3.4 17.5 - - - +
501A LEU* 3.8 4.5 - - - +
533A ASP* 3.3 9.2 - - - +
536A LYS* 2.8 28.3 + - - -
702A CA 2.7 24.4 - - - -
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Residues in contact with TYR 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A THR* 4.4 3.6 + - + +
210A LEU* 3.6 5.4 - - - +
211A TYR* 3.3 44.2 + + + -
214A PHE* 3.9 27.8 - + + -
494A THR* 2.9 48.6 + - + +
497A ASP* 1.4 72.1 - - - +
499A LEU* 1.4 55.6 + - - +
501A LEU* 3.1 8.2 + - + +
502A PHE* 2.8 31.9 + - - +
552A ILE* 3.3 38.5 - - + +
555A TRP* 3.5 47.1 - + + -
559A PHE* 4.5 3.8 - + - -
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Residues in contact with LEU 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ARG* 5.5 0.9 - - - +
405A LEU* 3.9 26.0 - - + -
408A ASN* 3.4 40.4 - - + +
495A PHE* 2.9 27.6 + - + +
496A ASP* 3.8 11.7 - - + +
497A ASP 3.4 0.2 - - - -
498A TYR* 1.4 74.9 - - - +
500A GLU* 1.4 53.5 + - - +
502A PHE* 3.5 4.1 - - + +
503A LEU* 2.8 65.7 + - + +
555A TRP* 3.7 11.5 - - + -
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Residues in contact with GLU 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A GLN* 5.2 2.8 - - - +
444A ASN* 3.1 20.0 + - - +
448A GLU* 3.0 30.1 - - - +
496A ASP* 3.4 15.9 + - - +
497A ASP 3.4 9.2 - - - +
498A TYR 3.2 0.2 - - - -
499A LEU* 1.4 77.6 - - + +
501A LEU* 1.3 60.5 + - + +
503A LEU* 3.6 9.3 + - + +
504A GLN* 3.0 34.3 + - - +
525A ASN* 4.5 5.0 + - - -
529A GLU* 3.0 14.5 - - - +
701A CA 2.3 24.6 - - - -
702A CA 3.0 3.9 - - - -
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Residues in contact with LEU 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A TYR* 3.8 26.9 - - + +
214A PHE* 3.9 23.1 - - + -
215A LEU* 3.7 27.6 - - + -
218A PHE* 3.3 25.0 - - + -
497A ASP 3.8 10.1 - - - +
498A TYR* 3.1 8.6 + - - +
500A GLU* 1.3 78.4 - - + +
502A PHE* 1.4 60.1 + - - +
504A GLN* 3.4 11.6 - - - +
505A PHE* 2.9 24.9 + - - +
526A ASN* 3.5 26.5 - - - +
529A GLU* 5.1 3.4 - - + -
559A PHE* 3.9 8.7 - - + -
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Residues in contact with PHE 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A LEU* 3.7 24.0 - - + -
409A PHE* 4.1 16.2 - + + -
498A TYR 2.8 12.7 + - - +
499A LEU* 3.1 14.3 + - + +
501A LEU* 1.4 75.9 - - - +
503A LEU* 1.4 64.2 + - + +
505A PHE* 3.3 5.4 + + - +
506A GLY* 2.9 23.7 + - - -
555A TRP* 3.7 15.7 - + + -
558A ALA* 3.3 34.3 - - + -
559A PHE* 3.6 30.9 - + + -
562A MET* 3.5 33.7 - - + +
711A 79M 3.7 22.0 - - + -
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Residues in contact with LEU 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ASN* 4.6 5.8 - - + +
409A PHE* 4.7 3.6 - - - -
412A CYS* 3.8 22.4 - - + -
413A PHE* 3.7 27.2 - - + -
499A LEU* 2.8 50.4 + - + +
500A GLU* 3.9 6.7 - - + +
502A PHE* 1.4 77.3 - - + +
504A GLN* 1.4 59.4 + - - +
506A GLY* 3.1 2.3 + - - +
507A TYR* 3.0 54.5 + - + +
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Residues in contact with GLN 504 (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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218A PHE* 3.6 12.0 - - + -
437A LEU* 5.2 2.0 - - + -
441A GLN* 2.9 30.9 + - - +
500A GLU* 3.0 21.2 + - - +
501A LEU* 3.4 15.1 - - - +
502A PHE 3.3 0.2 - - - -
503A LEU* 1.4 75.2 - - - +
505A PHE* 1.4 60.8 + - - +
507A TYR* 3.2 16.4 + - + +
508A VAL* 3.1 30.2 + - - +
522A ALA* 3.7 25.7 + - + +
525A ASN* 3.1 10.1 - - - +
526A ASN* 2.8 42.8 + - - +
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Residues in contact with PHE 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A PHE* 3.5 25.7 - + + -
253A TRP* 3.8 28.5 - + - -
254A SER* 4.0 17.0 - - - -
257A ILE* 3.8 15.9 - - + -
258A LEU* 3.9 17.9 - - + -
501A LEU 2.9 17.0 + - - +
502A PHE* 3.5 5.6 - + - +
504A GLN* 1.4 74.4 - - - +
506A GLY* 1.3 51.7 + - - +
508A VAL* 4.6 3.6 - - - -
509A SER* 2.7 42.4 + - - -
559A PHE* 3.2 46.9 - + + -
562A MET* 3.7 21.1 - - + -
563A SER* 4.1 7.0 - - - -
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Residues in contact with GLY 506 (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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413A PHE* 3.5 19.7 - - - -
502A PHE 2.9 9.1 + - - -
503A LEU 3.1 6.8 + - - -
505A PHE* 1.3 75.8 - - - +
507A TYR* 1.4 56.6 + - - +
510A LEU* 3.0 35.9 + - - +
562A MET* 3.7 23.1 - - - +
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Residues in contact with TYR 507 (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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412A CYS* 3.3 23.3 - - - -
413A PHE* 3.7 22.7 - + - -
416A LEU* 4.0 3.4 - - + -
433A LEU* 3.8 29.1 - - + +
436A LEU* 3.5 44.0 + - + +
437A LEU* 3.7 35.0 - - + -
441A GLN* 6.2 1.6 - - + -
503A LEU* 3.0 36.7 + - + +
504A GLN* 3.2 10.7 + - + +
506A GLY* 1.4 74.5 - - - +
508A VAL* 1.4 58.2 + - + +
511A PHE* 3.3 31.5 + - - +
518A ALA* 4.0 6.8 - - + +
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Residues in contact with VAL 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LEU* 3.8 18.8 - - + -
225A MET* 3.8 17.5 - - + -
250A ASN* 3.6 1.4 + - - -
253A TRP* 3.7 23.8 - - + -
437A LEU* 5.6 0.4 - - + -
504A GLN 3.1 18.5 + - - +
505A PHE* 4.1 3.4 - - - +
507A TYR* 1.4 74.8 - - + +
509A SER* 1.3 65.0 + - - +
512A SER* 2.7 35.9 + - - +
518A ALA* 3.8 10.3 - - + +
519A ALA* 3.7 34.8 - - + +
522A ALA* 4.2 4.5 - - + -
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Residues in contact with SER 509 (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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250A ASN* 3.3 15.8 + - - +
253A TRP* 4.5 6.5 - - - -
254A SER* 3.8 18.6 - - - -
505A PHE* 2.7 33.3 + - - -
508A VAL* 1.3 73.9 - - - +
510A LEU* 1.3 70.7 + - - +
562A MET* 3.8 9.9 + - - +
563A SER* 5.2 0.4 - - - -
566A SER* 3.4 17.4 - - - -
570A ASN* 3.0 25.5 + - - -
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Residues in contact with LEU 510 (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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409A PHE* 5.3 0.7 - - + -
413A PHE* 3.8 25.4 - - + -
417A PHE* 3.6 28.0 - - + -
506A GLY 3.0 15.2 + - - +
509A SER* 1.3 85.4 + - - +
511A PHE* 1.3 72.8 + - + +
512A SER 3.7 1.5 + - - -
562A MET* 3.7 28.0 - - - +
565A ILE* 4.0 4.0 - - + -
566A SER* 3.7 26.2 - - - +
569A THR* 3.3 36.4 - - + +
570A ASN* 4.0 8.0 - - - +
573A LEU* 3.8 7.6 - - - +
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Residues in contact with PHE 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A PHE* 4.1 4.7 - + - -
416A LEU* 3.9 38.8 - - + -
417A PHE* 4.5 9.2 - + - -
420A ALA* 4.0 20.2 - - + -
421A PHE* 4.3 4.0 - + - -
429A LEU* 3.8 15.9 - - + -
433A LEU* 3.8 33.9 - - + -
507A TYR* 3.3 18.6 + - - +
510A LEU* 1.3 103.6 - - + +
512A SER* 1.3 57.6 + - - +
513A CYS 3.3 2.9 - - - +
514A VAL* 3.9 7.6 - - + +
515A TYR* 3.0 27.9 + - - +
569A THR* 4.0 14.1 - - + -
573A LEU* 4.1 15.9 - - + -
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Residues in contact with SER 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A MET* 3.4 12.2 - - - +
246A PHE* 3.3 26.3 - - - -
250A ASN* 3.7 16.0 - - - +
507A TYR 4.7 0.7 - - - -
508A VAL* 2.7 31.5 + - - +
510A LEU 3.7 2.6 + - - -
511A PHE* 1.3 75.6 - - - +
513A CYS* 1.3 64.5 + - - +
515A TYR 3.6 6.8 + - - -
516A PRO* 3.3 27.1 + - - +
518A ALA* 4.2 6.8 - - - +
519A ALA* 5.0 2.1 + - - +
570A ASN* 5.1 0.2 + - - -
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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
------------------------------------------------------------
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