Contacts of the helix formed by residues 492 - 508 (chain B) in PDB entry 3OFN
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 SER 492 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484B GLU* 4.2 8.5 + - - -
488B LYS* 4.6 17.7 - - - +
490B GLU* 4.2 2.8 - - - +
491B LEU* 1.3 75.1 - - - +
493B LYS* 1.3 54.4 + - - +
494B GLU* 4.0 16.3 + - - +
495B LEU* 2.8 25.9 + - - +
496B LEU* 2.7 33.1 + - - +
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Residues in contact with LYS 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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491B LEU 3.9 1.3 + - - +
492B SER* 1.3 72.4 - - - +
494B GLU* 1.3 59.3 + - - +
496B LEU* 3.6 15.5 - - + +
497B ALA* 2.9 32.1 + - - +
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Residues in contact with GLU 494 (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* 4.1 15.7 - - - +
493B LYS* 1.3 81.8 + - - +
495B LEU* 1.3 56.1 + - - +
497B ALA* 4.3 3.4 - - - +
498B SER* 3.2 22.2 + - - -
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Residues in contact with LEU 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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481B LEU* 3.8 40.3 - - + +
484B GLU* 3.5 48.0 - - + +
485B ILE* 4.3 11.2 - - + +
488B LYS* 5.0 3.1 - - + -
490B GLU 4.4 6.1 - - - +
491B LEU* 3.8 27.8 - - + +
492B SER* 2.8 20.1 + - - +
494B GLU* 1.3 77.9 - - - +
496B LEU* 1.3 60.2 - - - +
497B ALA 3.5 0.2 - - - -
498B SER* 3.5 3.4 - - - -
499B LEU* 3.0 27.1 + - + +
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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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387B GLN* 5.4 6.1 - - + +
388B VAL* 4.8 4.0 - - + -
448B TYR* 3.7 26.9 + - + +
491B LEU* 3.7 39.7 - - + +
492B SER 2.7 17.2 + - - +
493B LYS* 3.4 16.8 + - + +
495B LEU* 1.3 71.3 - - - +
497B ALA* 1.3 60.0 + - - +
498B SER 3.2 0.2 - - - -
499B LEU* 3.5 6.0 + - + +
500B LYS* 2.9 27.4 + - - +
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Residues in contact with ALA 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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493B LYS 2.9 17.2 + - - +
494B GLU* 4.6 3.8 - - - +
496B LEU* 1.3 73.4 - - - +
498B SER* 1.3 58.9 + - - +
500B LYS* 3.4 16.4 - - + +
501B SER* 3.1 27.5 + - - -
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Residues in contact with SER 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B HIS* 5.3 4.3 + - - -
481B LEU* 3.2 28.5 - - - +
494B GLU 3.2 20.4 + - - -
495B LEU* 3.5 11.4 - - - -
496B LEU 3.2 0.2 - - - -
497B ALA* 1.3 76.3 - - - +
499B LEU* 1.3 63.0 + - - +
501B SER* 3.6 5.1 + - - -
502B ALA* 3.3 22.2 + - - +
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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
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444B VAL* 4.3 18.6 - - + -
445B PRO* 4.3 26.7 - - + -
448B TYR* 3.7 38.8 - - + -
470B PHE* 5.6 2.4 - - + -
474B LEU* 5.1 9.0 - - + -
481B LEU* 3.7 20.5 - - + +
482B LEU* 5.7 1.1 - - + -
485B ILE* 4.5 11.2 - - + -
491B LEU* 4.6 12.3 - - + -
495B LEU* 3.0 17.0 + - + +
496B LEU* 3.6 5.2 - - - +
498B SER* 1.3 72.6 - - - +
500B LYS* 1.3 59.9 + - - +
502B ALA* 3.1 5.3 + - + +
503B THR* 2.6 35.4 + - - +
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Residues in contact with LYS 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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448B TYR* 3.2 32.6 + - + +
454B HIS* 4.9 9.3 + - + +
496B LEU 2.9 13.6 + - - +
497B ALA* 3.4 16.4 - - + +
499B LEU* 1.3 73.5 - - - +
501B SER* 1.3 62.5 + - - +
503B THR* 3.0 12.5 + - - -
504B GLU* 3.2 40.9 + - - +
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Residues in contact with SER 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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478B HIS* 6.4 0.4 - - - -
497B ALA 3.1 13.9 + - - -
498B SER* 3.8 6.5 - - - -
499B LEU 3.3 0.2 - - - -
500B LYS* 1.3 77.2 - - - +
502B ALA* 1.3 59.0 + - - +
503B THR 3.0 0.5 + - - -
504B GLU* 3.2 14.5 + - - +
505B SER* 2.8 33.9 + - - -
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Residues in contact with ALA 502 (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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470B PHE* 3.7 4.1 - - + -
473B TYR* 3.6 7.6 - - - -
474B LEU* 4.1 12.1 - - + -
478B HIS* 3.5 40.1 - - + +
481B LEU* 4.9 1.3 - - + -
498B SER 3.3 10.8 + - - +
499B LEU* 3.1 11.5 + - + +
501B SER* 1.3 77.9 + - - +
503B THR* 1.3 57.3 + - - +
505B SER* 3.9 9.0 - - - -
506B PHE* 3.3 25.1 + - - +
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Residues in contact with THR 503 (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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445B PRO 5.5 0.5 + - - -
448B TYR* 3.8 12.5 - - + -
449B ALA* 4.1 21.1 - - + -
454B HIS* 3.8 35.9 - - + +
466B PHE* 5.4 1.6 - - + -
470B PHE* 4.1 19.6 - - + -
499B LEU* 2.6 26.8 + - - +
500B LYS* 3.3 7.1 + - - -
501B SER 3.0 0.6 + - - -
502B ALA* 1.3 75.5 - - - +
504B GLU* 1.3 60.0 + - - +
505B SER 3.2 1.1 - - - -
506B PHE* 3.2 4.3 + - - +
507B VAL* 2.9 33.2 + - + +
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Residues in contact with GLU 504 (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 HIS* 3.6 20.0 - - + +
500B LYS* 3.2 43.3 + - - +
501B SER* 3.8 13.9 + - - +
503B THR* 1.3 72.4 - - - +
505B SER* 1.3 64.1 + - - +
507B VAL* 3.6 10.3 - - - +
508B ALA* 3.1 24.4 + - - +
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Residues in contact with SER 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B TYR* 2.8 23.6 + - - -
478B HIS* 5.0 0.6 + - - -
501B SER* 2.8 21.2 + - - -
502B ALA* 3.8 8.3 - - - -
504B GLU* 1.3 78.8 - - - +
506B PHE* 1.3 58.6 + - - +
508B ALA* 3.7 10.5 + - - +
509B THR* 3.3 15.3 - - - +
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Residues in contact with PHE 506 (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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466B PHE* 3.5 39.9 - + - -
469B SER* 3.3 43.3 - - - -
470B PHE* 3.5 24.2 - + + -
473B TYR* 3.5 31.6 - + + -
502B ALA 3.3 14.4 + - - +
503B THR 3.2 4.6 + - - +
505B SER* 1.3 77.0 + - - +
507B VAL* 1.3 62.4 + - - +
509B THR* 2.8 41.4 + - + +
510B PHE* 4.1 15.3 - + - +
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Residues in contact with VAL 507 (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 HIS* 3.5 40.2 - - + +
458B ILE* 5.1 9.4 - - + +
466B PHE* 5.0 10.8 - - + -
503B THR* 2.9 27.8 + - + +
504B GLU* 3.3 9.4 + - - +
506B PHE* 1.3 74.0 - - - +
508B ALA* 1.3 58.0 + - - +
509B THR* 3.0 10.6 + - - -
510B PHE* 4.0 11.7 + - - +
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Residues in contact with ALA 508 (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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504B GLU 3.1 17.0 + - - +
505B SER* 3.8 8.1 - - - +
506B PHE 3.4 0.2 - - - -
507B VAL* 1.3 77.2 - - - +
509B THR* 1.3 57.5 + - - +
510B PHE 4.0 1.3 + - - -
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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
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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