Contacts of the helix formed by residues 513 - 525 (chain A) in PDB entry 1OY6
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 PHE 513 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356A TYR 6.2 0.2 - - - -
360A GLN* 4.7 21.6 + - + -
514A GLY* 1.3 63.9 - - - +
515A TRP* 3.2 58.6 + + + +
516A PHE* 3.4 39.2 + + - +
517A ASN* 3.6 13.5 + - - -
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Residues in contact with GLY 514 (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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513A PHE* 1.3 75.5 - - - +
515A TRP* 1.3 60.4 + - - +
516A PHE 3.3 0.2 - - - -
517A ASN* 3.6 16.1 - - - +
518A ARG* 3.0 45.5 + - - +
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Residues in contact with TRP 515 (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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356A TYR 5.8 0.7 - - - -
357A LEU* 4.3 44.9 - - + +
513A PHE* 3.2 54.0 - + + +
514A GLY* 1.3 76.7 - - - +
516A PHE* 1.3 66.6 + + + +
518A ARG* 3.2 34.9 + - - +
519A MET* 2.8 30.0 + - - +
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Residues in contact with PHE 516 (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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357A LEU 4.2 15.3 - - - -
358A PHE* 4.0 22.4 - - - -
360A GLN* 4.1 33.0 - - + -
513A PHE* 3.6 46.9 - + - +
514A GLY 3.3 0.4 - - - -
515A TRP* 1.3 79.5 - + + +
517A ASN* 1.3 60.4 + - - +
519A MET* 3.2 3.8 + - - -
520A PHE* 2.9 61.5 + + + +
973A ARG* 5.5 3.8 - - - -
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Residues in contact with ASN 517 (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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513A PHE 3.6 16.9 + - - -
514A GLY* 3.6 15.7 + - - +
515A TRP 3.3 0.2 - - - -
516A PHE* 1.3 78.5 - - - +
518A ARG* 1.3 56.2 + - + +
520A PHE* 4.2 2.9 - - - +
521A GLU* 3.0 31.7 + - - +
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Residues in contact with ARG 518 (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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514A GLY* 3.0 30.8 + - - +
515A TRP* 3.2 27.8 + - - +
516A PHE 3.1 0.6 - - - -
517A ASN* 1.3 76.2 - - + +
519A MET* 1.3 59.7 + - - +
521A GLU* 4.1 9.2 - - - +
522A LYS* 3.0 55.7 + - + +
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Residues in contact with MET 519 (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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358A PHE* 5.2 17.3 - - + -
515A TRP 2.8 20.8 + - - +
516A PHE* 3.8 6.5 - - - +
518A ARG* 1.3 72.8 - - - +
520A PHE* 1.3 86.9 + - + +
521A GLU 3.2 0.2 + - - -
522A LYS* 4.2 1.6 - - - +
523A SER* 2.8 49.4 + - - +
972A LEU* 4.2 17.3 - - - -
973A ARG* 4.7 24.0 - - + +
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Residues in contact with PHE 520 (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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516A PHE* 2.9 53.3 + + + +
517A ASN* 4.7 2.2 - - - +
519A MET* 1.3 93.7 - - + +
521A GLU* 1.3 66.0 - - - +
523A SER* 4.2 3.8 - - - -
524A THR* 3.4 26.7 + - - -
973A ARG* 5.8 8.1 - - - -
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Residues in contact with GLU 521 (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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517A ASN 3.0 24.4 + - - +
518A ARG* 3.6 11.5 - - - +
519A MET 3.1 1.0 - - - -
520A PHE* 1.3 76.4 - - - +
522A LYS* 1.3 72.0 + - - +
524A THR* 4.0 0.2 - - - -
525A HIS* 2.6 62.6 + - + +
526A HIS* 3.3 22.0 + - + -
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Residues in contact with LYS 522 (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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518A ARG* 3.0 42.9 + - + +
519A MET* 4.2 2.2 - - - +
521A GLU* 1.3 94.0 + - - +
523A SER* 1.3 64.0 + - - +
525A HIS 2.9 18.9 - - - +
526A HIS* 3.8 34.3 - - + -
527A TYR* 2.9 15.1 + - + +
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Residues in contact with SER 523 (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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519A MET* 2.8 43.9 + - - +
520A PHE* 4.2 4.7 - - - -
522A LYS* 1.3 72.6 - - - +
524A THR* 1.3 54.3 + - - +
527A TYR* 3.7 10.1 - - - -
528A THR* 2.2 40.1 + - - -
968A VAL 4.9 0.5 + - - -
969A ARG 4.7 9.9 + - - -
972A LEU* 4.2 22.6 - - - +
973A ARG 5.6 0.2 + - - -
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Residues in contact with THR 524 (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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520A PHE* 3.4 19.2 + - - +
521A GLU 3.1 2.2 + - - -
523A SER* 1.3 77.4 + - - +
525A HIS* 1.3 73.9 + - + +
528A THR* 3.6 12.9 - - - -
529A ASP* 2.9 18.1 - - - +
969A ARG* 5.0 20.4 + - + +
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Residues in contact with HIS 525 (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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521A GLU* 2.6 43.7 + - + +
522A LYS 2.9 2.5 - - - +
524A THR* 1.3 84.0 - - + +
526A HIS* 1.3 70.7 + - + +
527A TYR 2.4 21.7 + - - -
528A THR 2.8 14.7 + - - -
529A ASP* 3.2 21.5 + - - +
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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