Contacts of the strand formed by residues 528 - 535 (chain F) in PDB entry 4OMC
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 528 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263F VAL* 3.8 28.9 - - + -
305F CYS* 4.6 4.9 - - - -
491F LEU* 3.9 13.2 - - + +
492F THR* 3.1 6.2 - - - +
493F LEU* 2.9 56.9 + - + +
498F ARG* 3.6 26.2 - - + -
501F LEU* 4.7 6.1 - - + -
503F ILE* 4.8 1.3 - - + -
516F LEU* 3.8 32.1 - - + -
519F ARG* 6.2 0.2 - - - -
522F ASP* 5.4 0.9 - - - -
526F ASP 4.7 1.6 - - - -
527F GLY* 1.3 77.3 - - - -
529F ASN* 1.3 60.3 + - - +
530F ASP 3.8 0.2 - - - -
531F TRP* 3.9 22.0 - + + -
533F PHE* 3.8 29.8 - + + -
604F FMT 3.6 5.4 - - - -
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Residues in contact with ASN 529 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268E ARG* 4.7 20.1 + - - +
492F THR* 4.3 11.8 + - - +
526F ASP 5.1 2.2 + - - +
528F PHE* 1.3 70.7 - - - +
530F ASP* 1.3 75.7 + - - +
531F TRP* 3.2 3.0 + - - -
604F FMT 3.0 23.1 + - - +
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Residues in contact with ASP 530 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E ASP* 4.6 6.1 - - - +
267E ALA* 5.2 3.3 - - - +
268E ARG* 3.8 28.3 + - - +
490F ARG* 2.9 49.9 + - - +
491F LEU 3.1 6.0 + - - -
492F THR* 2.8 24.0 + - - +
529F ASN* 1.3 77.5 - - - +
531F TRP* 1.3 61.6 + - - +
532F ALA 3.6 0.5 + - - -
565F LYS* 3.1 24.4 + - - +
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Residues in contact with TRP 531 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263F VAL* 3.7 29.1 - - + +
264F ASP* 3.5 28.3 - - - -
265F GLY* 4.5 2.5 - - - -
304F ASN 2.8 29.0 + - - -
305F CYS* 3.8 11.3 - - - +
306F ASP 4.2 0.2 - - - -
307F GLY* 3.8 19.1 - - - -
310F ASN* 4.2 10.2 - - - +
489F ALA 3.4 0.9 - - - +
490F ARG* 3.3 1.1 - - - -
491F LEU 2.9 26.7 + - - +
528F PHE* 3.9 27.6 - + + -
529F ASN 3.2 2.2 - - - -
530F ASP* 1.3 76.4 - - - +
532F ALA* 1.3 60.7 + - - +
533F PHE* 3.3 41.3 + + + -
604F FMT 4.0 11.9 - - - +
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Residues in contact with ALA 532 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310F ASN* 2.6 28.8 + - - +
488F GLN* 3.7 19.6 + - - +
489F ALA 3.9 4.0 - - - -
490F ARG* 3.4 40.4 - - + +
530F ASP 3.6 2.2 + - - -
531F TRP* 1.3 76.9 - - - +
533F PHE* 1.3 59.3 + - - +
534F MET* 3.3 3.6 + - - +
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Residues in contact with PHE 533 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304F ASN* 4.2 9.0 - - + +
305F CYS* 5.1 1.1 - - - -
310F ASN* 3.9 5.4 - - - +
487F ALA 3.9 0.2 - - - +
488F GLN* 3.1 4.7 - - - -
489F ALA* 2.9 43.1 + - - +
491F LEU* 3.7 30.3 - - + -
503F ILE* 4.5 6.3 - - + -
515F LEU* 3.3 51.2 - - + +
516F LEU* 4.0 15.9 - - + -
528F PHE* 3.8 34.8 - + - -
531F TRP* 3.6 37.7 - + + -
532F ALA* 1.3 71.2 - - - +
534F MET* 1.3 58.4 + - - +
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Residues in contact with MET 534 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304F ASN* 3.4 3.9 + - - +
310F ASN* 3.1 46.4 + - - +
311F SER 3.7 15.9 - - - +
312F ILE* 4.0 16.8 - - + -
314F THR 5.5 0.4 - - - +
334F SER* 2.7 22.6 + - - -
335F SER* 3.3 37.8 + - - +
486F HIS* 4.1 17.9 - - + -
487F ALA 3.4 11.0 - - - +
488F GLN* 4.2 7.2 - - + +
515F LEU* 4.7 1.3 - - - -
532F ALA 4.0 3.4 - - - +
533F PHE* 1.3 75.6 - - - +
535F THR* 1.3 87.7 + - - +
536F THR* 3.7 13.2 - - + -
608F NA 4.1 2.9 - - - -
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Residues in contact with THR 535 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334F SER* 3.3 17.6 - - - -
485F GLU 4.4 1.2 - - - +
486F HIS* 3.9 2.9 - - - -
487F ALA* 3.0 42.4 + - + +
505F LEU* 4.6 9.9 - - + -
513F SER* 2.7 35.1 + - - +
515F LEU* 4.4 7.9 - - + -
534F MET* 1.3 82.3 - - - +
536F THR* 1.3 61.5 + - - +
537F HIS* 3.0 11.9 + - - +
538F SER* 5.0 8.2 + - - +
547F TRP* 5.8 2.0 - - + -
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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