Contacts of the strand formed by residues 528 - 535 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263C VAL* 3.9 27.4 - - + -
305C CYS* 4.6 4.7 - - - -
491C LEU 3.9 13.2 - - - +
492C THR* 3.2 6.1 - - - +
493C LEU* 2.9 56.8 + - + +
498C ARG* 3.7 27.8 - - + -
501C LEU* 4.7 6.3 - - + -
503C ILE* 4.7 1.6 - - + -
516C LEU* 3.8 30.3 - - + -
522C ASP* 5.3 0.7 - - - -
526C ASP 4.8 1.6 - - - -
527C GLY* 1.3 76.8 - - - -
529C ASN* 1.3 60.0 + - - +
530C ASP 3.8 0.4 - - - -
531C TRP* 3.8 22.9 - + + -
533C PHE* 3.7 27.6 - + + -
602C FMT 3.8 5.2 - - - -
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Residues in contact with ASN 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492C THR* 4.3 12.3 - - + +
526C ASP 5.7 2.0 - - - +
528C PHE* 1.3 70.9 - - - +
530C ASP* 1.3 76.1 + - - +
531C TRP* 3.2 2.6 + - - -
602C FMT 3.0 23.0 + - - +
268D ARG* 4.8 19.6 + - - +
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Residues in contact with ASP 530 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490C ARG* 2.9 47.8 + - - +
491C LEU 3.1 6.2 + - - -
492C THR* 2.9 25.0 + - - +
529C ASN* 1.3 78.2 + - - +
531C TRP* 1.3 62.5 + - - +
532C ALA 3.6 0.5 + - - -
565C LYS* 3.0 25.8 + - - +
233D ASP* 4.4 7.7 - - - +
267D ALA* 5.2 2.6 - - - +
268D ARG* 3.7 27.7 + - - +
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Residues in contact with TRP 531 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C VAL* 3.7 27.8 - - + -
264C ASP* 3.6 26.2 - - - -
265C GLY* 4.5 2.2 - - - -
304C ASN 2.8 28.8 + - - -
305C CYS* 3.9 5.6 - - - +
307C GLY* 3.8 24.5 - - - -
310C ASN* 4.2 10.6 - - - +
489C ALA 3.3 3.8 - - - +
490C ARG* 3.3 1.1 - - - -
491C LEU 2.9 26.2 + - - +
528C PHE* 3.8 27.6 - + + -
529C ASN 3.2 1.3 - - - -
530C ASP* 1.3 77.1 - - - +
532C ALA* 1.3 60.9 + - - +
533C PHE* 3.3 39.1 + + + -
602C FMT 4.0 13.7 - - - +
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Residues in contact with ALA 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C ASN* 2.6 30.6 + - - +
488C GLN* 3.7 21.4 + - + +
489C ALA 3.9 4.5 - - - -
490C ARG* 3.5 38.1 - - + +
530C ASP 3.6 2.2 + - - -
531C TRP* 1.3 76.4 - - - +
533C PHE* 1.3 60.3 + - - +
534C MET* 3.2 3.6 + - - +
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Residues in contact with PHE 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C ASN* 4.1 11.2 - - + +
305C CYS* 5.1 0.7 - - - -
310C ASN* 4.0 4.9 - - - +
488C GLN* 3.1 5.0 - - - -
489C ALA* 2.8 45.1 + - - +
491C LEU* 3.8 29.4 - - + -
503C ILE* 4.3 7.0 - - + -
515C LEU* 3.2 52.9 - - + +
516C LEU* 4.0 15.0 - - + -
528C PHE* 3.7 33.0 - + - -
531C TRP* 3.5 35.8 - + + -
532C ALA* 1.3 71.6 - - - +
534C MET* 1.3 58.9 + - - +
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Residues in contact with MET 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C ASN* 3.6 3.5 + - - +
310C ASN* 3.0 48.3 + - - +
311C SER 3.7 16.2 - - - +
312C ILE* 4.0 16.6 - - + -
314C THR 5.5 0.2 - - - +
334C SER* 2.7 17.4 + - - -
335C SER* 3.3 38.3 + - - +
486C HIS* 4.1 17.5 - - + -
487C ALA 3.3 11.0 - - - +
488C GLN* 4.1 7.0 - - + -
515C LEU* 4.7 1.6 - - - -
532C ALA 4.0 3.1 - - - +
533C PHE* 1.3 75.2 - - - +
535C THR* 1.3 92.3 + - - +
536C THR* 3.7 12.8 - - + -
608C NA 4.1 2.7 - - - -
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Residues in contact with THR 535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334C SER* 3.4 17.5 - - - -
485C GLU 4.4 1.0 - - - +
486C HIS* 3.9 3.3 - - - -
487C ALA* 3.0 42.0 + - + +
505C LEU* 4.5 14.6 - - + -
513C SER* 2.7 34.0 + - - +
515C LEU* 4.5 3.6 - - + -
534C MET* 1.3 82.6 - - - +
536C THR* 1.3 62.0 + - - +
537C HIS* 3.0 13.0 + - - +
538C SER* 5.1 8.1 + - - +
547C TRP* 5.7 1.8 - - + -
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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