Contacts of the strand formed by residues 528 - 535 (chain A) in PDB entry 4OMD
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A VAL* 3.8 33.0 - - + -
305A CYS* 4.5 4.5 - - - -
491A LEU 4.0 12.6 - - - +
492A THR* 3.1 5.7 - - - +
493A LEU* 2.8 61.6 + - + +
498A ARG* 3.6 28.7 - - + -
501A LEU* 4.8 3.8 - - + -
503A ILE* 4.8 1.3 - - + -
516A LEU* 3.8 29.8 - - + -
519A ARG* 5.4 0.2 - - - -
522A ASP* 5.4 0.9 - - - -
526A ASP 4.7 0.9 - - - -
527A GLY* 1.3 76.9 - - - -
529A ASN* 1.3 60.4 + - - +
530A ASP 3.7 0.2 - - - -
531A TRP* 3.7 23.8 - + + -
533A PHE* 3.7 26.9 - + + -
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Residues in contact with ASN 529 (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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492A THR* 4.1 11.8 - - + +
526A ASP 5.0 3.3 + - - +
527A GLY 4.4 0.2 + - - -
528A PHE* 1.3 71.1 - - - +
530A ASP* 1.3 75.6 + - - +
531A TRP* 3.3 6.0 + - - +
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Residues in contact with ASP 530 (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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490A ARG* 3.0 44.3 + - - +
491A LEU 3.1 6.3 + - - -
492A THR* 3.0 23.4 + - - +
529A ASN* 1.3 80.2 + - - +
531A TRP* 1.3 64.0 + - - +
532A ALA 3.7 1.9 + - - -
565A LYS* 2.9 28.1 + - - +
233B ASP* 5.0 4.8 - - - +
267B ALA* 5.8 1.0 - - - +
268B ARG* 4.1 14.9 + - - +
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Residues in contact with TRP 531 (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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263A VAL* 3.7 24.4 - - + +
264A ASP* 3.7 27.1 - - - -
265A GLY* 4.3 3.1 - - - -
304A ASN 2.7 28.6 + - - -
305A CYS* 3.8 10.1 - - - +
307A GLY* 3.7 24.7 - - - -
310A ASN* 4.2 10.4 - - - +
489A ALA 3.4 0.5 - - - +
490A ARG* 3.3 0.8 - - - -
491A LEU 3.0 27.0 + - - -
528A PHE* 3.7 26.9 - + + -
529A ASN 3.3 5.7 - - - +
530A ASP* 1.3 76.4 - - - +
532A ALA* 1.3 61.5 + - - +
533A PHE* 3.3 43.2 + + + -
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Residues in contact with ALA 532 (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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310A ASN* 2.6 30.6 + - - +
488A GLN* 3.8 17.8 + - + +
489A ALA 4.0 3.6 - - - -
490A ARG* 3.6 39.5 - - + +
530A ASP 3.7 2.4 + - - -
531A TRP* 1.3 75.1 - - - +
533A PHE* 1.3 61.2 + - - +
534A MET* 3.2 3.6 + - - +
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Residues in contact with PHE 533 (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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304A ASN* 4.3 9.6 - - + +
305A CYS* 5.1 1.1 - - - -
310A ASN* 4.1 5.4 - - - +
487A ALA 3.9 0.5 - - - +
488A GLN* 3.2 4.0 - - - -
489A ALA* 2.8 44.5 + - - +
491A LEU* 3.9 27.6 - - + -
503A ILE* 4.3 7.2 - - + -
515A LEU* 3.4 46.7 - - + +
516A LEU* 3.8 22.9 - - + -
528A PHE* 3.7 34.1 - + - -
531A TRP* 3.6 41.5 - + + -
532A ALA* 1.3 71.0 - - - +
534A MET* 1.3 58.8 + - - +
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Residues in contact with MET 534 (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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304A ASN* 3.7 3.0 + - - +
310A ASN* 3.2 44.3 + - - +
311A SER 3.7 16.8 - - - +
312A ILE* 3.9 16.8 - - + -
314A THR 5.3 0.9 - - - +
334A SER* 2.9 15.8 + - - -
335A SER* 3.4 37.5 + - - +
486A HIS* 4.0 20.6 - - + -
487A ALA 3.4 10.5 - - - +
488A GLN* 4.2 8.1 - - + +
515A LEU* 4.8 0.9 - - - -
532A ALA 3.2 4.5 + - - +
533A PHE* 1.3 74.8 - - - +
535A THR* 1.3 89.4 + - - +
536A THR* 3.6 13.2 - - + -
606A NA 4.1 2.5 - - - -
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Residues in contact with THR 535 (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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334A SER* 3.3 19.1 - - - -
485A GLU 4.4 1.0 - - - +
486A HIS* 4.0 2.4 - - - -
487A ALA* 3.0 45.6 + - + +
505A LEU* 4.4 15.3 - - + -
513A SER* 2.7 34.3 + - - +
515A LEU* 4.4 3.1 - - + -
534A MET* 1.3 83.3 - - - +
536A THR* 1.3 61.0 + - - +
537A HIS* 3.2 9.7 + - - +
538A SER* 5.1 9.2 + - - +
547A TRP* 5.8 1.6 - - + -
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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