Contacts of the strand formed by residues 529 - 533 (chain A) in PDB entry 3OPY
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 PRO 529 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353A ILE 3.6 11.3 - - - +
354A VAL* 3.7 20.5 - - + -
355A GLY* 3.0 22.3 + - - -
518A ALA* 4.2 17.5 - - + +
527A PRO 3.6 9.2 - - - +
528A SER* 1.3 85.8 - - - +
530A VAL* 1.3 66.4 + - - +
531A ILE* 4.4 3.6 - - + -
540A ARG* 4.0 24.7 - - + +
541A GLN 3.1 13.5 - - - +
542A PRO* 4.3 0.2 - - + -
543A LEU* 4.1 5.0 - - - +
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Residues in contact with VAL 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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317A LEU* 4.9 2.5 - - + -
355A GLY* 3.3 13.5 - - - +
357A VAL* 3.7 29.2 - - + -
364A MET* 4.5 10.3 - - + -
365A CYS 5.7 0.9 - - - +
529A PRO* 1.3 70.1 - - - +
531A ILE* 1.3 68.7 + - - +
532A SER* 3.1 17.3 + - - +
540A ARG* 3.8 0.5 - - - -
541A GLN 2.6 31.4 + - - +
543A LEU* 3.5 44.9 - - + -
546A SER* 4.3 16.8 - - - +
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Residues in contact with ILE 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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354A VAL* 3.7 21.8 - - + -
355A GLY 2.8 15.1 + - - +
356A LEU* 3.9 14.1 - - + -
357A VAL* 4.5 8.7 + - - +
367A THR* 5.7 0.2 - - - +
511A GLN* 3.4 36.8 + - + +
514A ASP* 3.7 19.5 - - - +
515A ALA* 3.9 12.6 - - - -
518A ALA* 3.8 25.1 - - + -
529A PRO* 4.4 3.8 - - + -
530A VAL* 1.3 75.4 - - - +
532A SER* 1.3 57.2 + - - +
538A ILE* 3.6 29.4 - - + -
539A VAL 3.8 2.7 - - - +
540A ARG* 3.8 10.8 - - + -
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Residues in contact with SER 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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365A CYS 5.0 0.9 + - - -
366A GLY* 3.6 13.9 + - - -
367A THR* 3.5 22.5 - - - -
511A GLN* 3.5 7.5 + - - +
530A VAL* 3.1 22.9 + - - +
531A ILE* 1.3 72.5 - - - +
533A ILE* 1.3 55.5 + - - +
538A ILE* 3.4 9.4 - - - +
539A VAL* 2.8 37.6 + - - +
541A GLN* 3.3 21.5 - - - +
546A SER* 5.1 0.2 + - - -
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Residues in contact with ILE 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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367A THR* 2.8 17.6 + - - +
368A ASP* 2.7 33.4 + - + +
369A SER* 3.4 34.1 - - - +
503A PHE* 4.4 8.1 - - + -
506A PHE* 4.2 16.2 - - + -
507A LEU* 3.6 29.2 - - + -
511A GLN* 4.1 0.9 - - - +
532A SER* 1.3 74.0 - - - +
534A LEU* 1.4 68.7 + - - +
536A ASN* 4.1 28.9 - - - +
537A LYS 3.5 8.5 - - - +
538A ILE* 3.7 14.8 - - + -
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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