Contacts of the strand formed by residues 528 - 531 (chain A) in PDB entry 2O1S
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 THR 528 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499A VAL* 5.1 4.5 - - + -
501A ARG 3.1 18.4 - - - +
502A ARG* 3.8 8.0 - - - +
503A GLY* 2.8 21.4 + - - +
506A LEU 2.7 10.1 + - - -
507A ALA* 4.0 3.4 - - + -
508A ILE* 2.7 35.0 + - - +
522A ALA* 4.9 0.2 - - - -
527A ALA* 1.3 73.9 - - - +
529A LEU* 1.3 55.6 + - - +
530A VAL* 4.3 9.4 - - + -
546A MSE 3.9 27.6 - - + -
550A HIS* 2.6 29.9 + - + +
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Residues in contact with LEU 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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499A VAL* 3.5 3.6 - - - -
500A LYS* 2.6 46.3 + - + -
501A ARG* 2.9 29.8 + - + +
508A ILE* 3.5 29.6 - - + +
510A ASN* 4.8 1.1 - - + -
515A MSE 3.6 37.0 - - + -
518A ALA* 4.2 14.8 - - + +
519A ALA* 4.0 20.2 - - + -
522A ALA* 4.0 9.2 - - + -
527A ALA 3.7 0.8 + - - -
528A THR* 1.3 73.2 - - - +
530A VAL* 1.3 60.4 + - - +
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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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498A ILE 3.7 16.4 - - - +
499A VAL* 4.0 12.8 - - + +
500A LYS 5.1 0.2 - - - -
507A ALA* 5.6 0.2 - - + -
508A ILE 2.9 7.1 + - - +
509A LEU* 3.8 23.6 - - + -
510A ASN* 2.8 33.4 + - - +
515A MSE 4.2 3.5 - - - +
528A THR* 4.3 4.5 - - + -
529A LEU* 1.3 80.1 - - - +
531A ASP* 1.3 66.1 + - - +
532A MSE 3.8 26.9 - - - -
542A LEU* 3.9 12.1 - - + -
546A MSE 3.9 23.6 - - - -
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Residues in contact with ASP 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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450A THR 5.1 1.2 - - - +
452A SER* 2.8 28.3 + - - -
456A GLU* 4.2 13.3 - - - +
497A GLY* 3.4 1.0 - - - -
498A ILE* 2.9 46.4 + - + +
500A LYS* 4.4 12.6 + - + +
510A ASN* 3.2 21.2 - - - +
512A GLY 4.9 1.6 + - - -
515A MSE 3.5 21.8 - - + +
530A VAL* 1.3 71.2 - - - +
532A MSE 1.3 63.8 + - - +
533A ARG* 3.3 12.7 + - - +
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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