Contacts of the strand formed by residues 506 - 511 (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 LEU 506 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504A GLU 2.6 11.9 + - - +
505A LYS* 1.3 96.7 - - + +
507A ALA* 1.3 53.9 + - - +
508A ILE* 5.2 2.2 - - + -
525A LEU* 4.1 19.7 - - + +
527A ALA* 3.0 20.4 - - + +
528A THR 2.7 31.5 + - - -
550A HIS* 3.4 8.1 - - - -
552A ALA* 3.5 30.5 - - + +
554A VAL* 4.2 17.9 - - + -
615A ILE* 3.8 29.6 - - + -
618A TRP* 5.3 0.7 - - + -
619A LEU* 4.8 11.4 - - + -
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Residues in contact with ALA 507 (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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506A LEU* 1.3 72.9 - - - +
508A ILE* 1.3 63.8 + - - +
509A LEU* 3.8 6.6 + - + +
528A THR* 3.4 12.8 - - + -
546A MSE 4.2 17.3 - - + -
550A HIS* 3.5 31.8 - - + +
552A ALA 3.2 6.7 + - - -
553A LEU* 3.3 10.8 - - + +
554A VAL* 2.9 24.5 + - - +
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Residues in contact with ILE 508 (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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506A LEU* 5.2 3.1 - - + -
507A ALA* 1.3 74.1 - - - +
509A LEU* 1.3 65.8 + - - +
518A ALA* 4.2 9.9 - - + +
521A VAL* 3.7 31.2 - - + -
522A ALA* 3.8 24.7 - - + +
525A LEU* 5.5 0.4 - - + -
527A ALA* 4.2 11.4 - - + -
528A THR 2.7 14.8 + - - +
529A LEU* 3.5 15.5 - - + +
530A VAL* 2.9 28.2 + - - +
554A VAL* 3.3 23.3 - - + +
556A VAL* 4.2 21.5 - - + -
615A ILE* 4.8 5.4 - - + -
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Residues in contact with LEU 509 (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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507A ALA* 4.3 13.0 - - + +
508A ILE* 1.3 76.4 - - - +
510A ASN* 1.3 61.0 + - - +
511A PHE* 4.0 3.9 - - + -
530A VAL* 3.8 29.6 - - + -
532A MSE 3.9 31.9 - - + -
542A LEU* 5.0 0.2 - - + -
543A ILE* 4.5 9.0 - - + -
546A MSE 4.3 15.0 - - + -
553A LEU* 4.2 22.0 - - + -
554A VAL 2.6 15.2 + - - +
555A THR* 3.3 9.8 - - + -
556A VAL 2.9 25.5 + - - +
569A VAL* 4.3 19.5 - - + -
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Residues in contact with ASN 510 (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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508A ILE 3.7 0.6 + - - -
509A LEU* 1.3 72.3 - - - +
511A PHE* 1.3 64.9 + - - +
512A GLY 3.1 19.7 + - - +
514A LEU* 3.6 6.3 + - - +
515A MSE 3.2 50.9 - - + +
518A ALA* 4.1 9.4 - - + +
529A LEU* 4.8 2.5 - - + -
530A VAL 2.8 18.3 + - - +
531A ASP* 3.2 16.3 - - - +
532A MSE 2.9 30.3 + - - +
533A ARG 4.3 0.3 + - - -
556A VAL* 3.8 18.3 + - + +
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Residues in contact with PHE 511 (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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437A LEU* 5.2 1.9 - - + +
450A THR* 3.6 15.6 - - + +
475A ARG* 5.8 0.9 + - - -
509A LEU* 4.0 9.2 - - + -
510A ASN* 1.3 76.9 + - - +
512A GLY* 1.3 57.6 + - - +
514A LEU* 5.2 1.4 + - - +
532A MSE 3.2 38.1 - - + -
533A ARG 5.5 0.4 - - - +
534A PHE 3.5 18.8 - - - -
535A VAL* 3.8 18.6 - - + -
538A LEU* 3.9 11.9 - - + -
555A THR* 4.4 8.1 - - + -
556A VAL* 2.7 28.9 + - - +
557A GLU* 3.5 21.8 - - + +
558A GLU 4.3 3.1 + - - -
565A ALA* 3.6 27.1 - - + -
566A GLY 4.8 0.2 - - - -
569A VAL* 3.8 28.9 - - + -
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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