Contacts of the strand formed by residues 582 - 587 (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 VAL 582 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A LEU* 3.2 20.2 - - + +
555A THR* 3.9 21.8 - - + -
569A VAL* 4.5 3.1 - - + -
570A ASN* 3.5 25.4 - - - +
573A LEU* 3.4 25.8 - - + -
580A VAL 3.1 16.8 - - - +
581A PRO* 1.3 74.6 - - - +
583A LEU* 1.3 63.8 + - - +
584A ASN* 3.5 14.4 + - - +
618A TRP* 3.5 6.6 - - - -
574B MSE 3.1 33.8 - - - +
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Residues in contact with LEU 583 (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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553A LEU 2.9 12.0 + - - +
554A VAL* 3.4 6.2 - - + +
555A THR* 2.8 27.2 + - - +
582A VAL* 1.3 70.5 - - - +
584A ASN* 1.3 68.6 + - - +
585A ILE* 3.4 20.5 + - + -
614A LYS* 4.1 8.7 - - + +
615A ILE* 3.7 45.8 - - + +
618A TRP* 3.5 46.0 - - + +
574B MSE 5.3 0.2 - - - -
575B ALA* 5.5 5.4 - - - +
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Residues in contact with ASN 584 (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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555A THR* 3.0 19.0 + - - +
557A GLU* 5.6 2.2 - - - +
561A ILE* 3.6 40.0 - - + +
566A GLY* 3.3 16.3 - - - +
567A SER 4.4 0.4 - - - +
570A ASN* 2.8 42.3 - - - +
582A VAL* 3.5 10.3 + - - +
583A LEU* 1.3 78.7 - - - +
585A ILE* 1.3 62.8 + - - +
571B GLU* 4.6 10.3 + - - +
574B MSE 4.3 6.5 - - - +
575B ALA* 5.5 2.6 - - - +
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Residues in contact with ILE 585 (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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554A VAL* 3.7 21.5 - - + -
555A THR* 2.7 19.8 + - - +
556A VAL* 4.2 13.0 - - + -
557A GLU* 3.2 28.3 + - - +
561A ILE* 4.3 1.3 - - - -
583A LEU* 3.9 24.0 - - + -
584A ASN* 1.3 75.3 - - - +
586A GLY* 1.3 60.4 + - - +
606A LEU* 3.9 20.4 - - + -
611A MSE 4.1 41.3 - - + +
614A LYS* 4.2 21.5 - - + +
615A ILE* 4.4 2.5 - - + -
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Residues in contact with GLY 586 (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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557A GLU* 3.3 17.3 - - - -
559A ASN 3.7 5.6 - - - -
561A ILE* 3.6 16.7 - - - +
585A ILE* 1.3 79.0 - - - +
587A LEU* 1.3 66.0 + - - -
588A PRO* 3.7 5.2 - - - +
604A LEU 5.2 1.0 - - - +
606A LEU* 3.9 18.6 - - - +
614A LYS* 4.6 6.6 + - - +
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Residues in contact with LEU 587 (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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422A GLY 5.2 2.5 - - - -
423A ILE* 3.9 23.1 - - + -
434A ALA* 3.5 34.1 - - + -
558A GLU* 4.2 6.1 - - + +
559A ASN* 2.8 42.3 + - - +
560A ALA* 3.7 4.9 - - + +
561A ILE* 3.2 25.1 + - - +
586A GLY* 1.3 72.5 - - - -
588A PRO* 1.3 75.1 - - + +
592A ILE* 4.3 11.7 - - + -
604A LEU* 4.0 12.6 - - + -
606A LEU* 3.9 26.0 - - + -
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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