Contacts of the strand formed by residues 582 - 587 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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553C LEU* 3.3 20.6 - - + +
555C THR* 4.0 20.6 - - + -
569C VAL* 4.7 3.8 - - + -
570C ASN* 3.6 20.4 - - - +
573C LEU* 3.5 24.5 - - + -
580C VAL 3.2 17.7 + - - +
581C PRO* 1.3 75.6 - - - +
583C LEU* 1.3 62.5 + - - +
584C ASN* 3.7 13.7 + - - +
618C TRP* 3.4 5.6 - - - -
574D MSE 3.2 42.0 - - + +
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Residues in contact with LEU 583 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553C LEU 3.0 8.1 + - - -
554C VAL* 3.4 9.5 - - + +
555C THR 3.0 25.2 + - - +
582C VAL* 1.3 72.3 - - - +
584C ASN* 1.3 70.5 + - - +
585C ILE* 3.5 19.5 + - + -
614C LYS* 4.1 7.2 - - + +
615C ILE* 3.9 44.0 - - + +
618C TRP* 3.5 47.4 - - + +
574D MSE 5.1 0.4 - - - -
575D ALA* 5.7 4.7 - - - +
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Residues in contact with ASN 584 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555C THR* 3.0 18.7 + - - +
557C GLU* 5.5 1.6 - - - +
561C ILE* 3.1 41.2 - - + +
566C GLY* 3.4 23.7 - - - +
567C SER 4.4 1.5 - - - +
570C ASN* 2.8 34.6 + - - +
582C VAL* 3.7 7.0 + - - +
583C LEU* 1.3 80.2 - - - +
585C ILE* 1.3 60.8 + - - +
571D GLU* 4.6 9.1 + - - +
574D MSE 4.3 11.3 - - - +
575D ALA* 5.7 1.4 - - - +
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Residues in contact with ILE 585 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554C VAL* 3.8 19.7 - - + -
555C THR* 2.8 19.3 + - - +
556C VAL* 4.3 6.3 - - + -
557C GLU* 3.3 28.1 + - - +
561C ILE* 4.0 2.2 - - - -
583C LEU* 4.0 25.1 - - + -
584C ASN* 1.3 74.7 - - - +
586C GLY* 1.3 60.7 + - - +
606C LEU* 3.7 12.8 - - + -
611C MSE 3.4 57.4 - - + +
614C LYS* 4.3 19.5 - - + +
615C ILE* 4.7 2.9 - - + -
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Residues in contact with GLY 586 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557C GLU* 3.3 18.2 - - - -
559C ASN 3.7 2.7 - - - -
561C ILE* 3.5 18.7 - - - +
585C ILE* 1.3 79.7 - - - +
587C LEU* 1.3 66.7 + - - -
588C PRO* 3.6 6.6 - - - +
604C LEU 5.2 0.2 - - - +
606C LEU* 4.0 19.6 - - - +
614C LYS* 4.5 6.3 + - - +
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Residues in contact with LEU 587 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422C GLY 5.3 2.9 - - - -
423C ILE* 3.8 35.0 - - + -
432C GLN* 5.9 0.7 - - + -
434C ALA* 3.2 38.4 - - + -
558C GLU* 4.5 5.4 - - + +
559C ASN* 2.8 34.0 + - - +
560C ALA* 3.7 5.9 - - + +
561C ILE* 3.2 25.1 + - - +
562C MSE 5.1 0.2 + - - -
586C GLY* 1.3 71.4 - - - -
588C PRO* 1.3 73.4 - - + +
592C ILE* 4.2 15.0 - - + -
604C LEU* 3.9 11.7 - - + -
606C LEU* 3.8 15.5 - - + -
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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