Contacts of the strand formed by residues 582 - 587 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A MSE 3.2 38.7 - - - +
553B LEU* 3.1 20.0 - - + +
555B THR* 4.0 20.0 - - + +
569B VAL* 4.5 4.5 - - + -
570B ASN* 3.5 25.4 - - - +
573B LEU* 3.5 23.6 - - + -
580B VAL 3.4 15.9 - - - +
581B PRO* 1.3 74.5 - - - +
583B LEU* 1.3 62.9 + - - +
584B ASN* 3.6 14.9 + - - +
618B TRP* 3.5 4.9 - - - -
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Residues in contact with LEU 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A MSE 5.7 0.2 - - - -
575A ALA* 5.6 4.5 - - - +
553B LEU 2.8 12.4 + - - +
554B VAL* 3.4 9.8 - - + +
555B THR 2.9 23.4 + - - +
582B VAL* 1.3 71.6 - - - +
584B ASN* 1.3 68.3 + - - +
585B ILE* 3.3 15.7 + - + -
614B LYS* 4.0 6.3 - - + +
615B ILE* 3.6 44.9 - - + +
618B TRP* 3.5 49.5 - - + +
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Residues in contact with ASN 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571A GLU* 4.3 10.9 - - - +
574A MSE 4.5 6.4 - - - +
575A ALA* 6.2 1.0 - - - +
555B THR* 2.8 25.8 + - - +
557B GLU* 5.6 2.5 - - - +
561B ILE* 3.5 39.3 - - + +
566B GLY* 3.6 15.5 + - - -
567B SER 4.5 1.3 - - - -
570B ASN* 2.8 40.3 + - - +
582B VAL* 3.6 10.8 + - - +
583B LEU* 1.3 76.2 - - - +
585B ILE* 1.3 62.7 + - - +
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Residues in contact with ILE 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514B LEU* 5.8 0.2 - - + -
554B VAL* 3.8 19.7 - - + -
555B THR* 2.8 20.8 + - - +
556B VAL* 4.3 15.7 - - + -
557B GLU* 3.1 29.8 + - - +
561B ILE* 4.3 1.1 - - - -
583B LEU* 4.0 23.1 - - + -
584B ASN* 1.3 74.6 - - - +
586B GLY* 1.3 61.6 + - - +
606B LEU* 3.9 21.8 - - + -
611B MSE 4.1 40.4 - - + +
614B LYS* 4.3 19.1 - - + +
615B ILE* 4.5 2.7 - - + -
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Residues in contact with GLY 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B GLU* 3.2 18.6 - - - -
559B ASN 3.6 4.0 - - - -
561B ILE* 3.5 19.1 - - - +
585B ILE* 1.3 78.9 - - - +
587B LEU* 1.3 66.7 + - - -
588B PRO* 3.7 4.3 - - - +
604B LEU 5.4 0.3 - - - +
606B LEU* 3.9 17.8 - - - +
614B LYS* 4.6 5.6 + - - +
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Residues in contact with LEU 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B GLY* 5.2 2.7 - - - -
423B ILE* 3.9 17.0 - - + -
434B ALA* 3.4 34.3 - - + -
558B GLU* 4.2 9.6 - - + +
559B ASN* 2.8 36.8 + - - +
560B ALA* 3.7 4.8 - - - -
561B ILE* 3.1 27.1 + - - +
586B GLY* 1.3 71.1 - - - -
588B PRO* 1.3 73.9 - - + +
592B ILE* 4.6 11.9 - - + -
604B LEU* 3.7 27.6 - - + -
606B LEU* 3.8 16.8 - - + -
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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