Contacts of the strand formed by residues 582 - 587 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574C MSE 3.3 51.6 - - + +
553D LEU* 3.1 25.1 - - + +
555D THR* 3.8 22.0 - - + -
569D VAL* 4.9 2.9 - - + -
570D ASN* 2.9 24.0 - - - +
573D LEU* 4.4 7.9 - - + -
580D VAL 3.6 4.5 - - - +
581D PRO* 1.3 74.9 - - - +
583D LEU* 1.3 62.8 + - - +
584D ASN* 3.6 21.1 + - - +
618D TRP* 3.6 5.6 - - - -
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Residues in contact with LEU 583 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574C MSE 4.9 0.4 - - - -
575C ALA* 5.6 5.4 - - + -
553D LEU 2.9 8.8 + - - +
554D VAL* 3.4 7.2 - - + +
555D THR 2.9 26.0 + - - +
582D VAL* 1.3 70.4 - - - +
584D ASN* 1.3 70.1 + - - +
585D ILE* 3.5 20.7 + - + -
614D LYS* 3.9 12.3 - - + +
615D ILE* 3.8 41.3 - - + +
618D TRP* 3.5 47.1 - - + +
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Residues in contact with ASN 584 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571C GLU* 4.6 11.7 + - - +
574C MSE 4.5 6.3 - - - +
575C ALA* 5.7 1.2 - - - +
555D THR* 2.9 18.6 + - - +
557D GLU* 5.4 2.2 - - - +
561D ILE* 3.3 42.0 - - + +
566D GLY* 3.5 21.8 - - - +
567D SER 4.6 1.5 - - - +
570D ASN* 2.9 32.7 + - - +
582D VAL* 3.6 11.8 + - - +
583D LEU* 1.3 77.6 - - - +
585D ILE* 1.3 61.7 + - - +
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Residues in contact with ILE 585 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554D VAL* 3.8 20.4 - - + -
555D THR* 2.9 19.6 + - - +
556D VAL* 4.5 13.5 - - + -
557D GLU* 3.4 28.1 + - - +
561D ILE* 4.2 2.0 - - - -
583D LEU* 4.1 21.5 - - + -
584D ASN* 1.3 74.8 - - - +
586D GLY* 1.3 60.9 + - - +
606D LEU* 3.7 22.2 - - + -
611D MSE 4.1 42.2 - - + +
614D LYS* 4.4 20.6 - - + +
615D ILE* 4.6 1.8 - - + -
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Residues in contact with GLY 586 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557D GLU* 3.4 17.9 - - - -
559D ASN 3.8 3.4 - - - -
561D ILE* 3.6 18.2 - - - +
585D ILE* 1.3 79.1 - - - +
587D LEU* 1.3 65.3 + - - -
588D PRO* 3.8 6.1 - - - +
604D LEU 5.2 0.5 - - - +
606D LEU* 3.9 18.9 - - - +
614D LYS* 4.6 7.0 + - - +
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Residues in contact with LEU 587 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422D GLY* 5.2 1.3 - - - -
423D ILE* 4.1 9.6 - - + -
434D ALA* 3.2 35.7 - - + -
558D GLU* 4.0 8.5 - - + +
559D ASN* 3.0 34.2 + - - +
560D ALA* 3.7 6.5 - - + +
561D ILE* 3.1 27.2 + - - +
586D GLY* 1.3 71.4 - - - -
588D PRO* 1.3 73.8 - - + +
590D PHE 6.0 0.2 - - - +
592D ILE* 3.6 28.0 - - + -
604D LEU* 3.8 8.7 - - + -
606D LEU* 3.8 25.6 - - + -
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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