Contacts of the strand formed by residues 585 - 590 (chain D) in PDB entry 3P23
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 ILE 585 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604C GLU* 4.7 13.0 - - + -
576D VAL* 3.6 23.8 - - + -
578D GLY 3.9 11.0 - - - +
579D HIS* 4.0 19.3 - - + +
580D GLY 4.7 0.2 - - - +
583D GLY 4.0 6.1 - - - +
584D THR* 1.3 75.8 - - - +
586D VAL* 1.3 67.7 + - - +
587D TYR* 3.2 55.7 + - + +
598D VAL 3.8 1.0 - - - +
599D LYS* 3.6 0.7 - - - -
600D ARG* 2.8 58.3 + - + +
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Residues in contact with VAL 586 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576D VAL* 3.9 1.9 - - - -
577D LEU* 2.9 34.7 + - + +
578D GLY* 3.2 22.0 + - - +
580D GLY* 5.7 3.4 - - - +
584D THR* 4.7 2.9 - - + -
585D ILE* 1.3 80.4 - - - +
587D TYR* 1.3 71.9 + - - +
597D ALA* 4.2 15.5 - - + -
598D VAL 3.2 7.6 - - - +
599D LYS* 3.7 38.4 - - + -
642D ILE* 5.4 2.5 - - + -
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Residues in contact with TYR 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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604C GLU* 4.6 6.5 + - - -
571D PHE* 3.4 54.0 - + + -
572D CYS 4.2 8.7 - - - +
573D PRO* 4.4 11.2 - - + -
574D LYS* 5.0 1.8 - - - -
575D ASP 3.9 6.3 - - - +
576D VAL* 3.8 21.5 - - + -
577D LEU* 4.0 4.8 - - - +
585D ILE* 3.2 54.0 - - + +
586D VAL* 1.3 76.5 - - - +
588D ARG* 1.3 60.0 + - - +
597D ALA* 3.3 6.8 - - - +
598D VAL* 2.6 44.3 + - + +
600D ARG* 3.5 29.1 + - + -
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Residues in contact with ARG 588 (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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572D CYS* 3.9 14.9 + - - +
575D ASP* 2.8 52.3 + - - +
577D LEU* 3.3 35.1 - - + +
587D TYR* 1.3 76.5 - - - +
589D GLY* 1.3 66.1 + - - +
595D ASP* 5.1 10.3 - - + -
596D VAL 3.6 9.2 - - - +
644D LEU* 4.4 22.3 - - + +
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Residues in contact with GLY 589 (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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570D SER 3.9 1.1 - - - -
571D PHE* 3.8 21.5 - - - -
572D CYS 4.6 0.4 - - - -
587D TYR 4.0 1.4 + - - -
588D ARG* 1.3 76.6 - - - +
590D MET* 1.3 65.7 + - - +
595D ASP* 3.5 9.9 - - - +
596D VAL* 2.8 33.1 + - - +
598D VAL* 4.1 5.3 - - - +
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Residues in contact with MET 590 (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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569D ILE* 3.6 6.9 - - - +
570D SER* 2.8 44.0 + - - +
571D PHE* 4.5 0.2 - - - +
589D GLY* 1.3 75.2 - - - +
591D PHE* 1.3 61.7 + - - +
592D ASP 4.9 2.0 - - - +
593D ASN* 4.3 11.2 - - - +
594D ARG 3.4 21.5 - - - +
595D ASP* 3.5 24.5 - - - +
596D VAL* 4.0 4.2 - - - +
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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