Contacts of the strand formed by residues 583 - 590 (chain D) in PDB entry 1O23
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 LYS 583 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580D SER 4.8 8.1 - - - +
581D PRO 4.5 2.2 - - - +
582D HIS* 1.3 70.8 - - - +
584D VAL* 1.3 58.8 + - - +
614D ASP* 3.3 19.7 - - + +
645D TYR* 3.7 26.1 + - + -
646D ASP* 2.6 44.7 + - - +
647D TYR* 3.3 14.0 - - - +
648D ASN* 3.0 50.6 + - - +
649D CYS 3.1 7.8 + - - -
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Residues in contact with VAL 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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582D HIS* 3.9 24.9 - - + +
583D LYS* 1.3 71.9 - - - +
585D ALA* 1.3 68.8 + - - +
586D ILE* 4.1 7.6 - - + -
613D LEU* 4.5 11.2 - - + -
614D ASP 3.0 8.1 + - - -
615D TYR* 3.0 16.8 - - + +
616D GLY 2.9 23.7 + - - -
647D TYR* 3.4 5.2 - - - -
649D CYS* 3.4 19.7 - - - +
651D VAL* 3.3 34.1 - - + -
666D TYR 3.7 15.3 - - - +
667D ARG* 4.4 1.8 - - + -
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Residues in contact with ALA 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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584D VAL* 1.3 73.0 - - - +
586D ILE* 1.3 61.7 + - - +
587D ILE* 3.8 5.2 + - + +
616D GLY 3.5 5.4 - - - -
618D TYR* 4.3 3.4 - - + -
641D ALA* 3.8 19.1 - - + -
647D TYR* 3.4 36.2 - - + -
649D CYS 3.0 7.6 + - - +
650D PHE* 3.5 12.9 - - + -
651D VAL 3.0 23.2 + - - +
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Residues in contact with ILE 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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584D VAL* 4.1 17.5 - - + +
585D ALA* 1.3 75.3 - - - +
587D ILE* 1.3 59.6 + - - +
588D ILE* 4.1 5.0 - - + +
600D TRP* 3.8 25.8 - - + -
608D LEU* 3.6 33.4 - - + -
615D TYR* 4.5 7.2 - - + -
616D GLY 2.8 14.0 + - - +
617D ILE* 3.5 25.8 - - + -
618D TYR* 2.8 35.0 + - - +
651D VAL* 3.3 21.1 - - + +
653D SER* 4.4 9.0 - - - -
666D TYR* 4.7 5.8 - - + -
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Residues in contact with ILE 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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585D ALA* 4.3 8.5 - - + +
586D ILE* 1.3 76.6 - - - +
588D ILE* 1.3 63.6 + - - +
589D PRO* 3.8 2.9 - - - +
618D TYR* 3.6 8.7 - - + -
620D ILE* 3.8 23.1 - - + -
634D LEU* 3.9 23.7 - - + +
637D GLY* 3.3 34.8 - - - +
638D PHE* 3.3 11.2 - - - +
641D ALA* 4.9 1.3 - - + -
650D PHE* 3.9 15.9 - - + -
651D VAL 2.8 9.4 + - - +
652D PHE* 3.4 26.4 - - + -
653D SER 2.8 27.7 + - - +
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Residues in contact with ILE 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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586D ILE* 4.6 9.2 - - + +
587D ILE* 1.3 79.0 - - - +
589D PRO* 1.3 73.6 - - - +
590D PHE* 3.4 3.4 + - + +
597D LEU* 4.3 6.7 - - + -
600D TRP* 3.9 45.8 - - + +
617D ILE* 4.4 6.1 - - + -
618D TYR 2.9 13.2 + - - +
619D VAL* 3.7 22.7 - - + -
620D ILE 3.0 23.1 + - - -
653D SER 3.2 17.0 - - - +
654D ASP 5.0 0.2 - - - +
655D VAL* 3.2 32.3 - - + +
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Residues in contact with PRO 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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588D ILE* 1.3 88.1 - - - +
590D PHE* 1.3 60.1 + - - +
620D ILE* 3.9 5.4 - - + +
628D PHE* 4.1 13.5 - - + -
630D ARG* 4.1 29.6 - - + +
633D LEU* 4.2 9.4 - - + -
634D LEU* 3.5 23.1 - - + -
653D SER 3.3 16.4 - - - +
654D ASP* 3.6 14.1 - - - +
655D VAL* 4.4 0.7 - - - +
810D UPG 2.9 36.8 + - - +
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Residues in contact with PHE 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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588D ILE* 3.7 1.1 - - + +
589D PRO* 1.3 75.3 - - - +
591D ARG* 1.3 73.1 + - - +
592D ASN* 4.0 7.4 - - - -
593D ARG* 3.4 39.9 - - + -
594D GLN* 3.5 23.6 - - + -
597D LEU* 4.0 15.7 - - + -
619D VAL* 3.4 30.5 - - + -
620D ILE 2.8 13.2 + - - +
621D ASN* 3.1 28.8 - - + -
622D GLN* 2.8 30.7 + - - +
628D PHE* 3.8 8.7 - - - -
633D LEU* 4.1 0.4 - - - +
655D VAL* 3.9 17.5 - - + -
795D LYS* 4.2 14.8 - - - -
810D UPG 3.2 7.0 - - - -
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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