Contacts of the strand formed by residues 523 - 530 (chain D) in PDB entry 5Y7K
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 523 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424D GLY 5.6 3.0 + - - +
516D PHE* 3.5 48.6 - - + -
517D ILE 3.5 5.2 - - - -
518D ILE* 4.8 8.1 - - + +
522D THR* 1.3 82.5 - - - +
524D PHE* 1.3 66.0 + - - +
525D TRP* 4.3 23.0 - - + +
586D GLN* 4.1 10.7 - - - +
590D ILE* 4.3 1.7 - - - +
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Residues in contact with PHE 524 (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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516D PHE* 3.3 3.2 - - - -
517D ILE* 2.9 38.9 + - + +
519D LEU* 3.7 38.4 - - + -
522D THR* 3.4 39.3 - - + -
523D LYS* 1.3 74.7 - - - +
525D TRP* 1.3 62.7 + - - +
526D TYR* 3.9 0.7 + - - -
578D PHE* 3.5 24.1 - + + -
579D ASP 3.4 16.4 - - - +
580D GLY* 3.8 7.2 - - - -
581D ARG* 3.8 36.8 - - + -
586D GLN* 5.1 2.9 - - - -
590D ILE* 4.0 21.3 - - + -
605D ASP* 4.6 3.8 - - - -
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Residues in contact with TRP 525 (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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423D LYS 5.5 0.9 - - - -
424D GLY 3.7 18.8 + - - -
425D MET* 4.3 26.0 - - + -
426D PRO* 3.2 37.0 - - + +
427D GLY 5.8 2.5 - - - +
514D LEU* 3.6 23.6 - - + -
515D ASP* 3.2 37.0 - - - -
516D PHE* 3.8 28.8 - + + +
523D LYS* 4.4 21.8 - - + +
524D PHE* 1.3 79.3 - - - +
526D TYR* 1.3 60.9 + - - +
555D ALA* 3.9 13.9 - - + +
578D PHE* 3.8 1.8 - - - -
579D ASP* 3.0 37.3 + - + +
586D GLN* 4.3 12.6 + - - +
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Residues in contact with TYR 526 (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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513D LYS* 3.7 20.9 - - + +
514D LEU* 3.3 5.7 - - - +
515D ASP* 2.8 52.3 + - + +
516D PHE* 3.3 36.5 + - - -
517D ILE* 3.9 16.6 - - + -
524D PHE 4.4 0.7 - - - -
525D TRP* 1.3 74.7 - - - +
527D GLN* 1.3 63.5 + - - +
528D MET* 4.0 31.4 - - + -
555D ALA* 3.7 5.6 - - - -
577D SER 3.2 15.0 - - - +
578D PHE* 3.9 14.6 - - + -
613D PHE* 3.7 22.4 - + + -
616D MET* 3.6 19.7 - - + +
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Residues in contact with GLN 527 (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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512D LYS* 3.3 30.3 + - + +
513D LYS 3.2 9.9 - - - +
514D LEU* 4.6 8.3 - - + -
526D TYR* 1.3 74.9 - - - +
528D MET* 1.3 66.7 + - - +
529D ILE* 4.4 11.1 - - - +
554D LYS* 3.3 21.9 + - - +
555D ALA* 3.3 5.8 - - + +
556D ASP* 2.9 33.8 + - - +
560D ARG* 4.7 6.9 - - - +
575D VAL 5.5 1.1 + - - +
576D ALA* 3.2 4.2 - - - +
577D SER* 2.9 45.8 + - - +
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Residues in contact with MET 528 (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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512D LYS* 3.2 5.0 - - - -
513D LYS* 3.0 41.2 + - + +
526D TYR* 4.0 17.3 - - + -
527D GLN* 1.3 79.3 - - - +
529D ILE* 1.3 63.8 + - - +
530D LEU* 3.4 21.6 + - + +
542D LEU* 4.8 2.2 - - + -
574D ILE* 4.2 12.8 - - + -
575D VAL 3.5 4.3 - - - -
576D ALA* 3.9 11.9 - - + -
613D PHE* 3.4 49.1 - - + -
616D MET* 4.2 5.2 - - - +
618D PHE* 4.0 31.9 - - + -
619D VAL* 5.3 0.4 - - + -
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Residues in contact with ILE 529 (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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510D PRO* 3.8 16.4 - - + -
511D SER 3.4 2.9 - - - +
512D LYS* 3.8 35.2 - - + -
527D GLN* 4.4 10.1 - - - +
528D MET* 1.3 71.9 - - - +
530D LEU* 1.4 59.5 + - - +
562D ASN* 6.1 0.4 - - - +
564D ALA* 3.9 26.5 - - + +
565D THR* 4.7 3.6 - - - +
568D ALA* 3.6 25.4 - - + +
574D ILE* 3.6 5.2 - - - -
575D VAL* 2.9 42.6 + - + +
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Residues in contact with LEU 530 (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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510D PRO* 3.2 6.4 - - - +
511D SER* 2.6 48.8 + - - +
513D LYS* 4.2 26.5 - - + +
528D MET* 3.9 21.5 - - + +
529D ILE* 1.4 71.6 - - - +
531D PRO* 1.3 72.6 - - + +
534D PHE* 3.7 51.6 - - + -
568D ALA* 4.2 0.2 - - - -
574D ILE* 3.8 25.8 - - + -
618D PHE* 4.8 1.3 - - + -
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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