Contacts of the strand formed by residues 560 - 566 (chain A) in PDB entry 5ZR1
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 THR 560 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467A ILE* 4.2 29.1 - - + +
470A ASP* 4.0 15.0 - - - +
471A SER 5.1 2.9 - - - +
506A PRO* 5.0 3.0 - - + +
507A ASP 3.1 19.0 + - - -
508A PHE* 3.2 13.4 - - - +
509A LEU* 3.1 22.7 + - - +
559A LYS* 1.3 76.6 - - - +
561A ILE* 1.3 61.6 + - - +
562A VAL* 5.8 1.1 - - - -
592A LYS* 3.5 38.2 - - + +
594A ILE* 6.1 2.2 - - + -
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Residues in contact with ILE 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A TYR* 4.4 10.1 - - + -
509A LEU* 3.4 15.5 - - + +
511A VAL* 4.7 12.3 - - + -
528A LEU* 4.8 6.3 - - + -
532A VAL* 3.7 21.5 - - + -
549A TYR* 3.6 37.5 - - + +
550A PHE* 4.2 8.7 - - + -
559A LYS 3.6 7.0 - - - +
560A THR* 1.3 80.7 - - - +
562A VAL* 1.3 65.4 + - - +
563A VAL* 4.3 11.0 - - + +
592A LYS 3.0 11.6 + - - +
593A LEU* 3.4 19.4 - - + +
594A ILE* 2.9 26.3 + - - +
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Residues in contact with VAL 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A ALA* 6.0 2.2 - - + -
467A ILE* 4.1 21.8 - - + -
493A VAL* 4.2 16.8 - - + -
496A LEU* 5.1 2.0 - - + -
508A PHE* 3.7 31.4 - - + -
509A LEU 2.9 8.8 + - - -
510A TYR* 3.3 14.4 - - + -
511A VAL 3.2 19.9 + - - -
560A THR* 5.8 0.4 - - - -
561A ILE* 1.3 75.9 - - - +
563A VAL* 1.3 59.0 + - - +
594A ILE* 3.4 24.2 - - + +
596A ILE* 4.1 25.8 - - + -
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Residues in contact with VAL 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511A VAL* 3.5 9.9 - - + +
513A ILE* 3.7 28.5 - - + -
528A LEU* 3.9 26.7 - - + -
561A ILE* 3.8 2.6 - - + -
562A VAL* 1.3 74.7 - - - +
564A LEU* 1.3 64.6 + - - +
565A LEU* 4.0 6.6 + - + -
582A PHE* 4.5 10.5 - - + -
593A LEU* 3.8 17.9 - - + -
594A ILE 3.0 9.0 + - - +
595A VAL* 3.5 28.4 - - + -
596A ILE* 3.0 26.6 + - - +
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Residues in contact with LEU 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486A THR* 5.2 4.5 - - + -
489A VAL* 3.7 30.1 - - + -
490A ARG* 4.8 7.2 - - + +
510A TYR* 3.3 18.6 - - + +
511A VAL 2.8 15.3 + - - +
512A GLU* 3.3 32.5 - - - +
513A ILE* 2.8 35.0 + - - +
562A VAL 4.0 0.6 + - - -
563A VAL* 1.3 72.0 - - - +
565A LEU* 1.3 58.4 + - - +
566A ASP* 3.2 15.4 + - + +
596A ILE* 3.3 22.2 - - + +
598A VAL* 3.7 20.9 - - + -
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Residues in contact with LEU 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513A ILE* 3.6 28.3 - - + -
563A VAL* 3.9 5.1 - - + -
564A LEU* 1.3 68.4 - - - +
566A ASP* 1.3 64.1 + - - +
568A LEU* 3.9 31.5 - - + +
571A MET* 4.2 9.2 - - + -
578A ILE 5.5 0.4 - - - +
579A MET* 6.0 0.7 - - - -
582A PHE* 3.6 59.9 - - + -
583A PHE* 4.7 5.6 - - + -
595A VAL* 3.7 19.7 - - + -
596A ILE 3.0 12.4 + - - +
597A ALA* 3.8 4.6 - - + -
598A VAL* 3.3 23.4 + - - +
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Residues in contact with ASP 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486A THR* 3.3 34.1 + - - +
490A ARG* 5.0 1.9 + - - -
512A GLU* 4.9 5.9 - - - +
513A ILE 2.5 17.6 + - - +
514A ASN* 4.0 16.9 + - + +
515A GLY* 2.9 29.8 + - - -
564A LEU* 3.2 12.2 + - + +
565A LEU* 1.3 73.5 - - - +
567A GLU* 1.3 84.0 + - - +
571A MET* 4.1 1.9 - - - +
598A VAL* 3.3 25.1 - - + +
2001A AGS 5.1 1.0 + - - -
2002A MG 4.0 2.6 - - - -
232D TYR* 5.4 0.3 + - - -
267D ARG* 5.8 0.2 + - - -
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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