Contacts of the strand formed by residues 508 - 514 (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 PHE 508 (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* 4.4 10.5 - - + -
493A VAL* 4.0 4.7 - - + -
496A LEU* 3.2 44.4 - - + -
497A LEU* 3.6 39.9 - - + +
500A SER* 4.1 11.4 + - - -
505A ILE* 5.0 0.2 - - + -
506A PRO 4.3 3.8 - - - +
507A ASP* 1.3 74.2 - - - +
509A LEU* 1.3 68.3 + - - +
510A TYR* 4.1 22.4 - + + -
559A LYS* 3.9 10.0 + - - +
560A THR* 3.2 30.1 - - - +
562A VAL* 3.7 28.3 - - + -
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Residues in contact with LEU 509 (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* 3.8 50.9 - - + +
396A GLY* 5.8 0.2 - - - -
508A PHE* 1.3 79.6 - - - +
510A TYR* 1.3 71.2 + - - +
511A VAL* 3.7 26.0 - - + -
531A LYS* 4.0 20.0 - - + +
532A VAL* 4.8 2.9 - - + -
559A LYS* 4.4 3.6 - - + +
560A THR 3.1 9.1 + - - +
561A ILE* 3.4 15.7 - - + +
562A VAL 2.9 25.5 + - - +
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Residues in contact with TYR 510 (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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489A VAL* 5.2 0.8 - - + +
490A ARG* 4.0 11.0 - - + +
493A VAL* 3.7 42.4 - - + +
497A LEU* 5.6 10.1 - - + -
508A PHE* 4.1 14.8 - + + -
509A LEU* 1.3 83.7 - - - +
511A VAL* 1.3 63.7 + - - +
512A GLU* 2.4 43.8 + - + -
531A LYS* 6.1 0.7 - - - +
562A VAL* 3.3 21.3 - - + -
564A LEU* 3.3 25.5 - - + +
596A ILE* 6.0 0.7 - - + -
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Residues in contact with VAL 511 (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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509A LEU* 3.7 22.9 - - + -
510A TYR* 1.3 79.7 - - - +
512A GLU* 1.3 73.7 + - - +
513A ILE* 3.6 20.5 + - + -
528A LEU* 3.7 28.0 - - + -
531A LYS* 3.7 31.0 - - + -
532A VAL* 5.4 0.4 - - + +
561A ILE* 4.7 4.7 - - + -
562A VAL 3.2 6.9 + - - +
563A VAL* 3.9 5.4 - - + -
564A LEU* 2.8 30.8 + - - +
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Residues in contact with GLU 512 (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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490A ARG* 3.3 34.0 + - - +
510A TYR* 2.4 39.0 + - + -
511A VAL* 1.3 74.3 - - - +
513A ILE* 1.3 71.6 + - - +
514A ASN* 4.1 4.9 + - + +
518A MET* 5.4 1.0 - - - +
531A LYS* 6.0 1.4 - - - -
564A LEU* 3.3 19.1 - - - +
566A ASP* 4.9 6.9 - - - +
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Residues in contact with ILE 513 (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* 3.6 12.3 + - + -
512A GLU* 1.3 82.8 + - - +
514A ASN* 1.3 58.2 + - - +
518A MET* 4.1 9.6 - - + -
524A CYS* 3.9 26.9 - - + +
527A THR* 3.3 29.6 - - - +
528A LEU* 4.3 4.9 - - + +
563A VAL* 3.7 24.5 - - + -
564A LEU 2.8 17.9 + - - +
565A LEU* 3.9 19.5 - - + -
566A ASP* 2.5 36.8 + - - +
571A MET* 4.2 11.9 - - + -
582A PHE* 5.5 1.1 - - + -
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Residues in contact with ASN 514 (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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490A ARG* 6.2 0.4 - - - +
512A GLU* 4.1 5.7 + - + +
513A ILE* 1.3 75.8 - - - +
515A GLY* 1.3 71.7 + - - +
516A LEU 3.5 0.9 + - - -
517A LYS* 3.3 53.2 + - + +
518A MET* 3.3 25.9 + - - +
566A ASP* 3.5 19.5 + - + +
567A GLU* 2.9 22.9 - - - +
232D TYR* 3.6 19.4 + - - -
236D ASP* 4.7 0.6 + - - -
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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