Contacts of the strand formed by residues 356 - 361 (chain A) in PDB entry 1KYZ
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 356 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A HIS* 5.5 1.0 + - - -
187A THR* 3.9 23.7 + - + +
191A ILE* 4.5 4.7 - - + -
266A TRP* 4.0 17.6 + - + +
296A ALA* 3.9 15.7 - - + -
297A GLU* 3.7 26.7 - - - +
298A CYS* 4.6 5.5 - - - -
352A ASN* 3.1 1.9 - - - -
353A ALA* 2.5 45.4 + - - +
354A PHE 3.9 4.3 + - - -
355A ASN* 1.3 80.9 + - - +
357A TYR* 1.3 63.5 + - - +
358A ILE* 4.8 1.4 - - - +
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Residues in contact with TYR 357 (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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295A VAL 3.3 3.6 - - - +
296A ALA* 3.4 2.9 - - - -
297A GLU 2.8 34.9 + - - +
299A ILE* 3.6 50.3 - - + -
313A VAL* 6.4 0.2 - - + -
349A VAL* 4.0 22.9 - - + -
350A HIS 4.3 6.5 - - - -
352A ASN* 3.3 41.5 + - + +
355A ASN* 4.3 17.7 - - - -
356A THR* 1.3 74.7 - - - +
358A ILE* 1.3 62.2 + - - +
359A MET* 4.0 2.9 + - + +
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Residues in contact with ILE 358 (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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191A ILE* 3.6 48.5 - - + -
194A THR* 5.5 1.8 - - - +
195A TYR* 3.7 42.2 - - + -
263A PHE* 4.7 6.7 - - + -
294A ILE* 3.9 15.7 - - + -
295A VAL 3.4 1.6 - - - +
296A ALA* 3.7 20.0 - - + -
349A VAL* 3.7 1.0 - - - +
350A HIS* 2.7 35.9 + - + +
351A CYS 3.2 17.7 + - - +
353A ALA 5.4 1.3 - - - +
356A THR* 4.8 2.7 - - + +
357A TYR* 1.3 76.2 - - - +
359A MET* 1.3 58.4 + - - +
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Residues in contact with MET 359 (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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294A ILE* 3.6 2.1 - - - -
295A VAL* 2.7 53.7 + - + +
297A GLU* 4.2 14.6 - - + +
299A ILE* 3.9 26.5 - - + -
335A PHE* 3.5 51.1 - - + -
347A PHE* 3.6 31.2 - - + -
348A LYS 3.1 17.3 - - - +
349A VAL* 4.0 9.4 - - + -
350A HIS* 4.3 0.9 - - - +
357A TYR 4.7 1.6 - - - +
358A ILE* 1.3 79.5 - - - +
360A GLU* 1.3 56.4 + - - +
361A PHE* 4.2 1.8 - - + -
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Residues in contact with GLU 360 (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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195A TYR* 3.3 15.6 + - - +
197A GLY* 5.5 0.7 - - - -
292A LYS* 3.0 37.0 + - + +
293A VAL 3.0 9.6 - - - +
294A ILE* 4.8 1.6 - - - -
346A GLY 4.5 0.2 - - - -
347A PHE* 3.5 7.8 - - - -
348A LYS* 2.9 52.3 + - + +
350A HIS* 2.8 34.5 + - + +
359A MET* 1.3 73.3 - - - +
361A PHE* 1.3 67.6 + - - +
362A LEU 4.0 4.9 + - - -
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Residues in contact with PHE 361 (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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268A CYS* 5.7 2.5 - - - -
280A LEU* 4.0 25.8 - - + -
292A LYS* 2.8 23.0 - - - +
293A VAL* 2.7 34.1 + - + -
295A VAL* 3.5 32.3 - - + -
335A PHE* 3.6 29.2 - + - -
338A LEU* 4.7 1.1 - - + -
339A ALA* 3.7 30.5 - - + -
344A PHE* 3.5 19.6 - + + -
346A GLY 3.8 3.4 - - - -
347A PHE* 3.6 24.2 - + - -
359A MET* 4.2 4.5 - - + -
360A GLU* 1.3 78.9 - - - +
362A LEU* 1.3 69.8 + - - +
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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