Contacts of the strand formed by residues 356 - 362 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183E HIS* 5.3 1.7 + - - -
187E THR* 3.7 23.2 + - + +
191E ILE* 4.5 4.7 - - + -
265E LYS* 5.7 0.2 - - + -
266E TRP* 4.0 21.8 + - - +
296E ALA* 3.9 18.4 - - + -
297E GLU 3.8 23.8 - - - +
298E CYS* 4.6 4.4 - - - +
352E ASN* 3.1 1.3 - - - -
353E ALA* 2.7 42.8 + - - +
354E PHE 3.8 4.3 + - - -
355E ASN* 1.3 79.0 - - - +
357E TYR* 1.3 64.3 + - - +
358E ILE* 4.0 1.7 + - - +
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Residues in contact with TYR 357 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295E VAL 3.2 5.7 - - - +
296E ALA* 3.3 2.9 - - - -
297E GLU 2.8 38.5 + - - +
299E ILE* 3.6 46.4 - - + -
349E VAL* 3.9 25.1 - - + -
350E HIS 4.1 2.9 - - - -
351E CYS 3.7 5.4 - - - -
352E ASN* 3.5 35.5 + - + -
355E ASN* 4.0 17.0 - - - -
356E THR* 1.3 74.8 - - - +
358E ILE* 1.3 62.1 + - - +
359E MET* 3.9 2.7 + - + +
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Residues in contact with ILE 358 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E ILE* 3.5 47.3 - - + -
195E TYR* 3.6 39.9 - - + -
263E PHE* 4.7 7.4 - - + -
294E ILE* 3.8 17.0 - - + -
295E VAL 3.5 0.9 - - - +
296E ALA* 3.7 19.7 - - + -
349E VAL* 3.7 0.9 - - - +
350E HIS* 2.7 39.8 + - + +
351E CYS* 3.1 18.0 + - - +
353E ALA* 5.6 1.6 - - + +
356E THR* 4.9 2.9 - - + +
357E TYR* 1.3 74.0 - - - +
359E MET* 1.3 58.9 + - - +
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Residues in contact with MET 359 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294E ILE* 3.4 7.3 - - - +
295E VAL* 2.8 45.3 + - + +
297E GLU* 4.1 17.0 - - + +
299E ILE* 3.8 21.8 - - + -
332E GLN* 5.7 0.2 - - - -
335E PHE* 3.7 61.2 - - + -
347E PHE* 3.8 18.4 - - + -
348E LYS 3.2 7.9 - - - +
349E VAL* 4.1 18.2 - - + -
357E TYR* 4.4 2.0 - - + +
358E ILE* 1.3 78.9 - - - +
360E GLU* 1.3 65.9 + - - +
361E PHE* 4.3 7.2 - - + -
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Residues in contact with GLU 360 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E TYR* 2.5 38.0 + - + +
197E GLY* 4.1 3.6 - - - -
292E LYS* 3.5 28.3 - - + +
293E VAL 3.4 5.2 - - - +
294E ILE* 4.9 1.8 - - + -
347E PHE* 3.4 6.4 - - - -
348E LYS* 2.8 36.5 + - + +
350E HIS* 3.2 31.1 + - + +
359E MET* 1.3 78.5 - - - +
361E PHE* 1.3 65.5 + - - +
362E LEU* 3.6 22.8 + - + +
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Residues in contact with PHE 361 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268E CYS* 5.6 1.6 - - - -
280E LEU* 4.1 30.1 - - + -
292E LYS* 3.3 5.2 - - - -
293E VAL* 2.9 41.0 + - + +
295E VAL* 3.9 28.5 - - + -
335E PHE* 3.6 29.8 - + - -
338E LEU* 4.6 1.8 - - + -
339E ALA* 3.7 30.1 - - + -
344E PHE* 3.3 26.4 - + + -
346E GLY 3.7 5.2 - - - -
347E PHE* 3.6 25.6 - + - -
359E MET* 4.3 8.3 - - + -
360E GLU* 1.3 76.9 - - - +
362E LEU* 1.3 60.7 + - - +
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Residues in contact with LEU 362 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291E GLY 4.2 2.2 - - - +
292E LYS* 3.3 38.4 - - + -
344E PHE* 3.3 5.5 - - - +
345E GLN 2.9 23.2 + - - -
346E GLY* 2.9 30.1 + - - +
347E PHE 5.1 0.7 - - - +
348E LYS* 4.9 11.0 - - + -
360E GLU* 3.6 24.7 - - + +
361E PHE* 1.3 73.7 - - - +
363E LYS* 1.3 62.3 + - - +
364E LYS* 4.3 1.8 - - + -
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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