Contacts of the strand formed by residues 325 - 333 (chain A) in PDB entry 1KYO
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 GLY 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A PHE* 3.5 8.7 - - - -
265A GLU* 3.7 2.6 - - - -
266A GLY* 2.8 24.6 + - - -
267A GLU 3.9 6.3 - - - -
319A LEU 3.1 15.5 - - - -
321A TYR* 4.4 5.6 - - - -
324A SER* 1.3 83.7 + - - +
326A LEU* 1.3 72.9 + - - +
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Residues in contact with LEU 326 (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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163A LEU* 4.0 22.0 - - + -
164A HIS* 3.4 44.0 - - + +
167A ALA* 3.8 6.5 - - + -
168A PHE* 3.6 16.8 - - + -
243A PHE* 3.6 29.4 - - + -
263A ALA* 4.1 13.2 - - + -
264A VAL 3.4 4.0 - - - +
266A GLY* 3.8 1.7 - - - -
317A PHE* 3.5 11.8 - - + -
318A SER* 4.7 0.2 - - - -
319A LEU* 2.9 39.6 + - + +
321A TYR* 5.3 0.4 - - + -
325A GLY* 1.3 81.3 - - - +
327A TRP* 1.3 60.3 + - - +
328A GLY 4.1 0.2 - - - -
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Residues in contact with TRP 327 (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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263A ALA* 3.1 2.2 - - - -
264A VAL* 2.6 47.8 + - + +
266A GLY* 3.8 13.3 - - - +
277A ALA* 3.0 28.2 + - + -
280A ALA* 3.6 13.9 - - + +
281A ALA* 3.5 28.7 - - + +
284A PHE* 4.1 15.5 - + - -
316A HIS* 4.5 2.9 - - + -
317A PHE 3.8 7.2 - - - -
318A SER* 3.7 16.6 - - - +
326A LEU* 1.3 71.7 - - - +
328A GLY* 1.3 62.7 + - - +
350A TRP* 3.7 43.4 - + - -
353A LEU* 4.3 2.0 - - + -
420A TRP* 3.5 27.6 - + + -
425A LEU* 3.8 27.4 - - + -
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Residues in contact with GLY 328 (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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262A LEU 3.1 12.8 - - - -
263A ALA* 3.7 1.8 - - - -
316A HIS* 3.3 7.9 + - - +
317A PHE* 3.0 37.5 + - - +
327A TRP* 1.3 88.0 - - - +
329A PHE* 1.3 61.7 + - - -
350A TRP* 3.7 10.1 - - - -
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Residues in contact with PHE 329 (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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260A ILE* 4.4 0.6 - - + +
261A SER* 3.5 1.6 - - - -
262A LEU* 2.8 49.7 + - + +
301A LEU* 6.5 0.2 - - + -
314A PHE* 3.9 16.4 - + + -
315A ASN 3.3 11.7 - - - +
316A HIS* 3.6 25.6 - + + +
317A PHE* 3.8 5.9 - - - -
328A GLY* 1.3 76.0 - - - +
330A SER* 1.3 77.6 + - - +
331A THR* 3.5 31.0 - - + -
342A LEU* 4.8 7.2 - - + -
343A ILE* 4.5 13.5 - - + -
346A THR* 3.6 32.3 - - + -
347A LEU* 4.5 5.8 - - + -
350A TRP* 3.4 21.8 - + - -
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Residues in contact with SER 330 (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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156A PRO 5.6 2.9 - - - -
160A LEU* 4.0 12.8 - - - +
260A ILE 3.6 6.5 - - - -
261A SER* 3.0 20.0 + - - -
314A PHE* 3.2 0.9 - - - -
315A ASN* 2.9 48.3 + - - -
317A PHE* 3.1 19.6 - - - -
329A PHE* 1.3 77.0 - - - +
331A THR* 1.3 65.4 + - - +
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Residues in contact with THR 331 (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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258A ALA 3.8 0.9 - - - +
259A TRP* 3.4 5.2 - - - +
260A ILE* 2.8 63.4 + - + +
311A CYS* 3.8 6.6 - - - +
313A ASN* 2.9 16.8 + - - +
314A PHE* 3.8 4.1 - - - +
315A ASN* 5.3 0.2 - - - -
329A PHE* 3.5 26.7 - - + -
330A SER* 1.3 78.4 - - - +
332A ALA* 1.3 63.9 + - - +
333A THR* 5.7 1.3 - - + -
342A LEU* 3.7 23.4 - - + +
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Residues in contact with ALA 332 (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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257A LYS* 4.5 11.7 - - + +
258A ALA 3.7 4.9 - - - -
259A TRP* 3.6 28.9 - - + +
311A CYS* 3.4 1.9 - - - +
312A ASP* 2.8 31.6 + - + -
313A ASN* 2.9 32.1 + - - +
331A THR* 1.3 78.2 + - - +
333A THR* 1.3 54.5 + - - +
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Residues in contact with THR 333 (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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257A LYS* 3.4 6.7 - - - +
258A ALA* 3.1 47.1 + - + +
260A ILE* 5.3 4.0 - - + -
310A LEU 3.2 27.0 + - - +
311A CYS* 3.6 7.7 - - - +
312A ASP* 4.1 3.1 - - - +
331A THR* 5.2 0.7 - - + +
332A ALA* 1.3 77.1 - - - +
334A ARG* 1.3 65.1 + - - +
335A ASN* 2.8 19.8 + - - +
336A VAL* 4.7 0.7 - - - +
339A ILE* 4.3 20.4 - - + -
342A LEU* 4.7 11.0 - - + -
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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