Contacts of the strand formed by residues 313 - 320 (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 ASN 313 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A LYS* 4.8 5.2 + - - -
287A TYR* 3.1 24.5 - - - +
288A ASN* 4.0 10.0 + - + +
311A CYS* 3.4 4.6 - - - -
312A ASP* 1.3 98.5 - - - +
314A PHE* 1.3 61.2 + - - +
315A ASN* 4.9 6.4 + - - +
331A THR* 2.9 19.7 + - - +
332A ALA* 2.9 35.4 + - - +
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Residues in contact with PHE 314 (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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284A PHE 3.5 24.7 - - - -
286A SER* 3.6 4.6 - - - -
287A TYR* 2.7 77.7 + + + +
299A ILE* 4.9 3.6 - - + -
301A LEU* 4.1 22.4 - - + -
302A LEU* 4.2 17.5 - - + -
305A ILE* 4.5 7.4 - - + -
311A CYS* 3.8 13.7 - - - -
313A ASN* 1.3 75.1 - - - +
315A ASN* 1.3 64.6 - - - +
316A HIS* 3.8 20.6 - + - -
329A PHE* 3.9 10.8 - + + -
330A SER 3.2 13.2 - - - +
331A THR* 3.8 11.0 - - - +
342A LEU* 5.5 2.7 - - + -
346A THR* 6.2 0.2 - - - -
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Residues in contact with ASN 315 (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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160A LEU* 6.0 1.8 - - - +
285A GLY 3.5 7.2 - - - -
286A SER* 3.5 15.9 - - - +
313A ASN* 4.9 7.6 + - - +
314A PHE* 1.3 81.4 + - - +
316A HIS* 1.3 65.4 + - - +
317A PHE* 4.0 9.5 - - - +
329A PHE* 3.3 1.7 - - - -
330A SER* 2.9 47.3 + - - +
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Residues in contact with HIS 316 (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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281A ALA* 3.4 29.4 - - + +
284A PHE* 3.4 32.4 - + + +
285A GLY* 2.8 32.4 + - - +
286A SER* 5.7 0.3 - - - -
301A LEU* 4.7 6.2 - - + +
314A PHE* 3.8 19.1 - + - -
315A ASN* 1.3 79.9 - - - +
317A PHE* 1.3 61.7 + - - +
327A TRP* 4.5 3.6 - - + -
328A GLY 3.3 7.6 + - - +
329A PHE* 3.6 23.8 - + + +
346A THR* 4.3 4.5 - - + -
350A TRP* 3.0 35.5 + + - -
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Residues in contact with PHE 317 (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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160A LEU* 4.2 21.1 - - + -
163A LEU* 4.3 11.7 - - + -
261A SER* 5.3 0.2 - - - -
263A ALA* 4.0 7.4 - - + -
281A ALA* 3.6 12.4 - - - +
315A ASN* 4.0 15.9 - - - +
316A HIS* 1.3 74.2 - - - +
318A SER* 1.3 62.7 + - - +
319A LEU* 3.8 28.7 - - + -
326A LEU* 3.5 20.0 - - + -
327A TRP* 3.8 3.5 - - - -
328A GLY* 3.0 33.3 + - - +
329A PHE 3.8 14.8 - - - -
330A SER* 3.1 34.3 - - - -
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Residues in contact with SER 318 (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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266A GLY* 5.9 0.3 - - - -
267A GLU* 5.3 4.7 + - - +
274A TYR 4.9 0.5 + - - -
277A ALA* 3.5 24.7 - - - +
278A LYS* 3.1 54.1 + - - +
281A ALA* 4.3 2.9 - - - +
317A PHE* 1.3 75.9 - - - +
319A LEU* 1.3 66.0 + - - +
320A SER* 3.5 7.8 + - - -
326A LEU 3.8 4.9 - - - -
327A TRP* 3.7 13.9 - - - +
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Residues in contact with LEU 319 (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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160A LEU* 4.6 14.6 - - + -
164A HIS* 4.0 26.5 - - + +
266A GLY* 5.1 0.2 - - - -
267A GLU 3.7 4.5 + - - +
317A PHE* 3.8 37.9 - - + -
318A SER* 1.3 74.9 - - - +
320A SER* 1.3 59.0 + - - +
321A TYR* 4.1 18.4 - - + +
325A GLY* 3.1 6.2 - - - -
326A LEU* 2.9 43.8 + - + +
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Residues in contact with SER 320 (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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99A ASP* 4.8 0.3 - - - +
267A GLU* 3.0 21.3 + - - +
269A VAL* 3.9 15.3 - - - +
274A TYR* 3.3 37.7 + - - -
278A LYS* 4.7 2.3 - - - +
318A SER* 3.5 14.3 + - - -
319A LEU* 1.3 74.4 - - - +
321A TYR* 1.3 72.5 + - - +
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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