Contacts of the strand formed by residues 352 - 357 (chain B) 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 352 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146B LEU* 4.2 3.9 - - + +
149B ILE* 4.0 9.2 - - + -
150B THR* 3.0 35.5 - - + +
224B PHE 3.1 19.0 + - - +
225B LEU* 3.5 11.2 - - - +
226B GLY 3.3 5.0 + - - -
227B GLU* 2.7 45.2 + - - +
240B ALA 3.9 0.2 - - - +
241B ILE* 3.1 8.5 - - - +
242B GLY 3.1 36.7 + - - +
244B PRO* 4.4 0.4 - - - +
351B PHE* 1.3 78.2 - - - +
353B TYR* 1.3 61.3 + - - +
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Residues in contact with TYR 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B GLU 3.0 8.1 + - - +
228B GLU* 2.9 52.3 - - + +
229B ASN 3.1 2.4 + - - -
230B ARG* 4.0 8.1 - - - -
239B ALA* 3.8 21.0 - - + +
240B ALA 3.5 9.0 - - - -
241B ILE* 3.8 13.7 - - + -
301B ILE* 4.1 11.5 - - + +
351B PHE* 4.4 0.4 + - - -
352B ASN* 1.3 75.0 - - - +
354B VAL* 1.3 77.5 + - - +
355B ALA* 3.8 17.2 - - + +
363B PRO* 2.8 52.8 + - + +
364B TYR 3.9 11.7 - - - -
365B LEU* 3.7 20.3 - - + +
368B LEU* 4.0 15.0 - - + -
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Residues in contact with VAL 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ALA* 3.6 28.5 - - + +
145B GLN* 3.8 22.4 - - + -
146B LEU* 3.4 26.7 - - + -
149B ILE* 3.6 23.3 - - + -
229B ASN* 3.3 13.2 - - + +
231B VAL* 6.3 0.4 - - + -
238B VAL 4.0 0.7 - - - +
239B ALA* 3.7 1.9 - - - -
240B ALA* 3.1 30.7 + - + +
353B TYR* 1.3 85.4 - - - +
355B ALA* 1.3 60.6 + - - +
356B VAL* 5.0 3.6 - - + -
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Residues in contact with ALA 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B ASN 3.2 8.0 + - - +
230B ARG* 3.6 30.5 - - + +
231B VAL 3.1 23.8 + - - +
238B VAL 3.9 3.8 - - - -
239B ALA* 4.6 0.9 - - - +
353B TYR* 3.8 21.2 - - + +
354B VAL* 1.3 73.2 - - - +
356B VAL* 1.3 61.3 + - - +
359B VAL* 4.1 6.2 - - + +
362B LEU* 3.8 17.7 - - + -
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Residues in contact with VAL 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B PRO* 4.0 22.7 - - + +
141B SER* 4.5 7.9 - - - +
142B ALA* 3.9 33.4 - - + +
145B GLN* 5.5 0.4 - - + -
229B ASN 6.0 0.2 - - - +
231B VAL* 3.3 26.2 - - + +
233B PHE* 3.8 21.1 - - + -
236B ASP 4.8 0.2 - - - -
237B SER* 3.3 2.5 - - - -
238B VAL* 2.6 50.2 + - + +
354B VAL* 5.0 3.8 - - + -
355B ALA* 1.3 78.8 - - - +
357B GLY* 1.3 59.7 + - - +
362B LEU* 4.0 4.3 - - - +
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Residues in contact with GLY 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B VAL 3.0 9.7 + - - -
232B ARG* 3.8 7.4 - - - +
233B PHE* 3.5 38.5 + - - +
235B GLY 5.3 0.2 - - - -
236B ASP 4.2 3.8 - - - -
237B SER* 3.7 9.6 - - - -
355B ALA 4.1 0.4 + - - -
356B VAL* 1.3 76.0 - - - +
358B ASP* 1.3 57.0 + - - -
359B VAL* 2.8 14.7 + - - -
164M VAL* 4.6 4.0 - - - +
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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