Contacts of the strand formed by residues 352 - 357 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146M LEU* 4.3 3.4 - - + +
149M ILE* 4.0 11.2 - - + -
150M THR* 3.1 38.2 - - + +
224M PHE 3.3 13.2 + - - +
225M LEU* 3.7 13.9 - - - +
226M GLY 3.2 7.2 + - - -
227M GLU* 2.8 43.6 + - - +
240M ALA 3.8 0.2 - - - +
241M ILE* 3.0 9.4 - - - +
242M GLY* 2.9 37.8 + - - +
244M PRO* 4.3 0.8 - - - +
351M PHE* 1.3 78.0 - - - +
353M TYR* 1.3 61.4 + - - +
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Residues in contact with TYR 353 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227M GLU 2.9 10.6 + - - +
228M GLU* 3.1 45.8 - - + +
229M ASN 3.1 4.0 + - - -
230M ARG* 4.0 5.6 - - - -
239M ALA* 4.2 23.1 - - + +
240M ALA 3.5 12.3 - - - -
241M ILE* 4.1 9.2 - - + -
301M ILE* 4.4 10.3 - - + +
351M PHE* 3.9 13.9 + - + -
352M ASN* 1.3 74.1 - - - +
354M VAL* 1.3 65.1 + - - +
355M ALA* 4.0 14.7 - - + +
363M PRO* 2.7 49.3 + - + +
364M TYR* 3.5 15.7 - - - -
365M LEU* 3.8 15.0 - - + +
368M LEU* 3.9 15.9 - - + -
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Residues in contact with VAL 354 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142M ALA* 3.7 28.7 - - + +
145M GLN* 4.0 17.0 - - + -
146M LEU* 3.2 34.3 - - + +
149M ILE* 3.6 16.4 - - + -
229M ASN* 3.2 21.1 - - + +
231M VAL* 6.0 0.2 - - + -
238M VAL 3.9 1.7 - - - +
239M ALA* 3.6 1.0 - - - -
240M ALA* 2.9 38.1 + - + +
353M TYR* 1.3 79.7 - - - +
355M ALA* 1.3 60.9 + - - +
356M VAL* 4.0 4.9 + - + -
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Residues in contact with ALA 355 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229M ASN 3.3 6.1 + - - +
230M ARG* 3.4 27.6 - - + +
231M VAL 3.0 23.0 + - - -
238M VAL 3.5 4.5 - - - -
239M ALA* 4.3 1.3 - - - +
353M TYR* 4.0 20.5 + - + +
354M VAL* 1.3 73.2 - - - +
356M VAL* 1.3 62.2 + - - +
359M VAL* 3.6 6.4 - - + +
362M LEU* 3.7 20.6 - - + -
363M PRO 4.3 1.3 - - - +
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Residues in contact with VAL 356 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138M PRO* 4.4 10.1 - - + +
141M SER* 4.4 9.4 - - - +
142M ALA* 4.1 29.6 - - + -
145M GLN* 5.5 0.2 - - + -
231M VAL* 3.4 30.5 - - + +
233M PHE* 3.8 24.2 - - + -
236M ASP 5.0 0.2 - - - -
237M SER* 3.3 1.2 - - - -
238M VAL* 2.6 54.2 + - + +
354M VAL* 4.9 5.4 - - + -
355M ALA* 1.3 80.2 - - - +
357M GLY* 1.3 62.9 + - - +
359M VAL* 4.7 0.4 - - - -
362M LEU* 3.7 6.0 - - - +
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Residues in contact with GLY 357 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B VAL* 5.2 2.3 - - - +
231M VAL 3.1 6.7 + - - -
232M ARG* 3.9 1.2 - - - -
233M PHE* 3.4 39.1 + - - +
236M ASP 4.3 3.1 - - - -
237M SER* 3.7 12.1 - - - -
356M VAL* 1.3 78.5 - - - +
358M ASP* 1.3 55.8 + - - -
359M VAL* 2.6 22.7 + - - +
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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