Contacts of the strand formed by residues 238 - 245 (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 VAL 238 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B PRO* 3.7 32.3 - - + +
139B VAL* 4.4 10.1 - - + -
142B ALA* 4.4 4.4 - - + +
237B SER* 1.3 75.6 - - - +
239B ALA* 1.3 66.3 + - - +
240B ALA* 4.2 0.8 + - + -
288B PHE* 4.5 9.6 - - + -
289B VAL 3.2 27.1 - - - +
290B ARG* 3.7 18.4 - - + -
297B VAL* 4.2 1.1 - - - -
354B VAL 4.0 1.0 - - - +
355B ALA* 3.9 0.3 - - - -
356B VAL* 2.6 58.6 + - + +
362B LEU* 4.6 2.8 - - - +
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Residues in contact with ALA 239 (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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238B VAL* 1.3 73.5 - - - +
240B ALA* 1.3 59.8 + - - +
289B VAL* 2.7 40.6 + - + +
297B VAL* 3.8 17.6 - - + +
301B ILE* 3.6 27.3 - - + +
353B TYR* 3.8 20.4 - - - +
354B VAL 3.7 4.5 - - - -
355B ALA* 4.6 0.9 - - - +
362B LEU* 4.8 6.3 - - + -
363B PRO* 5.6 0.2 - - + -
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Residues in contact with ALA 240 (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* 4.5 3.6 - - + -
146B LEU* 4.5 1.1 - - + -
238B VAL* 4.2 0.9 + - + -
239B ALA* 1.3 75.3 - - - +
241B ILE* 1.3 67.7 + - - +
287B LEU 3.0 17.5 - - - +
288B PHE* 3.2 33.2 - - + -
301B ILE* 4.0 3.9 - - - +
353B TYR* 3.5 2.1 - - - -
354B VAL* 3.1 48.4 + - + +
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Residues in contact with ILE 241 (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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146B LEU* 4.0 5.4 - - - -
240B ALA* 1.3 79.2 - - - +
242B GLY* 1.3 58.8 - - - +
243B ILE* 5.3 4.9 - - + -
285B PHE* 3.5 8.3 - - + +
286B THR* 3.5 1.2 - - - -
287B LEU* 3.0 62.6 + - + +
301B ILE* 4.8 4.5 - - + -
304B ILE* 5.1 2.7 - - + -
305B VAL* 4.1 23.6 - - + -
308B LEU* 6.0 1.6 - - + -
348B LEU* 5.5 8.5 - - + -
351B PHE* 3.7 35.0 - - + -
352B ASN 3.1 14.4 - - - +
353B TYR* 3.8 17.3 - - + -
368B LEU* 5.5 0.2 - - + -
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Residues in contact with GLY 242 (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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146B LEU* 3.8 19.7 - - - +
150B THR* 4.9 0.9 - - - -
241B ILE* 1.3 73.5 - - - +
243B ILE* 1.3 63.5 + - - +
244B PRO* 4.0 0.8 - - - +
284B LEU* 4.3 10.3 - - - -
285B PHE 3.0 8.7 - - - -
286B THR* 4.6 0.2 - - - -
352B ASN* 3.1 41.9 + - - +
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Residues in contact with ILE 243 (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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225B LEU* 5.1 1.1 - - + -
241B ILE* 5.3 5.6 - - + -
242B GLY* 1.3 73.7 - - - +
244B PRO* 1.3 76.8 - - + +
245B VAL* 3.7 3.8 + - - +
253B TYR* 3.6 38.1 - - + +
284B LEU* 3.8 3.1 - - - +
285B PHE* 2.9 47.3 + - + +
346B PHE* 5.2 1.6 - - + -
348B LEU* 4.3 23.8 - - + -
349B GLY 5.9 1.3 - - - +
350B LYS 3.8 15.0 - - - +
351B PHE* 3.4 32.5 - - + +
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Residues in contact with PRO 244 (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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150B THR* 4.8 1.3 - - + -
151B PHE* 3.8 25.4 - - + -
223B PHE* 3.9 32.2 - - + +
224B PHE 4.6 2.7 - - - +
225B LEU* 3.6 31.2 - - + -
242B GLY 4.0 4.3 - - - +
243B ILE* 1.3 95.5 - - + +
245B VAL* 1.3 61.7 + - - +
253B TYR* 5.2 1.2 - - - -
283B GLY 3.3 7.9 - - - +
284B LEU* 3.6 9.4 - - + -
352B ASN* 4.4 5.6 - - - +
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Residues in contact with VAL 245 (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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220B GLU* 5.0 0.2 - - - +
223B PHE* 3.6 20.6 - - - -
243B ILE 3.7 9.6 - - - +
244B PRO* 1.3 78.2 - - - +
246B ASN* 1.3 71.4 + - - +
249B SER* 4.6 1.6 - - - -
250B LEU* 3.5 31.0 - - + +
253B TYR* 3.5 42.8 - - + -
276B LEU* 4.2 7.4 - - + -
282B GLY* 4.2 3.3 - - - -
283B GLY* 2.8 42.6 + - - +
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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