Contacts of the helix formed by residues 260 - 269 (chain C) in PDB entry 4KYI
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 SER 260 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123C ASP* 4.2 4.0 + - - -
210C ASN* 3.6 22.9 - - - +
212C ARG* 3.4 27.2 - - - +
213C LEU 3.2 13.9 + - - -
214C THR* 4.0 0.2 - - - +
215C LEU* 4.1 0.2 - - - +
259C GLN* 1.3 75.1 - - - +
261C ILE* 1.3 65.6 + - - +
262C ALA* 3.6 9.0 + - - +
263C GLN* 3.6 27.0 + - - +
264C VAL* 3.2 21.3 - - - +
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Residues in contact with ILE 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C SER* 4.5 0.7 - - - +
84C VAL* 6.0 0.7 - - + -
126C TYR* 3.5 35.0 - - + +
130C MET* 4.5 5.4 - - - -
213C LEU* 2.9 26.6 + - + +
214C THR 3.3 25.8 - - - +
215C LEU* 3.9 11.2 - - + +
218C LEU* 3.6 30.5 - - + -
236C LEU* 4.0 25.8 - - + -
260C SER* 1.3 69.9 - - - +
262C ALA* 1.3 66.7 + - - +
263C GLN 3.2 0.9 + - - -
264C VAL* 3.4 3.1 + - - +
265C VAL* 3.1 28.6 + - + +
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Residues in contact with ALA 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ARG* 3.3 38.1 - - + +
122C LEU* 3.5 18.3 - - + +
123C ASP* 3.4 30.2 + - - +
126C TYR* 3.5 11.0 - - + -
260C SER* 3.5 2.2 + - - +
261C ILE* 1.3 78.0 - - - +
263C GLN* 1.3 62.3 + - - +
265C VAL 4.1 0.2 - - - -
266C GLN* 3.4 16.6 + - - +
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Residues in contact with GLN 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C ARG* 4.0 17.6 - - + +
198C THR* 5.3 14.5 + - - +
212C ARG* 5.8 0.9 - - - -
259C GLN* 3.7 19.0 + - - +
260C SER* 3.6 32.6 + - - +
261C ILE 3.2 0.6 - - - -
262C ALA* 1.3 81.1 - - - +
264C VAL* 1.3 57.8 + - - +
266C GLN* 3.9 3.1 - - - +
267C TRP* 3.2 68.2 + - + +
279C ARG 5.0 2.8 + - - -
280C ASN* 5.3 2.2 - - - +
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Residues in contact with VAL 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C LEU* 4.7 5.8 - - + -
238C VAL* 3.6 24.1 - - + +
240C VAL* 3.9 12.6 - - + -
251C TYR* 3.4 31.9 - - + -
259C GLN* 3.5 26.7 - - + -
260C SER 3.2 19.3 - - - +
261C ILE 3.4 3.2 + - - +
263C GLN* 1.3 76.8 - - + +
265C VAL* 1.3 61.6 + - - +
266C GLN 3.3 0.7 - - - -
267C TRP* 3.6 12.5 - - + +
268C SER* 2.9 28.6 + - - -
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Residues in contact with VAL 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C SER 4.8 0.4 - - - +
76C ALA* 3.7 14.1 - - + +
77C MET* 3.5 37.9 - - + +
80C SER* 3.9 11.2 - - - +
118C PHE* 4.3 6.3 - - + -
122C LEU* 3.7 20.6 - - + -
126C TYR* 3.4 17.7 - - - +
236C LEU* 5.2 0.2 - - + -
238C VAL* 4.5 11.0 - - + -
261C ILE* 3.1 22.1 + - + +
264C VAL* 1.3 76.5 - - + +
266C GLN* 1.3 62.2 + - - +
268C SER* 3.6 1.6 + - - -
269C GLY* 3.2 19.4 + - - -
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Residues in contact with GLN 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C ARG 4.1 4.9 + - - -
115C GLY* 3.3 43.5 - - - +
116C ASP* 5.6 0.3 - - - -
118C PHE* 3.8 27.7 - - + -
119C ARG* 4.1 13.8 + - + +
122C LEU* 4.0 1.2 - - + +
262C ALA 3.4 16.3 + - - +
263C GLN* 3.9 3.7 - - - +
264C VAL 3.3 0.4 - - - -
265C VAL* 1.3 77.5 - - - +
267C TRP* 1.3 81.3 + - - +
269C GLY 3.5 1.6 + - - -
270C ALA* 3.0 41.9 + - - +
275C PHE* 4.5 5.7 - - + -
276C VAL 5.0 3.8 + - - -
278C GLY* 5.8 3.2 - - - +
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Residues in contact with TRP 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C VAL* 4.0 3.4 - - + -
251C TYR* 3.9 11.9 - + - -
259C GLN* 3.9 19.3 - - - -
263C GLN* 3.2 53.5 + - + +
264C VAL* 3.6 23.1 - - + +
265C VAL 3.3 0.2 - - - -
266C GLN* 1.3 93.9 + - - +
268C SER* 1.3 57.9 + - - +
270C ALA* 2.9 21.0 + - + +
278C GLY* 4.1 22.7 - - - -
279C ARG 3.8 19.0 + - - -
280C ASN* 3.6 21.5 - - + -
286C ILE* 3.6 43.7 - - + -
287C ALA 3.0 21.5 - - - +
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Residues in contact with SER 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C GLY 4.4 0.2 + - - -
72C ALA* 3.3 6.1 - - - -
73C SER* 2.8 29.1 + - - -
76C ALA* 3.7 15.6 - - - +
238C VAL* 5.1 1.8 - - - -
239C VAL 2.8 25.9 + - - -
240C VAL* 3.7 10.1 - - - +
264C VAL 2.9 17.3 + - - -
265C VAL 4.0 0.4 - - - -
267C TRP* 1.3 76.5 - - - +
269C GLY* 1.3 57.3 + - - +
288C ASP* 2.9 24.8 - - - +
289C GLY 3.0 7.8 + - - +
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Residues in contact with GLY 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C SER* 3.9 18.8 + - - -
74C ALA* 4.8 0.9 - - - -
118C PHE* 5.7 5.6 - - - -
265C VAL 3.2 14.7 + - - -
266C GLN* 3.6 3.4 - - - -
267C TRP 3.1 0.6 - - - -
268C SER* 1.3 76.9 - - - +
270C ALA* 1.3 58.6 + - - +
271C HIS* 3.2 7.8 + - - +
275C PHE* 3.9 14.5 - - - -
288C ASP* 4.1 5.9 - - - +
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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