Contacts of the helix formed by residues 187 - 197 (chain O) 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 GLY 187 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181O VAL* 3.3 31.2 - - - -
184O ARG* 3.8 6.1 + - - -
185O HIS 3.1 7.7 + - - -
186O GLY* 1.3 73.5 - - - +
188O CYS* 1.3 65.3 + - - -
190O TYR* 2.9 2.7 + - - +
191O ILE* 2.8 31.4 + - - +
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Residues in contact with CYS 188 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76O TRP* 3.4 30.3 - - + +
78O HIS* 3.5 17.0 - - + -
79O ASN* 5.8 1.1 - - - +
181O VAL* 4.3 6.8 - - - +
186O GLY 3.0 2.0 + - - +
187O GLY* 1.3 69.0 - - - +
189O ASP* 1.3 63.6 + - - +
191O ILE* 4.6 0.4 - - - -
192O PHE* 2.9 27.0 + - - +
252O THR* 3.5 19.1 - - - +
256O ASN* 2.8 43.1 - - - -
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Residues in contact with ASP 189 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71O ALA* 3.9 7.1 - - + +
72O PRO 3.1 22.8 - - - +
73O ALA* 3.2 22.1 - - - +
74O TYR* 3.0 17.4 + - - +
76O TRP* 2.6 33.5 + - - +
79O ASN* 5.5 0.9 - - - +
186O GLY* 3.0 14.1 + - - +
188O CYS* 1.3 77.6 - - - +
190O TYR* 1.3 57.4 - - - +
192O PHE* 3.8 1.7 - - - +
193O SER* 2.9 34.8 + - - -
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Residues in contact with TYR 190 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69O LEU 5.8 1.1 - - - -
71O ALA* 3.7 15.6 - - + +
184O ARG* 3.8 29.1 + - + -
185O HIS 3.1 24.9 - - - +
186O GLY* 3.6 3.6 + - - -
187O GLY 2.9 8.8 + - - +
189O ASP* 1.3 72.5 - - - +
191O ILE* 1.3 86.1 + - + +
193O SER* 3.9 0.9 - - - -
194O LEU* 3.0 37.6 + - + +
217O TYR* 3.5 34.5 - - + -
218O PHE* 3.5 17.7 - - - -
219O PRO* 4.2 7.9 - - + +
523O HEC 2.6 28.8 + - - -
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Residues in contact with ILE 191 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180O ILE* 3.9 26.9 - - + +
181O VAL* 4.4 11.2 - - + -
184O ARG* 4.9 0.2 - - + -
187O GLY* 2.8 27.3 + - - +
188O CYS 3.8 3.1 - - - +
190O TYR* 1.3 90.9 - - + +
192O PHE* 1.3 61.6 + - - +
194O LEU* 3.2 5.5 + - - +
195O LEU* 3.1 30.8 + - + +
252O THR* 3.2 29.8 - - + +
255O LEU* 4.7 13.0 - - + -
523O HEC 3.4 31.6 - - + +
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Residues in contact with PHE 192 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74O TYR* 3.4 39.9 - + - -
76O TRP* 3.8 18.6 - + + -
188O CYS 2.9 18.0 + - - +
189O ASP* 3.8 2.5 - - - +
191O ILE* 1.3 75.7 - - - +
193O SER* 1.3 67.8 + - - +
194O LEU 3.1 0.7 + - - -
195O LEU* 3.3 6.1 + - - +
196O THR* 3.0 45.9 + - + +
245O SER* 3.5 25.4 - - - -
248O ALA* 3.8 9.0 - - + -
249O LYS* 3.8 22.0 - - - -
252O THR* 4.0 7.2 - - - +
78Q LEU* 4.4 1.8 - - + -
142Q LEU* 3.4 24.9 - - + -
143Q PHE* 4.0 13.0 - + - -
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Residues in contact with SER 193 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71O ALA* 3.7 13.4 - - - +
72O PRO* 3.4 13.7 - - - +
74O TYR* 3.4 22.9 + - - -
189O ASP 2.9 24.2 + - - -
190O TYR 4.0 1.3 - - - -
192O PHE* 1.3 76.3 - - - +
194O LEU* 1.3 54.2 + - - +
196O THR* 3.5 7.2 - - - -
197O GLY* 2.6 33.1 + - - -
217O TYR* 3.1 28.3 - - - -
82Q ARG* 6.1 0.2 - - - +
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Residues in contact with LEU 194 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190O TYR* 3.0 42.2 + - + +
191O ILE* 3.3 4.3 - - - +
192O PHE 3.0 0.4 - - - -
193O SER* 1.3 74.3 - - - +
195O LEU* 1.3 69.2 + - + +
196O THR 3.1 1.0 + - - -
197O GLY 3.3 4.7 + - - -
198O TYR* 3.5 7.9 - - + +
215O ASN* 3.0 51.1 + - - +
217O TYR* 4.6 3.8 - - + +
218O PHE* 4.2 15.5 - - + +
223O ILE* 4.0 24.7 - - + -
225O MET* 5.3 3.4 - - + -
523O HEC 3.7 37.0 - - + -
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Residues in contact with LEU 195 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191O ILE* 3.1 14.0 + - + +
192O PHE* 3.8 5.6 - - - +
194O LEU* 1.3 81.7 - - + +
196O THR* 1.3 59.6 + - - +
198O TYR* 3.8 15.6 - - - -
225O MET* 3.9 26.2 - - + -
227O ARG* 4.8 7.4 + - - +
228O VAL* 5.4 1.9 + - + -
229O LEU* 3.8 41.5 + - + +
244O THR* 5.1 1.9 + - - -
248O ALA* 4.0 12.6 - - + -
251O VAL* 4.0 21.5 - - + -
252O THR* 4.2 13.2 - - - +
523O HEC 3.9 29.8 - - + -
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Residues in contact with THR 196 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74O TYR* 5.0 0.3 + - - -
192O PHE* 3.0 28.8 + - + +
193O SER* 3.4 8.7 + - - -
195O LEU* 1.3 77.6 - - - +
197O GLY* 1.3 53.9 + - - +
198O TYR* 2.7 23.3 + - - +
227O ARG* 5.5 6.5 + - - +
244O THR* 4.7 9.2 - - - +
245O SER* 4.3 10.5 - - - -
248O ALA* 3.9 22.0 - - + -
76Q ASP* 6.0 0.2 - - - +
78Q LEU* 3.6 32.0 - - + +
82Q ARG* 4.1 12.8 + - - -
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Residues in contact with GLY 197 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193O SER 2.6 26.4 + - - -
194O LEU 3.3 3.2 + - - -
196O THR* 1.3 69.8 + - - +
198O TYR* 1.3 55.9 + - - +
199O PRO* 3.0 16.5 - - - +
215O ASN* 4.0 7.0 - - - -
216O PRO* 3.1 15.6 - - - +
217O TYR* 3.5 17.2 - - - -
82Q ARG* 4.8 7.2 - - - -
131Q GLN* 5.8 2.0 + - - -
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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