Contacts of the helix formed by residues 187 - 197 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181D VAL* 3.4 30.3 - - - -
184D ARG* 3.3 9.5 + - - +
185D HIS 3.4 1.4 + - - -
186D GLY* 1.3 76.0 - - - +
188D CYS* 1.3 64.2 + - - -
190D TYR* 3.0 3.0 + - - +
191D ILE* 2.8 31.8 + - - +
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Residues in contact with CYS 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D TRP* 3.4 28.8 - - + +
78D HIS* 3.6 17.7 - - - -
79D ASN* 5.8 0.9 - - - +
181D VAL* 3.8 8.0 - - - +
186D GLY 3.3 1.8 + - - -
187D GLY* 1.3 69.7 - - - +
189D ASP* 1.3 57.4 + - - +
191D ILE* 4.6 0.7 - - - -
192D PHE* 2.8 34.1 + - - +
252D THR* 3.7 21.6 - - + +
256D ASN* 3.1 37.0 - - - -
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Residues in contact with ASP 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D ALA* 3.9 8.1 - - + +
72D PRO 3.1 22.9 - - - +
73D ALA* 3.6 13.2 - - - +
74D TYR* 3.0 22.3 + - - +
76D TRP* 2.7 30.7 + - - +
79D ASN* 5.4 0.9 - - - +
186D GLY* 3.2 12.3 + - - +
188D CYS* 1.3 79.5 - - - +
190D TYR* 1.3 56.5 + - - +
192D PHE* 4.1 1.6 - - - +
193D SER* 2.8 35.2 + - - -
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Residues in contact with TYR 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D LEU 6.0 0.9 - - - -
71D ALA* 3.9 14.1 - - + +
184D ARG* 4.1 22.4 - - + -
185D HIS 3.5 24.2 - - - +
186D GLY* 3.6 7.3 + - - -
187D GLY 3.0 7.1 + - - +
189D ASP* 1.3 77.9 - - - +
191D ILE* 1.3 83.5 + - + +
193D SER* 4.4 0.4 - - - -
194D LEU* 2.8 47.2 + - + +
217D TYR* 3.6 31.6 - - + -
218D PHE* 3.3 19.9 - - - -
219D PRO* 4.3 6.3 - - + +
503D HEC 2.8 28.4 + - + -
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Residues in contact with ILE 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D ILE* 3.9 37.7 - - + +
181D VAL* 4.2 15.9 - - + -
184D ARG* 4.6 2.2 - - + -
187D GLY 2.8 28.9 + - - +
188D CYS 3.9 2.7 - - - +
190D TYR* 1.3 88.4 - - + +
192D PHE* 1.3 62.8 + - - +
194D LEU* 3.3 4.8 + - - +
195D LEU* 3.0 37.0 + - + +
252D THR* 3.8 17.7 - - + +
255D LEU* 4.5 17.3 - - + -
503D HEC 3.9 20.4 - - + -
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Residues in contact with PHE 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D TYR* 3.2 47.8 - + - -
76D TRP* 3.7 18.8 - + + -
188D CYS 2.8 18.4 + - - +
189D ASP 4.1 1.8 - - - +
191D ILE* 1.3 77.3 - - - +
193D SER* 1.3 62.0 + - - +
195D LEU* 3.3 7.7 + - - +
196D THR* 3.0 43.5 + - + +
245D SER* 3.8 9.9 - - - -
248D ALA* 3.7 21.5 - - + -
249D LYS* 3.7 24.9 - - + -
252D THR* 3.6 7.8 + - - +
78F LEU* 5.1 0.4 - - + -
142F LEU* 3.4 24.2 - - + -
143F PHE* 3.8 12.8 - + - -
146F LEU* 4.8 0.2 - - + -
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Residues in contact with SER 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D ALA* 4.1 3.8 - - - -
72D PRO* 3.2 23.7 - - - +
74D TYR* 3.5 11.2 + - - -
189D ASP 2.8 24.9 + - - -
190D TYR* 3.8 3.1 - - - -
192D PHE* 1.3 78.0 - - - +
194D LEU* 1.3 58.0 + - - +
196D THR* 3.8 5.8 - - - -
197D GLY 2.8 28.4 + - - -
217D TYR* 3.5 36.2 - - - -
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Residues in contact with LEU 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D TYR* 2.8 46.4 + - + +
191D ILE 3.5 4.3 - - - +
193D SER* 1.3 73.4 - - - +
195D LEU* 1.3 65.2 + - + +
197D GLY 3.9 0.5 + - - -
198D TYR* 3.4 4.9 - - - +
215D ASN* 2.8 38.0 + - - +
217D TYR* 4.3 5.7 - - + +
218D PHE* 3.7 19.5 - - + +
223D ILE* 3.7 25.6 - - + -
225D MET* 4.2 13.0 - - + -
503D HEC 3.8 43.1 - - + -
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Residues in contact with LEU 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D ILE* 3.0 23.3 + - + +
192D PHE 3.5 6.7 - - - +
193D SER 3.3 0.2 - - - -
194D LEU* 1.3 81.0 - - + +
196D THR* 1.3 60.1 + - - +
198D TYR* 3.4 18.2 - - + -
225D MET* 4.5 10.5 - - + -
227D ARG* 4.9 6.6 + - - +
228D VAL* 5.3 3.8 - - + -
229D LEU* 4.5 18.3 + - + +
248D ALA* 4.2 16.2 - - + -
251D VAL* 4.1 21.5 - - + -
252D THR* 4.1 12.8 - - - +
255D LEU* 6.3 0.2 - - + -
503D HEC 3.9 54.1 - - + -
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Residues in contact with THR 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D TYR* 5.0 0.7 + - - -
192D PHE* 3.0 30.7 + - + +
193D SER* 3.4 7.3 + - - -
195D LEU* 1.3 75.6 - - - +
197D GLY* 1.3 57.2 + - - +
198D TYR* 3.0 13.6 + - - +
227D ARG* 5.4 7.8 + - - -
229D LEU* 6.6 0.2 - - + -
244D THR* 4.5 10.8 - - - +
245D SER* 4.1 22.0 - - - -
248D ALA* 3.8 26.0 - - + -
76F ASP* 5.7 1.1 - - - +
78F LEU* 3.8 18.7 - - + +
82F ARG* 3.9 12.4 + - - -
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Residues in contact with GLY 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D SER 2.8 22.5 + - - -
194D LEU 3.9 0.2 + - - -
195D LEU 3.7 0.8 - - - -
196D THR* 1.3 71.7 + - - +
198D TYR* 1.3 50.3 + - - +
199D PRO* 2.8 25.3 - - - +
215D ASN* 3.9 7.4 - - - +
216D PRO* 3.5 16.5 - - - +
217D TYR* 3.8 14.3 - - - -
82F ARG* 4.1 14.4 - - - -
131F GLN* 5.3 1.9 + - - -
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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