Contacts of the helix formed by residues 226 - 244 (chain H) in PDB entry 1KBY
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 THR 226 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119H ASP* 2.6 48.2 + - - +
120H LEU* 3.1 17.5 - - - -
121H PRO* 3.9 6.5 - - + -
220H LYS* 4.3 7.9 - - - +
224H GLU* 4.8 9.2 - - + +
225H VAL* 1.3 77.7 - - - +
227H LEU* 1.3 65.6 + - - +
228H LEU 3.7 1.0 + - - -
229H GLU* 2.9 43.6 + - - +
230H GLU* 2.9 17.2 + - - +
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Residues in contact with LEU 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H ARG* 6.1 1.8 - - - +
117H ARG* 3.4 41.2 + - + +
118H ARG* 3.4 15.7 - - + +
120H LEU* 2.8 20.6 + - + +
121H PRO 4.9 1.1 - - - +
122H GLU* 4.1 22.2 - - + +
226H THR* 1.3 71.2 - - - +
228H LEU* 1.3 62.2 + - - +
230H GLU* 3.4 22.4 + - - +
231H ASP* 3.2 24.1 + - - +
233M ARG* 3.9 9.4 - - - +
236M GLU* 3.9 28.9 - - + +
240M ASP* 4.1 14.4 - - - +
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Residues in contact with LEU 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H TRP* 3.8 33.9 - - + -
115H VAL 4.0 7.0 - - - +
116H ALA* 4.2 3.4 - - + -
117H ARG* 3.3 27.1 - - - +
118H ARG 3.1 10.0 + - - +
119H ASP* 3.7 32.5 - - + +
220H LYS* 5.6 0.2 - - - +
226H THR* 3.1 1.7 - - - +
227H LEU* 1.3 78.2 - - - +
229H GLU* 1.3 64.0 + - + +
231H ASP* 3.5 2.4 + - - +
232H LYS* 3.3 34.9 + - - +
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Residues in contact with GLU 229 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H ASP* 4.2 0.9 - - - +
217H PRO* 6.5 0.2 - - - -
218H THR 4.3 3.8 - - - +
219H ILE* 3.4 27.4 - - + +
220H LYS* 2.9 50.0 + - - +
221H SER 5.5 0.2 + - - -
224H GLU* 4.0 2.4 - - - +
225H VAL* 3.4 10.9 - - + -
226H THR* 2.9 42.9 + - - +
228H LEU* 1.3 78.3 - - + +
230H GLU* 1.3 66.3 + - - +
232H LYS* 3.5 6.8 + - + +
233H ILE* 3.0 32.7 + - + +
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Residues in contact with GLU 230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H ARG* 5.8 2.7 - - - +
122H GLU* 5.2 1.7 + - - +
131H ILE* 3.9 9.7 - - - +
178H PHE* 3.7 31.7 - - + -
225H VAL* 4.3 17.8 - - + +
226H THR 2.9 16.3 + - - +
227H LEU* 3.6 21.3 - - + +
229H GLU* 1.3 75.5 - - - +
231H ASP* 1.3 59.1 + - - +
233H ILE* 3.3 5.6 + - - +
234H CYS* 2.9 38.9 + - - -
230M GLY* 6.0 0.2 - - - -
233M ARG* 2.8 42.7 + - - -
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Residues in contact with ASP 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H SER 4.4 0.2 - - - +
114H TRP* 3.5 12.4 - - + +
115H VAL* 3.0 48.6 + - - +
117H ARG* 3.4 26.1 + - - -
227H LEU 3.2 11.3 + - - +
228H LEU 3.8 4.9 - - - +
229H GLU 3.3 0.2 - - - -
230H GLU* 1.3 80.9 - - - +
232H LYS* 1.3 56.5 + - - +
234H CYS* 4.9 2.7 - - - -
235H GLY* 3.0 24.3 + - - -
229M PHE* 4.9 7.4 - - - +
237M GLN* 4.9 0.9 + - - -
242M GLY* 4.1 0.5 - - - -
243M THR* 3.1 27.2 + - - +
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Residues in contact with LYS 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H TRP* 3.5 64.9 - - + +
217H PRO* 3.7 24.3 - - + +
228H LEU* 3.3 32.1 + - + +
229H GLU* 4.0 7.2 - - + +
230H GLU 3.3 0.2 - - - -
231H ASP* 1.3 74.5 - - - +
233H ILE* 1.3 61.0 + - - +
236H TYR* 3.1 28.9 + - - +
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Residues in contact with ILE 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178H PHE* 4.7 7.0 - - + -
190H LEU* 3.4 46.4 - - + +
192H PRO* 4.4 11.4 - - + -
216H ILE* 4.2 7.2 - - + -
217H PRO* 3.8 32.5 - - + +
218H THR 5.6 0.2 - - - -
219H ILE* 4.0 25.6 - - + -
225H VAL* 4.6 2.5 - - + -
229H GLU* 3.0 21.3 + - + +
230H GLU* 3.7 4.9 - - - +
232H LYS* 1.3 75.0 - - - +
234H CYS* 1.3 64.8 + - - +
236H TYR* 3.3 3.3 + - - +
237H VAL* 3.0 31.3 + - + +
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Residues in contact with CYS 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178H PHE* 4.2 16.8 - - - -
192H PRO* 4.1 25.1 - - - -
230H GLU* 2.9 24.2 + - - +
231H ASP* 4.3 2.5 - - - +
233H ILE* 1.3 73.8 - - - +
235H GLY* 1.3 67.5 + - - +
237H VAL* 3.5 3.2 + - - +
238H ALA* 3.1 25.8 + - - +
228M ARG 3.4 27.2 - - - +
229M PHE* 3.9 23.6 - - + -
230M GLY 5.2 0.7 - - - -
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Residues in contact with GLY 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H PRO 3.4 1.7 - - - +
112H ALA* 3.1 18.1 - - - -
113H SER 3.5 23.3 - - - -
231H ASP 3.0 14.8 + - - -
232H LYS* 4.3 0.4 - - - -
234H CYS* 1.3 76.4 - - - +
236H TYR* 1.3 62.7 + - - +
238H ALA 3.4 0.2 + - - -
239H GLY 3.0 18.4 + - - -
229M PHE* 4.2 13.1 - - - -
243M THR* 5.3 0.2 - - - -
247M ARG* 4.4 1.1 - - - -
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Residues in contact with TYR 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H MET* 3.9 50.2 - - + +
106H LYS* 5.0 6.3 - - + -
112H ALA* 4.3 8.6 + - - -
208H LEU* 4.1 14.8 - - + -
212H LEU* 2.8 38.3 + - - +
215H GLY* 3.4 18.4 - - - -
216H ILE* 3.6 33.7 - - + -
217H PRO* 3.7 16.6 - - + -
232H LYS 3.1 21.3 + - - +
233H ILE 3.4 4.5 - - - +
234H CYS 3.2 0.2 - - - -
235H GLY* 1.3 76.1 - - - +
237H VAL* 1.3 68.1 + - + +
239H GLY* 3.2 11.6 + - - -
240H GLY 3.5 6.9 + - - -
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Residues in contact with VAL 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191H LEU* 4.4 10.3 - - + -
192H PRO* 3.9 24.9 - - + -
195H MET* 3.8 32.5 - - + -
205H VAL* 6.1 1.1 - - + -
207H ALA* 2.9 29.3 - - + +
208H LEU* 4.0 22.7 - - + -
216H ILE* 4.8 4.9 - - + -
233H ILE* 3.0 22.1 + - + +
234H CYS 3.5 4.5 + - - +
236H TYR* 1.3 84.4 - - + +
238H ALA* 1.3 66.5 + - - +
240H GLY* 3.3 6.2 + - - -
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Residues in contact with ALA 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111H PRO* 3.9 11.0 - - - +
195H MET* 4.2 12.1 - - + -
234H CYS 3.1 19.0 + - - +
235H GLY 3.8 2.7 - - - +
237H VAL* 1.3 77.1 - - + +
239H GLY* 1.3 63.6 + - - +
240H GLY 3.1 1.3 + - - -
241H LEU* 3.2 22.7 + - - +
242H MET 4.4 0.3 + - - -
112L GLY* 4.1 11.5 - - - +
228M ARG* 4.5 7.4 - - + -
229M PHE* 3.6 29.4 - - + -
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Residues in contact with GLY 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105H MET* 3.7 6.3 - - - -
111H PRO* 3.5 25.1 + - - -
112H ALA* 3.8 9.9 - - - -
235H GLY 3.0 11.7 + - - -
236H TYR 3.2 6.1 + - - -
238H ALA* 1.3 79.1 - - - +
240H GLY* 1.3 56.5 + - - +
242H MET* 3.2 4.1 + - - +
243H TYR* 2.9 32.9 + - - +
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Residues in contact with GLY 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H MET* 3.8 19.3 - - - -
207H ALA 3.1 21.0 - - - +
208H LEU* 4.1 1.3 - - - -
236H TYR 3.5 5.1 + - - -
237H VAL 3.3 6.2 + - - -
238H ALA 3.1 2.0 - - - -
239H GLY* 1.3 75.6 - - - +
241H LEU* 1.3 64.0 + - - +
244H ALA* 2.7 33.4 + - - +
245H ALA 3.5 0.7 + - - -
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Residues in contact with LEU 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195H MET* 4.2 8.3 - - + -
206H ASN* 4.8 5.8 - - + -
207H ALA* 3.6 32.6 + - + +
237H VAL 4.1 0.6 + - - -
238H ALA 3.4 15.7 - - - +
239H GLY 3.2 0.2 - - - -
240H GLY* 1.3 79.5 - - - +
242H MET* 1.3 60.2 + - - +
245H ALA* 3.8 13.0 + - - +
112L GLY* 4.3 11.2 - - - +
113L ILE 5.6 0.7 - - - +
2M GLU* 4.9 15.0 - - - +
228M ARG* 3.4 29.8 - - - +
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Residues in contact with MET 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H PRO* 3.9 29.8 - - + -
238H ALA 4.4 0.4 + - - -
239H GLY 3.2 2.6 + - - -
241H LEU* 1.3 80.1 - - + +
243H TYR* 1.3 79.3 + - + +
245H ALA* 3.0 24.9 - - - +
246H PRO* 4.6 0.9 - - - +
11L VAL* 4.9 0.2 - - - -
12L PRO 3.9 16.8 - - - +
13L GLY* 3.7 28.3 - - - +
14L GLY* 3.8 6.5 - - - +
109L ARG* 3.4 28.0 - - + +
110L LYS* 3.8 15.3 - - + +
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Residues in contact with TYR 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H PRO* 4.4 6.4 - - + +
104H PRO* 3.5 41.6 - - + +
105H MET* 3.9 26.2 - - + -
109H VAL 3.9 11.3 + - - -
110H GLY* 4.0 0.7 - - - -
111H PRO* 3.3 37.6 - - + +
112H ALA* 4.3 4.0 - - + -
239H GLY* 2.9 28.7 + - - +
242H MET* 1.3 85.0 - - + +
244H ALA* 1.3 61.0 + - - +
246H PRO* 3.7 12.7 - - - +
11L VAL* 3.8 17.8 - - - +
12L PRO 5.7 1.1 - - - -
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Residues in contact with ALA 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105H MET* 5.1 0.2 - - - +
156H CYS* 4.8 12.4 - - - -
207H ALA 3.5 16.6 - - - +
208H LEU* 4.6 3.1 - - - -
209H SER* 4.6 6.7 + - - +
212H LEU* 3.7 28.9 - - + -
240H GLY* 2.7 24.9 + - - +
243H TYR* 1.3 72.9 - - - +
245H ALA* 1.3 65.0 + - - +
246H PRO* 2.8 20.6 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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