Contacts of the helix formed by residues 167 - 183 (chain B) in PDB entry 1HYH
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 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B VAL* 3.8 22.1 - - - +
146B ASP* 4.7 0.9 - - - -
165B GLY 3.2 2.8 - - - -
166B THR* 1.3 79.7 + - - +
168B THR* 1.3 61.1 + - - -
169B LEU 3.3 2.4 + - - -
170B LEU* 4.1 4.9 + - - +
171B ASP* 3.7 0.2 - - - +
198B HIS* 3.4 23.5 + - - -
274B SER* 4.2 8.1 - - - -
285B SER* 3.2 14.4 - - - -
330B NAD 4.5 3.8 - - - +
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Residues in contact with THR 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B THR 3.3 0.4 + - - -
167B GLY* 1.3 71.4 - - - -
169B LEU* 1.3 52.4 + - - +
170B LEU 3.2 1.6 - - - -
171B ASP* 3.3 25.4 - - - +
172B THR* 2.7 41.5 + - - -
194B ASN 2.5 27.1 + - - +
195B LEU 4.1 2.7 - - - +
196B GLY 4.0 9.9 - - - +
198B HIS 4.1 6.1 - - - +
202B GLN* 3.9 23.6 - - + +
272B VAL* 3.5 6.3 + - - +
285B SER* 2.8 33.2 + - - -
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B THR 3.1 16.0 + - - +
168B THR* 1.3 78.3 - - - +
170B LEU* 1.3 62.3 + - - +
172B THR* 3.4 5.6 + - + -
173B ALA* 3.1 22.0 + - - +
176B GLN* 5.4 0.2 - - - +
255B SER* 3.6 39.0 - - - +
258B ARG* 4.5 12.8 - - + +
259B ILE* 3.8 24.2 - - + -
271B LEU* 4.7 8.7 - - + -
272B VAL* 3.3 36.4 + - + +
273B VAL* 4.8 1.1 - - + -
72D ASN* 3.9 20.3 + - - +
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B THR* 4.6 2.2 + - - -
167B GLY 4.1 5.5 + - - +
169B LEU* 1.3 77.0 - - - +
171B ASP* 1.3 64.5 + - - +
173B ALA* 3.1 16.4 + - + +
174B ARG* 3.1 52.7 + - - +
198B HIS* 4.1 2.5 - - + -
248B THR* 4.9 0.7 - - - +
251B GLY* 3.6 31.4 - - - +
252B VAL* 3.8 21.5 - - + +
255B SER* 4.1 11.9 + - - +
330B NAD 3.7 21.5 - - - +
331B SO4 3.6 15.3 - - - +
68D ASP* 4.5 7.6 - - + -
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Residues in contact with ASP 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B THR* 3.3 26.3 + - - +
169B LEU 3.4 0.4 - - - -
170B LEU* 1.3 72.4 - - - +
172B THR* 1.3 64.9 + - - +
174B ARG* 3.3 21.4 + - - +
175B MET* 3.2 21.3 + - - +
194B ASN* 3.8 8.0 + - - +
198B HIS* 2.5 41.9 + - - +
199B GLY 5.0 1.2 + - - -
202B GLN* 3.5 36.0 + - - +
234B ALA* 5.2 1.1 - - - +
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Residues in contact with THR 172 (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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168B THR 2.7 28.8 + - - -
169B LEU* 3.7 7.6 - - + -
170B LEU 3.3 0.2 - - - -
171B ASP* 1.3 72.3 - - - +
173B ALA* 1.3 57.4 + - - +
175B MET* 3.2 8.2 + - + +
176B GLN* 2.9 46.4 + - - +
192B GLY 3.4 25.6 - - - +
193B TYR* 3.9 6.7 - - + -
194B ASN* 3.2 26.0 + - - +
272B VAL* 3.6 17.8 - - + +
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Residues in contact with ALA 173 (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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169B LEU 3.1 12.1 + - - +
170B LEU* 3.1 14.7 + - + +
172B THR* 1.3 77.6 - - - +
174B ARG* 1.3 55.1 + - - +
176B GLN* 3.4 14.5 + - - +
177B ARG* 2.9 26.5 + - - +
187B PRO* 5.3 0.3 - - - +
67D GLN 5.0 0.5 - - - +
68D ASP* 3.2 28.5 - - - +
71D ALA* 4.0 10.6 - - + +
72D ASN* 3.8 16.2 - - - +
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Residues in contact with ARG 174 (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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170B LEU* 3.1 34.9 + - - +
171B ASP* 3.6 22.9 + - - +
172B THR 3.2 0.2 - - - -
173B ALA* 1.3 71.9 - - - +
175B MET* 1.3 59.2 + - - +
177B ARG* 3.3 7.9 + - - +
178B ALA* 2.8 29.8 + - - +
234B ALA* 3.8 31.0 - - - +
235B ARG 5.7 1.4 + - - -
237B GLY* 4.7 2.6 + - - -
238B GLY* 3.6 30.5 - - - +
241B VAL* 5.2 1.8 - - - +
248B THR* 4.1 11.1 - - - +
331B SO4 2.7 41.2 + - - -
65D ASP* 5.2 2.8 + - - -
68D ASP* 3.0 39.7 + - + +
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Residues in contact with MET 175 (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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171B ASP 3.2 4.0 + - - +
172B THR* 3.3 16.6 - - + +
174B ARG* 1.3 78.7 - - - +
176B GLN* 1.3 62.7 + - + +
178B ALA* 3.3 1.3 + - - +
179B VAL* 2.9 53.2 + - + +
190B VAL* 4.2 8.5 - - - -
191B SER 4.6 2.2 - - - +
192B GLY* 3.9 24.5 - - - +
193B TYR* 4.1 2.0 - - - +
194B ASN* 3.4 28.0 - - - +
204B VAL* 3.8 17.9 - - + -
206B TRP* 4.5 4.3 - - + -
209B VAL* 3.8 28.9 - - + -
230B ILE* 5.7 0.4 - - + -
234B ALA* 3.8 16.0 - - + +
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Residues in contact with GLN 176 (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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172B THR* 2.9 34.2 + - - +
173B ALA* 3.4 10.0 + - - +
174B ARG 3.3 0.2 - - - -
175B MET* 1.3 85.8 - - + +
177B ARG* 1.3 51.8 + - - +
180B GLY* 2.8 31.5 + - - -
187B PRO* 3.0 35.7 + - + +
188B ARG* 4.3 6.1 + - - +
190B VAL* 3.0 42.2 + - + +
192B GLY 5.3 1.3 + - - +
258B ARG* 5.8 0.7 + - - -
71D ALA* 3.2 24.6 + - + +
72D ASN* 5.0 3.1 - - - +
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Residues in contact with ARG 177 (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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173B ALA 2.9 14.5 + - - +
174B ARG* 3.5 16.5 + - - +
176B GLN* 1.3 73.6 - - - +
178B ALA* 1.4 55.8 + - - +
180B GLY* 3.6 0.3 - - - -
181B GLU* 2.7 66.7 + - + +
187B PRO* 4.2 9.6 - - + +
233B GLU* 3.0 51.9 + - - +
237B GLY* 4.1 8.5 - - - -
64D ILE* 3.9 24.3 - - - +
67D GLN* 3.5 39.5 - - + +
68D ASP* 2.7 28.6 + - - +
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Residues in contact with ALA 178 (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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174B ARG 2.8 19.9 + - - +
175B MET 3.7 4.3 - - - +
177B ARG* 1.4 76.6 - - - +
179B VAL* 1.3 62.6 + - - +
181B GLU* 3.2 6.9 + - - +
182B ALA* 2.9 23.2 + - - +
230B ILE* 3.7 26.8 - - + +
233B GLU* 3.9 28.9 - - + -
234B ALA* 4.3 3.6 - - + +
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Residues in contact with VAL 179 (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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175B MET* 2.9 42.2 + - + +
178B ALA* 1.3 71.4 - - - +
180B GLY* 1.3 62.5 + - - +
182B ALA* 3.2 4.3 + - - -
183B PHE* 2.9 28.6 + - + +
190B VAL* 3.9 12.8 - - + -
206B TRP* 4.2 12.8 - - + -
209B VAL* 4.8 0.9 - - + -
211B VAL* 3.6 30.7 - - + -
216B ILE* 3.7 17.5 - - + -
230B ILE* 3.7 21.1 - - + -
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Residues in contact with GLY 180 (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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176B GLN 2.8 23.5 + - - -
177B ARG* 3.6 0.9 - - - -
179B VAL* 1.3 71.9 - - - +
181B GLU* 1.3 53.5 + - - +
183B PHE 3.2 0.2 + - - -
184B ASP* 2.7 33.4 + - - -
185B LEU* 3.0 35.2 + - - -
187B PRO* 4.8 2.9 - - - -
190B VAL* 4.1 5.8 - - - +
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Residues in contact with GLU 181 (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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177B ARG* 2.7 54.8 + - + +
178B ALA* 3.5 6.1 - - - +
180B GLY* 1.3 73.3 - - - +
182B ALA* 1.3 61.4 - - - +
184B ASP* 3.5 10.4 + - - +
233B GLU* 5.3 5.0 - - - +
67D GLN* 3.5 23.9 + - - +
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Residues in contact with ALA 182 (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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178B ALA 2.9 13.4 + - - +
179B VAL 3.6 7.4 - - - +
181B GLU* 1.3 78.8 - - - +
183B PHE* 1.4 69.0 + - + +
184B ASP* 3.8 0.3 + - - +
230B ILE* 4.2 23.8 - - + -
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Residues in contact with PHE 183 (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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179B VAL* 2.9 28.5 + - + +
182B ALA* 1.4 86.0 - - + +
184B ASP* 1.3 72.7 + - - +
185B LEU* 3.3 10.3 + - + -
211B VAL* 4.0 9.0 - - + -
212B MET* 3.6 35.0 - - + +
216B ILE* 3.6 25.1 - - + -
219B LEU* 3.8 37.2 - - + -
225B ILE* 4.8 16.4 - - + -
230B ILE* 4.9 6.7 - - + -
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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