Contacts of the helix formed by residues 169 - 182 (chain C) 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 LEU 169 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A ASN* 3.7 25.7 + - - +
166C THR 3.3 15.3 + - - +
168C THR* 1.3 74.8 - - - +
170C LEU* 1.3 61.6 + - - +
172C THR* 3.6 4.8 - - + -
173C ALA* 3.1 23.2 + - - +
255C SER* 3.9 35.0 - - - +
258C ARG* 4.8 5.2 - - - +
259C ILE* 3.9 20.6 - - + -
271C LEU* 4.7 16.4 - - + -
272C VAL* 3.5 40.0 + - + +
273C VAL* 5.0 1.3 - - + -
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Residues in contact with LEU 170 (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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68A ASP* 4.4 9.9 - - + +
166C THR* 4.8 1.7 + - - +
167C GLY 4.3 7.5 + - - +
168C THR 3.2 0.4 - - - -
169C LEU* 1.3 78.9 - - - +
171C ASP* 1.3 63.3 + - - +
173C ALA* 3.2 4.0 + - + +
174C ARG* 3.1 58.7 + - + +
198C HIS* 4.9 2.0 - - + -
248C THR* 4.6 2.0 - - - +
251C GLY* 3.7 29.2 - - - +
252C VAL* 3.8 23.1 - - + +
255C SER* 3.7 12.3 + - - +
330C NAD 3.4 28.5 - - + +
331C SO4 3.8 9.4 - - - +
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Residues in contact with ASP 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C THR* 3.0 29.4 + - - +
170C LEU* 1.3 76.6 - - - +
172C THR* 1.3 61.3 + - - +
174C ARG* 3.3 21.2 + - - +
175C MET* 3.1 17.5 + - - +
194C ASN* 3.7 13.8 + - - +
198C HIS* 2.7 37.5 + - - -
199C GLY 5.2 0.7 + - - -
202C GLN* 3.7 32.2 + - - +
234C ALA* 5.4 0.7 - - - +
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Residues in contact with THR 172 (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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168C THR 2.6 25.4 + - - -
169C LEU* 3.6 7.6 - - + -
171C ASP* 1.3 71.2 - - - +
173C ALA* 1.3 57.4 + - - +
175C MET* 2.9 7.1 + - + +
176C GLN* 2.8 46.6 + - - +
192C GLY 3.5 24.9 - - - +
193C TYR* 4.0 6.1 - - + -
194C ASN* 3.2 27.5 + - - +
272C VAL* 3.6 20.9 - - + +
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Residues in contact with ALA 173 (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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67A GLN 4.9 0.7 - - - +
68A ASP* 3.2 27.1 - - - +
71A ALA* 3.9 11.8 + - + +
72A ASN* 3.6 17.0 - - - +
169C LEU 3.1 17.7 + - - +
170C LEU* 3.2 8.7 + - + +
172C THR* 1.3 75.7 - - - +
174C ARG* 1.3 57.3 + - - +
176C GLN* 3.4 15.0 + - - +
177C ARG* 3.0 24.9 + - - +
187C PRO* 5.2 0.5 - - - +
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Residues in contact with ARG 174 (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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65A ASP* 5.3 2.0 + - - -
68A ASP* 3.1 39.5 + - - +
170C LEU* 3.1 41.8 + - + +
171C ASP* 3.5 20.6 + - - +
172C THR 3.2 0.2 - - - -
173C ALA* 1.3 73.7 - - - +
175C MET* 1.3 65.3 + - - +
177C ARG* 3.4 4.9 + - - +
178C ALA* 3.1 18.5 + - - +
198C HIS* 5.5 0.2 - - - -
234C ALA* 3.5 36.9 + - + +
235C ARG* 6.0 0.6 - - - +
237C GLY 5.5 0.2 - - - -
238C GLY* 3.8 23.5 - - - +
241C VAL* 5.1 2.0 - - - +
248C THR* 3.9 18.6 + - - +
331C SO4 3.5 31.7 + - - -
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Residues in contact with MET 175 (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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171C ASP 3.1 6.2 + - - +
172C THR* 2.9 23.0 + - + +
174C ARG* 1.3 74.7 - - - +
176C GLN* 1.3 70.6 + - + +
178C ALA* 3.1 4.1 + - - +
179C VAL* 2.8 47.0 + - + +
190C VAL* 4.3 4.9 - - - -
191C SER 4.3 3.6 - - - +
192C GLY 3.6 32.1 - - - +
193C TYR 4.2 3.1 - - - +
194C ASN* 3.5 17.7 - - - +
204C VAL* 3.8 27.8 - - + -
206C TRP* 4.4 9.4 - - + -
209C VAL* 4.1 17.7 - - + -
230C ILE* 5.4 0.9 - - + -
234C ALA* 4.1 10.9 - - + +
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Residues in contact with GLN 176 (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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71A ALA* 3.1 24.5 + - + +
72A ASN* 5.1 2.6 - - - +
172C THR* 2.8 27.7 + - - +
173C ALA* 3.4 18.2 - - - +
175C MET* 1.3 91.8 - - + +
177C ARG* 1.3 55.3 + - - +
180C GLY* 2.8 27.9 + - - -
187C PRO* 3.1 35.8 + - + +
188C ARG* 4.5 4.8 + - - +
190C VAL* 3.0 33.5 + - + +
192C GLY 5.1 1.4 + - - -
258C ARG* 5.8 0.5 + - - -
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Residues in contact with ARG 177 (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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64A ILE* 4.0 16.5 - - - +
67A GLN* 3.5 39.0 - - + +
68A ASP* 2.7 30.1 + - - +
173C ALA 3.0 17.2 + - - +
174C ARG* 3.6 6.4 + - - +
175C MET 3.3 0.2 - - - -
176C GLN* 1.3 75.7 - - - +
178C ALA* 1.3 59.5 + - - +
180C GLY* 3.7 0.6 - - - -
181C GLU* 2.9 56.1 + - + +
187C PRO* 4.2 10.3 - - + +
233C GLU* 3.3 45.1 + - - +
234C ALA* 3.8 13.3 + - - +
237C GLY* 3.8 15.6 - - - -
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Residues in contact with ALA 178 (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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174C ARG 3.1 17.0 + - - +
175C MET 3.6 3.6 - - - +
177C ARG* 1.3 76.6 - - - +
179C VAL* 1.3 60.8 + - - +
181C GLU* 3.3 6.3 + - - +
182C ALA* 3.0 27.4 + - - +
230C ILE* 3.7 31.3 - - + +
233C GLU* 4.0 23.7 - - + +
234C ALA* 4.1 6.5 - - + +
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Residues in contact with VAL 179 (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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175C MET* 2.8 27.3 + - - +
178C ALA* 1.3 72.4 - - - +
180C GLY* 1.3 67.6 + - - +
182C ALA* 3.0 7.1 + - - +
183C PHE* 2.9 32.5 + - + +
190C VAL* 3.7 14.8 - - + -
206C TRP* 4.0 19.1 - - + -
209C VAL* 4.7 0.9 - - + -
211C VAL* 3.5 32.1 - - + -
216C ILE* 4.1 13.2 - - + -
230C ILE* 3.6 21.1 - - + -
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Residues in contact with GLY 180 (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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176C GLN 2.8 20.3 + - - -
177C ARG* 3.8 1.3 - - - -
179C VAL* 1.3 76.7 - - - +
181C GLU* 1.3 54.8 + - - +
184C ASP* 2.8 26.9 + - - -
185C LEU* 2.9 37.7 + - - +
187C PRO* 5.0 1.6 - - - -
190C VAL* 4.3 4.9 - - - -
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Residues in contact with GLU 181 (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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64A ILE* 5.4 0.5 - - - +
67A GLN* 3.6 22.1 + - - +
177C ARG* 2.9 50.4 + - + +
178C ALA* 3.7 5.6 - - - +
179C VAL 3.2 0.4 - - - -
180C GLY* 1.3 76.3 - - - +
182C ALA* 1.3 63.0 + - - +
183C PHE 3.3 0.7 + - - -
184C ASP* 3.4 9.7 + - - +
233C GLU* 5.0 8.5 - - + +
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Residues in contact with ALA 182 (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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178C ALA 3.0 13.9 + - - +
179C VAL* 3.4 12.1 - - - +
181C GLU* 1.3 78.6 - - - +
183C PHE* 1.3 62.3 + - + +
225C ILE* 3.8 27.9 - - + +
230C ILE* 4.7 7.9 - - + -
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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