Contacts of the helix formed by residues 167 - 183 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A VAL* 3.8 23.6 - - - +
146A ASP* 4.8 0.9 - - - -
165A GLY 3.1 5.0 - - - -
166A THR* 1.3 84.6 + - - +
168A THR* 1.3 59.3 + - - -
169A LEU 3.2 2.6 + - - -
170A LEU* 3.9 7.3 + - - +
171A ASP* 3.5 6.9 - - - +
198A HIS* 3.6 15.3 + - - -
274A SER* 4.1 5.8 - - - -
285A SER* 3.4 12.3 - - - -
330A NAD 4.7 1.0 - - - +
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Residues in contact with THR 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A THR 3.3 0.6 + - - -
167A GLY* 1.3 68.7 - - - -
169A LEU* 1.3 57.5 + - - +
170A LEU 3.1 2.0 - - - -
171A ASP* 3.2 24.0 - - - +
172A THR* 2.7 29.9 + - - -
194A ASN 2.6 28.4 + - - +
195A LEU 4.2 2.0 - - - -
196A GLY 3.8 17.3 - - - +
198A HIS 4.3 4.3 - - - +
202A GLN* 3.7 27.1 - - + +
272A VAL* 3.5 6.8 + - - +
285A SER* 2.8 24.4 + - - -
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Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A THR 2.9 16.5 + - - +
167A GLY 3.2 0.2 + - - -
168A THR* 1.3 77.3 - - - +
170A LEU* 1.3 60.8 + - - +
172A THR* 3.8 3.3 + - + -
173A ALA* 3.3 20.6 + - - +
255A SER* 3.6 34.3 - - - +
258A ARG* 4.8 5.4 - - + +
259A ILE* 3.8 21.8 - - + -
271A LEU* 4.5 17.0 - - + -
272A VAL* 3.3 39.2 + - + +
273A VAL* 4.8 0.4 - - + -
72C ASN* 3.8 25.9 + - - +
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Residues in contact with LEU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A THR* 4.5 1.9 + - - -
167A GLY 3.9 5.9 + - - +
168A THR 3.1 0.2 - - - -
169A LEU* 1.3 76.7 - - - +
171A ASP* 1.3 66.0 + - - +
173A ALA* 2.9 17.7 + - + +
174A ARG* 3.0 44.6 + - + +
198A HIS* 4.2 5.2 - - + -
248A THR* 5.0 0.2 - - - +
251A GLY* 3.6 33.4 - - - +
252A VAL* 3.7 15.7 - - + +
255A SER* 4.1 10.1 + - - +
330A NAD 3.2 26.7 - - - +
331A SO4 3.4 21.3 - - - +
68C ASP* 4.6 4.9 - - + -
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Residues in contact with ASP 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A THR* 3.2 28.5 - - - +
170A LEU* 1.3 76.2 - - - +
172A THR* 1.3 61.7 + - - +
174A ARG* 3.2 19.9 + - - +
175A MET* 3.1 21.1 + - - +
194A ASN* 3.8 7.5 + - - +
198A HIS* 2.6 36.9 + - - -
199A GLY* 4.8 1.6 + - - -
202A GLN* 3.4 40.4 + - - +
234A ALA* 5.1 1.6 - - - +
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Residues in contact with THR 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A THR 2.7 24.7 + - - -
169A LEU* 3.9 7.0 - - + -
171A ASP* 1.3 71.9 - - - +
173A ALA* 1.3 57.1 + - - +
175A MET* 3.2 8.0 + - + +
176A GLN* 2.8 45.1 + - - +
192A GLY 3.4 25.6 - - - +
193A TYR* 4.0 7.0 - - + -
194A ASN* 3.1 29.3 + - - +
272A VAL* 3.7 15.1 - - + +
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Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A LEU 3.3 11.6 + - - +
170A LEU* 2.9 13.7 + - + +
172A THR* 1.3 78.3 - - - +
174A ARG* 1.3 56.9 + - - +
176A GLN* 3.6 13.8 + - - +
177A ARG* 3.0 26.2 + - - +
187A PRO* 5.4 0.3 - - - +
255A SER* 5.1 0.7 - - - +
67C GLN 4.9 0.5 - - - +
68C ASP* 3.2 28.4 - - - +
71C ALA* 3.9 11.0 - - + +
72C ASN* 3.8 16.2 - - - +
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Residues in contact with ARG 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LEU* 3.0 39.5 + - - +
171A ASP* 3.4 22.7 + - - +
173A ALA* 1.3 74.2 - - - +
175A MET* 1.3 60.8 + - - +
177A ARG* 3.3 8.6 + - - +
178A ALA* 2.9 30.3 + - - +
198A HIS* 4.8 0.2 - - - -
234A ALA* 3.9 28.3 - - - +
235A ARG 5.9 0.4 + - - -
237A GLY* 4.9 0.9 - - - -
238A GLY* 3.6 28.9 - - - +
241A VAL* 5.4 1.6 - - - +
248A THR* 4.0 14.3 + - - +
252A VAL 5.9 0.2 - - - +
331A SO4 3.2 38.6 + - - -
65C ASP* 5.1 2.6 + - - -
68C ASP* 2.9 41.0 + - + +
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Residues in contact with MET 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ASP 3.1 6.1 + - - +
172A THR* 3.3 17.0 - - + +
174A ARG* 1.3 74.2 - - - +
176A GLN* 1.3 69.5 + - + +
178A ALA* 3.2 2.5 + - - +
179A VAL* 2.8 47.2 + - + +
190A VAL* 4.1 8.3 - - - -
191A SER 4.5 1.1 - - - +
192A GLY* 3.7 33.7 - - - +
193A TYR 4.0 2.7 - - - +
194A ASN* 3.3 30.5 - - - +
204A VAL* 4.0 18.8 - - + -
206A TRP* 4.5 4.3 - - + -
209A VAL* 3.9 18.4 - - + -
230A ILE* 5.4 0.7 - - + -
234A ALA* 3.9 14.8 - - + +
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Residues in contact with GLN 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU 5.4 0.3 - - - +
172A THR* 2.8 35.0 + - - +
173A ALA* 3.6 8.0 - - - +
174A ARG 3.4 0.2 - - - -
175A MET* 1.3 93.7 - - + +
177A ARG* 1.3 50.9 + - - +
179A VAL 3.7 0.3 - - - -
180A GLY* 2.8 32.1 + - - -
187A PRO* 3.0 43.2 + - + +
188A ARG* 4.3 5.1 + - - +
190A VAL* 3.1 30.7 + - + +
192A GLY 5.3 1.1 - - - +
258A ARG* 6.0 0.2 + - - -
71C ALA* 3.3 24.6 + - + +
72C ASN* 5.1 2.3 - - - +
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Residues in contact with ARG 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ALA 3.0 15.7 + - - +
174A ARG* 3.5 17.6 + - - +
175A MET 3.2 0.2 - - - -
176A GLN* 1.3 72.1 - - - +
178A ALA* 1.3 62.1 - - - +
180A GLY* 3.1 1.8 + - - -
181A GLU* 2.9 61.7 + - + +
187A PRO* 4.2 11.4 - - + +
233A GLU* 3.5 44.6 + - - +
237A GLY* 4.1 12.7 - - - -
64C ILE* 4.1 19.1 - - - +
67C GLN* 3.5 41.6 - - + +
68C ASP* 2.7 28.8 + - - +
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Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ARG 2.9 17.8 + - - +
175A MET 3.7 3.6 - - - +
177A ARG* 1.3 82.3 - - - +
179A VAL* 1.3 62.3 + - - +
180A GLY 3.3 0.2 + - - -
181A GLU* 3.3 7.5 + - - +
182A ALA* 3.2 20.6 + - - +
230A ILE* 3.8 33.0 - - + +
233A GLU* 3.9 20.6 - - + -
234A ALA* 4.3 4.5 - - + +
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A MET* 2.8 37.7 + - - +
176A GLN 4.1 2.2 - - - +
178A ALA* 1.3 72.8 - - - +
180A GLY* 1.3 61.8 + - - +
182A ALA* 3.4 5.0 + - - -
183A PHE* 3.1 33.2 + - + +
190A VAL* 4.1 9.8 - - + +
206A TRP* 4.1 5.4 - - + -
209A VAL* 4.8 0.7 - - + -
211A VAL* 3.5 32.3 - - + -
216A ILE* 3.7 22.0 - - + -
230A ILE* 3.5 21.8 - - + -
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Residues in contact with GLY 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A GLN 2.8 23.7 + - - -
177A ARG* 3.1 2.6 + - - -
179A VAL* 1.3 73.9 - - - +
181A GLU* 1.3 51.6 + - - +
183A PHE 3.4 0.3 + - - -
184A ASP* 2.7 32.2 + - - -
185A LEU* 2.9 32.9 + - - +
187A PRO* 4.9 3.1 - - - -
190A VAL* 4.4 4.7 - - - +
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Residues in contact with GLU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ARG* 2.9 55.6 + - + +
178A ALA* 3.3 6.5 + - - +
180A GLY* 1.3 75.3 - - - +
182A ALA* 1.3 63.4 + - - +
184A ASP* 3.3 12.2 + - - +
233A GLU* 4.8 8.8 - - - +
64C ILE* 5.8 0.2 - - - +
67C GLN* 3.7 15.2 + - - +
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ALA 3.2 10.6 + - - +
179A VAL 3.6 7.9 - - - +
180A GLY 3.3 0.2 - - - -
181A GLU* 1.3 81.4 - - - +
183A PHE* 1.3 70.8 + - + +
184A ASP* 3.7 0.5 + - - +
225A ILE* 5.9 2.7 - - + -
230A ILE* 4.3 21.1 - - + -
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Residues in contact with PHE 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A VAL* 3.1 39.0 + - + +
182A ALA* 1.3 85.7 - - + +
184A ASP* 1.3 71.4 - - - +
185A LEU* 3.2 21.6 + - + +
211A VAL* 3.9 13.2 - - + -
212A MET* 4.2 24.1 - - + +
216A ILE* 3.8 17.5 - - + -
219A LEU* 3.6 36.1 - - + -
225A ILE* 4.7 12.8 - - + -
230A ILE* 5.0 4.3 - - + -
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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
------------------------------------------------------------
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