Contacts of the helix formed by residues 154 - 171 (chain G) in PDB entry 2HOI
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 ARG 154 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F A 4.1 16.6 + - - -
152G SER* 3.3 8.0 - - - +
153G ASP* 1.3 78.9 - - - +
155G CYS* 1.3 64.7 + - - +
156G GLN* 3.3 22.0 - - + +
157G ASP* 2.7 45.8 + - - +
158G ILE* 3.2 21.0 + - - +
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Residues in contact with CYS 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153G ASP 3.5 3.9 + - - -
154G ARG* 1.3 69.6 - - - +
156G GLN* 1.3 65.9 + - - +
158G ILE* 3.3 10.0 + - - +
159G ARG* 3.1 22.5 + - - +
224G TRP* 4.0 20.1 - - - -
227G VAL* 4.1 25.1 - - + -
242G VAL* 4.1 12.8 - - + -
246G GLY* 3.4 34.1 - - - +
248G ALA* 4.5 9.9 - - - -
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Residues in contact with GLN 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F A 4.4 16.9 + - - +
6F G 3.2 20.5 + - - -
154G ARG* 3.9 19.7 - - + +
155G CYS* 1.3 78.8 - - - +
157G ASP* 1.3 67.5 + - - +
159G ARG* 2.8 29.4 + - - +
160G ASN* 3.0 51.3 + - - +
242G VAL* 3.6 31.3 + - + +
246G GLY* 5.5 1.0 - - - -
264G ILE* 5.4 0.2 - - - +
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Residues in contact with ASP 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149G MET* 3.2 32.3 - - + +
152G SER* 2.8 34.4 + - - +
154G ARG* 2.7 43.5 + - - +
155G CYS 3.3 0.8 - - - -
156G GLN* 1.3 77.7 - - - +
158G ILE* 1.3 60.6 + - - +
160G ASN* 3.9 7.8 - - - +
161G LEU* 3.0 33.6 + - - +
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Residues in contact with ILE 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152G SER 3.8 13.2 - - - +
153G ASP* 3.5 28.7 - - - +
154G ARG 3.2 9.3 + - - +
155G CYS* 3.3 6.7 + - - +
157G ASP* 1.3 77.6 - - - +
159G ARG* 1.3 61.3 + - - +
161G LEU* 4.0 1.9 - - - +
162G ALA* 3.2 22.3 + - - +
220G LEU 4.5 1.6 - - - +
223G ARG* 3.7 39.5 + - + +
224G TRP* 3.5 33.7 - - - +
227G VAL* 4.0 26.9 - - + -
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Residues in contact with ARG 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F G 2.6 35.3 + - - -
155G CYS 3.1 8.5 + - - +
156G GLN* 2.8 38.2 + - - +
158G ILE* 1.3 75.0 - - - +
160G ASN* 1.3 75.7 + - - +
162G ALA* 3.1 4.7 + - - +
163G PHE* 2.9 27.4 + - - +
224G TRP* 3.4 39.6 - - + -
239G PHE* 3.7 20.3 - - + -
240G CYS 2.8 26.7 + - - -
242G VAL* 3.7 9.1 - - + +
256G LEU* 3.8 20.3 - - - +
260G ALA* 6.1 1.0 - - - +
264G ILE* 4.2 15.1 - - + +
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Residues in contact with ASN 160 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156G GLN* 3.0 40.6 + - - +
157G ASP* 3.9 8.9 + - - +
159G ARG* 1.3 103.0 + - - +
161G LEU* 1.3 58.0 + - - +
163G PHE* 3.5 4.6 + - - +
164G LEU* 3.1 34.6 + - + +
264G ILE* 3.5 32.7 + - + +
267G ALA* 5.7 5.5 - - - +
268G THR* 5.2 5.2 + - - +
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Residues in contact with LEU 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142G PHE* 4.0 21.8 - - + -
145G VAL* 4.3 19.7 - - + -
146G ARG* 4.4 13.2 - - + -
149G MET* 3.8 40.8 - - + +
150G GLU* 4.0 6.3 - - - +
157G ASP 3.0 17.7 + - - +
158G ILE* 4.0 4.0 - - - +
160G ASN* 1.3 74.5 - - - +
162G ALA* 1.3 60.9 + - - +
164G LEU* 3.5 5.5 + - + -
165G GLY* 3.0 24.9 + - - -
220G LEU* 3.8 31.6 - - + +
223G ARG* 4.0 8.5 - - - +
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Residues in contact with ALA 162 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158G ILE 3.2 13.8 + - - +
159G ARG 3.4 8.5 - - - +
161G LEU* 1.3 75.9 - - - +
163G PHE* 1.3 58.3 + - - +
165G GLY* 3.4 1.2 + - - -
166G ILE* 3.0 33.8 + - - +
220G LEU* 3.7 30.2 - - - +
221G VAL* 4.2 8.3 - - + +
224G TRP* 3.8 15.5 - - + -
239G PHE* 3.9 12.6 - - + -
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Residues in contact with PHE 163 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159G ARG 2.9 12.0 + - - +
160G ASN 3.6 6.3 - - - +
162G ALA* 1.3 73.8 - - - +
164G LEU* 1.3 64.7 + - + +
166G ILE* 3.3 2.7 + - - +
167G ALA* 2.8 29.1 + - + +
174G ILE* 4.1 7.4 - - + -
177G ILE* 3.7 39.9 - - + -
239G PHE* 3.6 17.9 - + + -
261G LEU* 3.5 50.9 - - + -
264G ILE* 3.8 33.2 - - + -
265G PHE* 3.5 37.0 - + - -
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Residues in contact with LEU 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137G PHE* 4.2 21.0 - - + -
142G PHE* 4.3 6.5 - - + -
145G VAL* 3.9 25.8 - - + -
160G ASN* 3.1 22.8 + - + +
161G LEU* 3.9 8.5 - - + +
162G ALA 3.4 0.2 - - - -
163G PHE* 1.3 86.2 - - + +
165G GLY* 1.3 57.0 + - - +
167G ALA* 3.4 5.6 + - - +
168G TYR* 2.9 33.3 + - - +
264G ILE* 4.4 6.7 - - + -
265G PHE* 3.7 35.7 - - + -
268G THR* 3.8 26.0 - - + +
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Residues in contact with GLY 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142G PHE* 3.7 24.2 - - - -
161G LEU 3.0 13.6 + - - -
162G ALA 3.7 3.6 - - - -
163G PHE 3.2 0.4 - - - -
164G LEU* 1.3 75.8 - - - +
166G ILE* 1.3 55.5 + - - +
168G TYR* 3.8 1.6 - - - +
169G ASN* 2.8 32.6 + - - +
217G VAL* 3.7 19.0 - - - +
220G LEU* 4.5 1.8 - - - -
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Residues in contact with ILE 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162G ALA 3.0 13.7 + - - +
163G PHE* 3.8 3.8 - - - +
165G GLY* 1.3 73.1 - - - +
167G ALA* 1.3 56.3 + - - +
170G THR* 2.7 56.8 + - + +
172G LEU* 4.7 0.2 - - + -
177G ILE* 4.3 21.5 - - + -
180G ILE* 4.5 11.0 - - + -
195G ILE* 4.4 9.2 - - + -
213G LEU* 4.1 18.6 - - + -
217G VAL* 4.0 0.4 - - - +
221G VAL* 3.8 22.7 - - + -
238G LEU* 3.6 31.2 - - + -
239G PHE* 3.6 19.3 - - + -
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Residues in contact with ALA 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163G PHE* 2.8 22.8 + - + +
164G LEU* 3.6 5.4 - - - +
166G ILE* 1.3 73.1 - - - +
168G TYR* 1.3 60.0 + - - +
170G THR* 4.5 0.9 - - - -
171G LEU* 3.2 23.2 + - - -
172G LEU 4.6 2.3 - - - +
177G ILE* 3.8 23.6 - - + -
265G PHE* 4.0 19.3 - - + -
288G GLY 6.0 0.7 - - - +
291G ALA* 3.5 23.8 - - + +
292G ARG* 4.7 0.5 + - - +
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Residues in contact with TYR 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G PHE* 3.7 32.1 - + + -
138G GLU 4.6 1.1 - - - -
139G ARG* 3.4 26.5 - - + +
142G PHE* 4.3 12.6 - + + -
164G LEU 2.9 17.4 + - - +
165G GLY* 3.9 3.4 - - - +
167G ALA* 1.3 75.3 - - - +
169G ASN* 1.3 67.4 + - - +
171G LEU* 3.6 9.5 - - - +
291G ALA* 3.7 13.9 - - + +
295G ALA* 3.7 17.4 - - - +
298G ASP* 2.7 39.8 + - - +
335H MET* 3.3 35.0 - - + +
338H LEU* 5.2 3.9 - - + +
339H LEU* 3.8 33.0 - - + -
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Residues in contact with ASN 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G GLY 2.8 18.3 + - - +
166G ILE 3.9 1.6 - - - +
168G TYR* 1.3 79.3 - - - +
170G THR* 1.3 58.4 + - - +
212G ALA 3.3 19.9 + - - +
213G LEU* 3.3 13.8 - - + -
214G SER* 2.8 36.9 + - - -
217G VAL* 3.7 6.2 - - + +
335H MET* 3.5 30.4 - - - +
336H VAL* 4.1 6.9 - - - +
339H LEU* 3.5 23.9 - - + +
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Residues in contact with THR 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166G ILE* 2.7 37.7 + - + +
167G ALA* 4.5 0.2 - - - -
169G ASN* 1.3 73.1 - - - +
171G LEU* 1.3 63.8 + - - +
172G LEU* 3.0 34.3 + - + +
195G ILE* 4.5 3.1 - - + -
211G LYS* 2.9 56.0 + - + -
212G ALA 4.7 3.4 - - - +
213G LEU* 3.7 26.5 - - + -
312G ALA 3.6 0.3 - - - +
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Residues in contact with LEU 171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167G ALA 3.2 16.2 + - - -
168G TYR 3.6 12.3 - - - +
170G THR* 1.3 80.9 + - - +
172G LEU* 1.3 61.5 + - - +
211G LYS* 5.2 0.7 - - - -
291G ALA 4.8 0.2 - - - +
292G ARG* 2.6 49.4 + - + +
295G ALA* 3.7 17.9 - - + -
299G MET* 3.9 19.3 - - + -
312G ALA* 3.6 12.3 - - + +
313G GLY* 3.9 12.6 - - - -
315G TRP* 3.8 28.9 - - + -
335H MET* 3.6 30.7 - - + -
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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
------------------------------------------------------------
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