Contacts of the helix formed by residues 178 - 193 (chain M) in PDB entry 1JH0
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 178 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74M PHE* 4.2 7.9 - - - -
92M PHE 4.2 12.1 - - - -
176M PRO 3.1 4.9 + - - -
177M TYR* 1.3 74.8 - - - +
179M ILE* 1.3 69.2 + - - +
180M PHE 3.7 0.7 - - - -
181M SER* 3.5 13.5 - - - -
182M HIS* 3.2 22.2 + - - +
859M SPO 3.5 14.8 - - - +
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Residues in contact with ILE 179 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74M PHE* 5.3 1.4 - - + -
89M LEU* 4.2 17.2 + - + +
90M PHE* 3.8 48.0 + - + +
92M PHE 4.9 0.4 + - - -
178M GLY* 1.3 70.9 - - - -
180M PHE* 1.3 72.0 + - + +
182M HIS* 2.7 32.1 + - + -
183M LEU* 3.7 3.8 - - - +
850M BCL 3.6 51.8 - - + -
859M SPO 3.7 29.1 - - + +
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Residues in contact with PHE 180 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169L TYR* 3.3 42.5 + + - +
174L MET* 3.7 19.3 - - + -
260L VAL* 6.2 0.2 - - + -
263L TRP* 3.5 33.9 - + + -
90M PHE* 3.2 52.2 + + + +
91M PHE* 3.9 33.9 - + + -
179M ILE* 1.3 84.4 - - + +
181M SER* 1.3 58.8 + - - +
183M LEU* 2.9 31.0 + - + +
184M ASP* 3.1 15.6 + - - +
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Residues in contact with SER 181 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90M PHE 4.6 1.2 + - - -
91M PHE 5.3 2.6 + - - -
92M PHE 4.6 1.7 + - - -
93M SER* 3.0 35.3 + - - -
95M GLU* 4.0 8.1 - - - -
176M PRO* 3.4 13.0 - - - +
178M GLY* 3.5 14.6 - - - -
179M ILE 3.3 0.2 - - - -
180M PHE* 1.3 79.4 - - - +
182M HIS* 1.3 60.0 + - - +
184M ASP* 3.3 13.2 + - - +
185M TRP* 3.0 25.8 + - - +
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Residues in contact with HIS 182 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175M VAL* 3.7 9.3 - - + +
176M PRO* 3.6 17.7 - - - +
178M GLY 3.2 14.3 + - - +
179M ILE* 2.7 27.3 + - + -
181M SER* 1.3 80.1 + - - +
183M LEU* 1.3 71.5 + - + +
185M TRP* 3.6 11.0 - - - +
186M THR* 3.1 25.8 + - - -
850M BCL 2.5 80.4 + + + -
859M SPO 3.6 21.7 - - + +
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Residues in contact with LEU 183 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166L ASN* 4.5 1.6 - - - +
168L HIS* 3.2 39.1 + - + +
169L TYR* 4.9 5.6 - - + +
174L MET* 3.8 29.2 - - + -
179M ILE 3.7 10.1 - - - +
180M PHE* 2.9 22.8 + - + +
182M HIS* 1.3 84.2 + - + +
184M ASP* 1.3 62.2 - - - +
186M THR* 3.1 11.2 + - - -
187M ASN* 3.1 10.6 + - - +
850M BCL 3.4 58.8 - - + +
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Residues in contact with ASP 184 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166L ASN* 4.0 9.2 + - - +
169L TYR* 3.2 34.0 + - - -
180M PHE* 3.1 11.8 + - - +
181M SER* 3.6 14.2 - - - +
183M LEU* 1.3 76.6 - - - +
185M TRP* 1.3 62.5 + - - +
187M ASN* 3.3 5.0 + - - +
188M ASN* 3.1 29.8 + - - +
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Residues in contact with TRP 185 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160M LEU* 3.9 26.7 - - + -
164M ARG* 5.1 1.1 - - - -
172M SER 5.2 2.1 + - - -
173M GLU* 3.4 22.3 + - - +
174M ALA 3.2 22.7 + - - -
175M VAL* 3.9 22.7 - - + -
176M PRO* 4.0 17.9 - - + -
181M SER 3.0 17.0 + - - +
182M HIS* 3.6 6.1 - - - +
183M LEU 3.2 0.2 - - - -
184M ASP* 1.3 77.7 - - - +
186M THR* 1.3 78.8 + - - +
188M ASN* 3.2 10.1 + - + +
189M PHE* 2.9 64.1 + + + -
850M BCL 4.2 14.4 - - + -
852M BCL 4.6 6.5 - - + -
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Residues in contact with THR 186 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168L HIS* 3.6 18.4 - - + -
851L BCL 4.0 6.7 - - + +
182M HIS 3.1 12.2 + - - -
183M LEU* 3.1 11.3 + - - -
185M TRP* 1.3 92.1 - - - +
187M ASN* 1.3 64.1 + - - +
189M PHE* 3.1 13.9 + - - +
190M SER 3.3 8.1 + - - -
850M BCL 3.5 26.6 - - + +
852M BCL 3.6 39.7 - - + +
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Residues in contact with ASN 187 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162L TYR* 2.6 39.2 + - - -
166L ASN* 3.7 33.4 - - - +
168L HIS* 4.1 1.5 - - + -
183M LEU 3.1 4.1 + - - +
184M ASP* 3.6 8.1 - - - +
186M THR* 1.3 78.2 - - - +
188M ASN* 1.3 67.8 + - - +
190M SER* 3.2 12.5 + - - -
191M LEU* 3.3 29.2 + - - +
852M BCL 3.2 18.7 - - + +
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Residues in contact with ASN 188 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184M ASP* 3.1 20.3 + - - +
185M TRP* 3.5 10.9 - - + +
187M ASN* 1.3 78.6 - - - +
189M PHE* 1.3 67.2 + - - +
190M SER 2.8 3.6 + - - -
191M LEU* 3.0 17.1 + - - +
192M VAL* 3.0 35.1 + - + +
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Residues in contact with PHE 189 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164M ARG* 3.2 42.8 - - - -
173M GLU* 5.7 0.9 - - - -
185M TRP* 2.9 43.8 + + + +
186M THR 3.1 9.8 + - - +
188M ASN* 1.3 76.3 - - - +
190M SER* 1.3 59.5 + - - +
192M VAL* 4.8 1.1 - - - -
193M HIS* 2.8 38.4 + + - +
196M LEU* 4.1 9.9 - - + -
284M ILE* 4.0 25.4 - - + -
287M SER* 3.5 32.8 - - - -
852M BCL 3.5 22.9 - - + -
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Residues in contact with SER 190 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162L TYR* 4.6 4.8 + - - -
186M THR 3.3 2.7 + - - -
187M ASN 3.2 10.0 + - - -
188M ASN 2.8 1.4 + - - -
189M PHE* 1.3 78.4 - - - +
191M LEU* 1.3 64.7 + - - +
193M HIS 3.0 10.6 + - - -
194M GLY 3.2 0.2 + - - -
195M ASN* 2.8 27.3 + - - -
196M LEU* 3.2 29.8 + - - -
852M BCL 3.7 40.1 - - - +
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Residues in contact with LEU 191 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162L TYR* 3.2 31.9 - - + +
187M ASN* 3.4 29.4 - - - +
188M ASN* 3.0 16.7 + - - +
190M SER* 1.3 80.5 + - - +
192M VAL* 1.3 65.4 + - + +
194M GLY* 3.1 14.6 + - - -
195M ASN* 4.4 4.9 - - + +
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Residues in contact with VAL 192 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188M ASN* 3.0 25.3 + - + +
189M PHE* 4.8 0.7 - - - -
191M LEU* 1.3 76.7 - - + +
193M HIS* 1.3 79.8 + - + +
194M GLY 3.3 2.1 + - - -
292M ASP 3.7 9.5 - - - +
293M ASN* 5.2 2.4 + - - -
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Residues in contact with HIS 193 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164M ARG* 3.2 30.2 + - - -
168M MET* 5.2 0.6 - - - +
173M GLU* 5.4 1.8 - - - -
189M PHE* 2.8 38.2 + + - +
190M SER 3.0 6.6 + - - +
192M VAL* 1.3 95.2 - - + +
194M GLY* 1.3 60.9 + - - +
195M ASN 3.6 1.1 + - - +
196M LEU* 4.3 5.4 - - + -
287M SER* 3.5 13.0 - - - -
288M GLY* 3.4 30.4 - - - -
291M VAL 4.2 5.2 - - - -
292M ASP* 3.6 9.4 - - - +
293M ASN* 3.9 3.6 - - - -
294M TRP* 2.9 42.7 + - + -
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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