Contacts of the helix formed by residues 162 - 185 (chain H) in PDB entry 4MNE
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 PRO 162 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160H ARG 4.1 4.0 - - - +
161H ILE* 1.3 91.9 - - + +
163H GLU* 1.3 67.2 + - - +
164H GLN* 3.1 19.2 + - + +
165H ILE* 3.2 17.1 + - + +
166H LEU* 3.1 18.4 + - - +
374H TRP* 3.4 33.7 - - + +
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Residues in contact with GLU 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161H ILE 3.6 1.6 + - - -
162H PRO* 1.3 72.5 - - - +
164H GLN* 1.3 63.6 + - - +
166H LEU* 3.2 15.0 + - - +
167H GLY 3.1 17.0 + - - -
329H VAL 4.5 0.7 - - - +
330H PHE* 3.4 23.8 - - + -
331H SER* 3.1 31.7 + - - -
334H PHE* 3.1 34.7 - - + +
360H PHE* 4.0 6.1 - - + -
363H ARG* 2.8 32.1 + - - +
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Residues in contact with GLN 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162H PRO* 3.8 22.4 - - + +
163H GLU* 1.3 78.6 - - - +
165H ILE* 1.3 73.5 + - - +
167H GLY* 3.0 12.7 + - - -
168H LYS* 3.4 14.0 + - - +
363H ARG* 5.9 2.2 - - - +
364H SER* 4.8 2.7 + - - -
367H GLU* 3.6 25.1 - - - +
369H VAL* 4.0 31.4 - - + +
374H TRP* 5.2 4.0 - - - -
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Residues in contact with ILE 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151H LEU* 6.3 0.4 - - + -
161H ILE* 4.6 8.1 - - + -
162H PRO* 3.5 33.2 - - + +
164H GLN* 1.3 78.0 - - + +
166H LEU* 1.3 63.6 + - - +
168H LYS* 3.1 10.8 + - + +
169H VAL* 3.0 29.9 + - + +
369H VAL* 3.8 24.9 - - + -
371H PHE* 3.5 35.0 - - + -
374H TRP* 3.4 44.2 - - + -
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Residues in contact with LEU 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161H ILE* 3.1 52.9 - - + +
162H PRO 3.1 9.4 + - - +
163H GLU* 3.5 12.3 - - - +
164H GLN 3.2 0.4 - - - -
165H ILE* 1.3 75.3 - - - +
167H GLY* 1.3 52.6 + - - +
169H VAL* 3.6 7.8 - - + +
170H SER* 2.4 39.5 + - - -
253H LEU* 3.7 17.5 - - + +
256H MET* 3.5 31.0 - - + -
257H ALA* 3.5 29.4 - - + +
330H PHE* 6.1 0.2 - - + -
334H PHE* 4.2 10.5 - - + -
360H PHE* 4.4 1.3 - - - -
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Residues in contact with GLY 167 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163H GLU 3.1 6.3 + - - -
164H GLN 3.0 10.5 + - - -
166H LEU* 1.3 75.9 - - - +
168H LYS* 1.3 57.8 + - - +
170H SER* 3.3 4.2 + - - -
171H ILE* 3.1 30.0 + - - +
360H PHE* 3.5 24.2 - - - -
361H ILE* 5.7 0.9 - - - +
364H SER* 3.8 18.6 - - - -
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Residues in contact with LYS 168 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164H GLN 3.4 10.2 + - - +
165H ILE* 3.1 9.0 + - + +
167H GLY* 1.3 72.8 - - - +
169H VAL* 1.3 61.2 + - - +
171H ILE* 3.2 13.8 + - + +
172H ALA* 2.9 28.8 + - - +
204H ILE* 3.9 13.3 - - + +
364H SER* 2.6 31.5 + - - +
365H ASP* 4.2 9.5 + - - +
367H GLU* 2.7 27.4 + - - +
369H VAL* 4.1 28.0 - - + +
371H PHE* 5.9 9.2 - - + -
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Residues in contact with VAL 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151H LEU* 4.0 32.3 - - + -
161H ILE* 5.1 2.7 - - + -
165H ILE* 3.0 26.5 + - + +
166H LEU* 3.6 15.0 - - + +
168H LYS* 1.3 76.7 - - - +
170H SER* 1.3 57.8 + - - +
172H ALA* 3.2 2.6 + - - +
173H VAL* 2.9 47.6 + - + +
196H ILE* 4.4 9.6 - - + -
204H ILE* 4.0 17.9 - - + +
253H LEU* 4.6 5.2 - - + -
256H MET* 4.5 11.9 - - + -
371H PHE* 5.2 2.5 - - + -
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Residues in contact with SER 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166H LEU 2.4 29.3 + - - -
167H GLY 3.5 6.5 - - - -
168H LYS 3.3 0.2 - - - -
169H VAL* 1.3 74.4 - - - +
171H ILE* 1.3 60.4 + - - +
173H VAL* 4.0 0.7 - - - +
174H ILE* 3.0 34.6 + - - +
249H MET* 4.3 9.2 - - - -
253H LEU* 3.3 22.1 - - - +
337H PHE* 3.9 24.0 - - - -
360H PHE* 3.8 10.7 - - - -
361H ILE* 5.1 2.7 - - - -
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Residues in contact with ILE 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H TYR* 5.6 4.0 - - + +
167H GLY 3.1 16.3 + - - +
168H LYS* 3.5 18.6 - - + +
169H VAL 3.1 0.2 - - - -
170H SER* 1.3 75.9 - - - +
172H ALA* 1.3 58.7 + - - +
174H ILE* 3.0 6.8 + - - +
175H LYS* 2.7 63.2 + - + +
356H MET* 4.3 8.1 - - + -
361H ILE* 4.6 20.2 - - + +
364H SER* 4.3 5.4 - - - +
365H ASP* 3.8 44.0 - - + +
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Residues in contact with ALA 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H TYR* 3.7 24.6 - - + +
168H LYS 2.9 13.0 + - - +
169H VAL 3.2 7.8 + - - +
171H ILE* 1.3 75.6 - - - +
173H VAL* 1.3 54.6 + - + +
175H LYS 3.8 0.2 - - - -
176H GLY* 2.7 33.4 + - - -
204H ILE* 3.6 44.6 - - + +
206H LEU* 4.8 3.2 - - + +
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Residues in contact with VAL 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169H VAL* 2.9 27.6 + - + +
172H ALA* 1.3 77.0 - - + +
174H ILE* 1.3 57.5 + - - +
176H GLY* 3.3 0.5 + - - -
177H LEU* 2.8 51.9 + - + +
191H VAL* 4.4 11.9 - - + -
196H ILE* 3.9 29.6 - - + -
206H LEU* 3.9 18.8 - - + +
249H MET* 3.5 39.0 - - + -
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Residues in contact with ILE 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170H SER 3.0 19.7 + - - +
171H ILE* 3.0 4.9 + - - +
173H VAL* 1.3 73.7 - - - +
175H LYS* 1.3 54.7 + - - +
177H LEU* 3.5 3.2 + - - +
178H THR* 2.5 41.2 + - - +
249H MET* 3.9 17.7 - - + -
337H PHE* 3.8 20.2 - - + -
352H LEU* 3.7 33.9 - - + +
355H LEU* 3.8 26.5 - - + -
356H MET* 4.0 21.5 - - - -
361H ILE* 4.2 13.2 - - + -
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Residues in contact with LYS 175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H TYR* 3.5 46.4 + - + -
171H ILE* 2.7 33.8 + - + +
172H ALA 3.9 0.7 - - - +
174H ILE* 1.3 72.4 - - - +
176H GLY* 1.3 63.3 + - - +
178H THR* 3.2 8.2 + - - -
179H TYR* 2.9 23.7 + - - +
356H MET* 3.8 34.4 - - + +
365H ASP* 4.8 8.4 + - - -
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Residues in contact with GLY 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H TYR* 3.8 15.6 - - - +
126H ILE* 4.0 7.1 - - - +
172H ALA 2.7 23.2 + - - -
173H VAL 3.6 0.9 - - - -
175H LYS* 1.3 73.1 - - - +
177H LEU* 1.3 61.9 + - - +
179H TYR* 3.2 7.5 + - - +
180H LEU* 3.2 25.8 + - - +
206H LEU* 4.0 14.1 - - - -
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Residues in contact with LEU 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173H VAL* 2.8 40.1 + - + +
174H ILE* 3.8 5.6 - - - +
176H GLY* 1.3 71.9 - - - +
178H THR* 1.3 62.3 + - - +
180H LEU* 3.6 6.9 + - + +
181H ARG* 3.3 25.6 + - - +
186H ILE 5.0 0.3 - - - +
188H HIS* 3.8 31.0 - - + +
191H VAL* 4.3 4.7 - - + -
206H LEU* 3.8 13.0 - - + +
242H VAL* 4.8 8.1 - - + +
245H ASP* 4.2 32.1 - - + +
246H ILE* 4.9 5.4 - - + +
249H MET* 4.9 4.3 - - + -
352H LEU* 3.9 24.5 - - + +
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Residues in contact with THR 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174H ILE* 2.5 30.1 + - - +
175H LYS* 3.5 8.4 - - - +
177H LEU* 1.3 74.8 - - - +
179H TYR* 1.3 66.0 + - - +
181H ARG* 3.4 30.8 - - - +
182H GLU* 2.9 48.6 + - - +
352H LEU* 4.1 10.1 - - - +
356H MET* 5.7 1.4 - - - -
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Residues in contact with TYR 179 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120H GLU 3.7 3.1 + - - -
121H CYS* 3.5 7.5 - - + -
122H ASN* 2.6 49.5 + - - +
123H SER* 3.7 24.5 - - - +
125H TYR* 6.0 0.7 - - + -
126H ILE* 4.3 9.0 - - + -
175H LYS 2.9 12.2 + - - +
176H GLY* 3.2 8.7 + - - +
178H THR* 1.3 74.8 - - - +
180H LEU* 1.3 61.6 + - + +
182H GLU* 4.9 1.3 - - - -
183H LYS* 2.7 63.3 + - + +
184H HIS* 3.1 35.9 + + - -
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Residues in contact with LEU 180 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H CYS* 4.6 9.2 - - - -
126H ILE* 3.9 25.1 - - + -
176H GLY 3.2 15.5 + - - +
177H LEU* 3.9 5.8 - - + +
178H THR 3.3 0.2 - - - -
179H TYR* 1.3 89.3 - - + +
181H ARG* 1.3 57.1 + - - +
184H HIS* 2.9 31.2 + - + +
185H LYS 3.0 7.1 + - - -
186H ILE* 3.4 26.4 + - + +
188H HIS* 4.6 19.1 - - + +
206H LEU* 4.7 1.3 - - + -
209H PHE* 3.8 51.1 - - + -
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Residues in contact with ARG 181 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177H LEU 3.3 16.9 + - - +
178H THR* 3.4 21.3 - - - +
180H LEU* 1.3 78.1 - - - +
182H GLU* 1.3 91.5 + - - +
185H LYS* 3.2 27.2 + - - +
186H ILE 3.4 17.9 + - - +
242H VAL* 4.4 24.9 - - + -
352H LEU* 3.1 37.6 - - + +
353H LYS* 4.6 19.2 - - - +
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Residues in contact with GLU 182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178H THR* 2.9 36.4 + - - +
179H TYR 4.1 0.7 - - - +
181H ARG* 1.3 111.8 + - - +
183H LYS* 1.3 80.1 + - - +
185H LYS* 4.5 11.3 + - - -
353H LYS* 5.0 8.1 - - - -
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Residues in contact with LYS 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179H TYR* 2.7 51.0 + - + +
182H GLU* 1.3 95.2 + - - +
184H HIS* 1.3 82.5 + - + +
185H LYS* 5.7 2.9 - - - -
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Residues in contact with HIS 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H VAL* 4.6 14.3 - - + +
120H GLU* 3.5 37.5 + - + +
121H CYS* 3.7 17.2 - - - -
179H TYR* 3.1 46.5 + + - -
180H LEU* 2.9 13.1 + - + +
183H LYS* 1.3 89.8 + - + +
185H LYS* 1.3 74.0 + - - +
186H ILE* 4.0 19.4 - - + +
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Residues in contact with LYS 185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180H LEU 3.0 3.8 + - - -
181H ARG* 3.2 17.8 + - - +
182H GLU 4.5 12.3 + - - -
183H LYS 5.7 2.2 - - - -
184H HIS* 1.3 80.8 - - - +
186H ILE* 1.3 66.6 + - - +
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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