Contacts of the helix formed by residues 187 - 200 (chain F) in PDB entry 1ZMC
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 187 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185F GLY 3.5 4.4 + - - -
186F ALA* 1.3 80.4 - - - +
188F VAL* 1.3 60.5 + - - -
189F ILE 3.4 2.2 - - - -
190F GLY 3.4 3.9 + - - +
191F VAL* 2.9 28.7 + - - +
208F GLU* 4.3 0.2 + - - -
214F GLY 4.4 2.0 - - - -
215F GLY* 4.1 14.6 - - - -
277F CYS* 5.5 0.4 + - - +
481F NAD 3.7 28.1 + - - -
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Residues in contact with VAL 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187F GLY* 1.3 67.3 - - - -
189F ILE* 1.3 83.2 + - + +
191F VAL* 3.2 5.4 + - - +
192F GLU* 2.9 35.7 + - + +
214F GLY 3.4 20.5 + - - +
327F LEU* 6.2 3.8 - - + -
356F SER* 6.4 0.4 - - - -
357F VAL 4.8 7.4 - - - +
358F ILE* 3.7 31.9 - - + -
366F TRP* 5.1 4.9 - - + -
481F NAD 4.2 14.8 + - - +
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Residues in contact with ILE 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F SER* 4.1 4.7 - - - -
187F GLY 3.4 0.2 - - - -
188F VAL* 1.3 85.9 - - + +
190F GLY* 1.3 62.8 + - - +
192F GLU* 3.9 6.8 - - - +
193F LEU* 3.0 38.0 + - + +
277F CYS* 3.5 23.6 - - + -
280F ARG* 4.0 17.7 - - + -
480F FAD 3.5 61.0 - - + -
481F NAD 5.0 7.7 + - - +
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Residues in contact with GLY 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F VAL* 4.0 21.1 - - - +
185F GLY 4.2 8.5 - - - -
186F ALA* 5.4 0.2 - - - -
187F GLY* 3.4 7.6 + - - +
188F VAL 3.3 0.4 - - - -
189F ILE* 1.3 79.2 - - - +
191F VAL* 1.3 58.8 + - - +
193F LEU* 4.1 2.0 - - - +
194F GLY* 2.8 27.4 + - - -
206F ALA* 6.1 0.9 - - - -
235F PHE* 4.3 3.1 - - - -
277F CYS* 3.8 20.0 - - - +
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Residues in contact with VAL 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186F ALA* 3.6 11.4 - - + +
187F GLY 2.9 22.5 + - - +
188F VAL* 3.8 7.0 - - - +
190F GLY* 1.3 77.6 - - - +
192F GLU* 1.3 58.2 + - - +
195F SER* 2.9 29.1 + - - -
213F VAL* 3.5 28.5 - - + -
214F GLY* 4.7 1.8 - - - +
226F PHE* 3.7 21.8 - - + -
230F LEU* 3.9 10.5 - - + -
235F PHE* 3.4 8.6 - - + -
237F PHE* 4.7 6.7 - - + -
358F ILE* 4.5 3.1 - - + -
360F THR* 3.7 21.1 - - + -
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Residues in contact with GLU 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F SER* 4.3 7.4 + - - -
54F LYS* 2.6 26.8 + - - -
57F LEU* 3.7 20.2 - - + +
188F VAL* 2.9 25.2 + - - +
189F ILE* 3.9 5.6 - - - +
191F VAL* 1.3 77.2 - - - +
193F LEU* 1.3 64.7 + - + +
195F SER* 3.3 1.7 + - - -
196F VAL* 3.0 28.0 + - - +
357F VAL 4.2 2.3 - - - +
358F ILE* 3.7 18.1 - - + -
359F TYR* 2.8 38.1 + - - +
360F THR* 4.2 9.6 - - + -
480F FAD 4.4 7.9 + - - +
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Residues in contact with LEU 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F SER* 5.0 8.5 - - - -
56F LEU* 5.9 1.1 - - + -
168F SER* 3.6 36.6 - - - -
171F ALA* 3.7 22.4 - - + +
172F LEU* 3.8 28.3 - - + -
181F MET* 4.7 0.9 - - - -
189F ILE* 3.0 28.8 + - + +
190F GLY 4.1 0.4 - - - +
192F GLU* 1.3 78.9 - - + +
194F GLY* 1.3 61.8 + - - +
196F VAL* 3.3 9.9 + - + +
197F TRP* 3.3 32.7 + - + +
275F LEU* 3.7 23.3 - - + -
480F FAD 4.9 2.7 - - + -
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Residues in contact with GLY 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F MET* 4.1 15.9 - - - +
183F VAL* 4.5 2.6 - - - +
190F GLY 2.8 16.5 + - - -
193F LEU* 1.3 76.8 - - - +
195F SER* 1.3 59.5 + - - +
196F VAL 3.3 0.2 + - - -
197F TRP* 3.3 1.7 + - - -
198F GLN* 2.9 30.0 + - - +
204F VAL* 3.9 9.0 - - - +
235F PHE* 3.7 17.9 - - - -
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Residues in contact with SER 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F LEU* 5.0 0.9 - - - -
191F VAL 2.9 19.1 + - - -
192F GLU 3.8 3.6 - - - -
194F GLY* 1.3 76.0 - - - +
196F VAL* 1.3 63.2 + - - +
198F GLN* 3.8 6.1 + - - +
199F ARG* 3.2 48.7 + - - +
230F LEU* 4.6 3.7 - - - +
233F GLN* 4.2 11.6 + - - -
235F PHE* 3.4 17.3 - - - -
360F THR* 4.2 17.1 - - - +
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Residues in contact with VAL 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F SER* 4.7 1.3 - - - +
56F LEU* 3.9 26.0 - - + +
57F LEU* 3.6 39.0 - - + +
60F SER* 3.8 14.9 - - - +
88F MET* 6.4 0.2 - - - -
192F GLU 3.0 19.4 + - - +
193F LEU* 3.6 14.8 - - + +
194F GLY 3.2 0.2 - - - -
195F SER* 1.3 79.2 - - - +
197F TRP* 1.3 77.2 + - + +
199F ARG* 3.3 3.9 + - - +
200F LEU* 3.2 32.9 + - + +
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Residues in contact with TRP 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F LEU* 5.3 2.6 - - + +
85F LEU* 3.8 22.9 - - + -
89F MET* 3.9 15.3 - - + -
171F ALA* 3.1 26.4 + - + +
174F LEU* 3.4 40.8 - - + +
176F LYS 4.3 0.9 - - - -
177F VAL* 3.8 30.6 - - + +
178F PRO* 4.0 12.3 - - + -
181F MET* 3.9 29.8 - - + -
193F LEU* 3.3 28.7 + - + +
196F VAL* 1.3 86.0 - - + +
198F GLN* 1.3 66.0 + - - +
200F LEU* 3.1 30.6 + - + +
201F GLY 3.3 0.9 + - - -
202F ALA* 2.9 32.1 + - + +
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Residues in contact with GLN 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194F GLY 2.9 19.1 + - - +
195F SER* 3.8 10.2 + - - +
197F TRP* 1.3 75.1 - - - +
199F ARG* 1.3 79.6 + - - +
201F GLY* 3.2 11.6 + - - -
202F ALA 3.3 20.8 + - - +
204F VAL* 3.8 10.9 - - + +
233F GLN* 3.0 39.9 + - - +
234F GLY* 4.1 23.3 - - - +
235F PHE* 4.2 10.3 - - + +
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Residues in contact with ARG 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F LEU* 2.9 40.6 + - - +
60F SER* 3.1 36.4 + - - +
61F HIS* 3.5 14.6 - - - +
63F TYR* 3.3 19.6 - - - -
64F HIS* 4.4 22.6 + - + +
195F SER* 3.2 32.3 + - - +
196F VAL 3.5 5.4 - - - +
197F TRP 3.2 0.2 - - - -
198F GLN* 1.3 91.3 - - - +
200F LEU* 1.3 60.3 + - - +
201F GLY 3.2 0.9 + - - -
233F GLN* 5.2 3.6 + - - +
359F TYR 5.3 0.2 + - - -
360F THR* 3.7 5.5 - - - +
361F HIS* 3.1 45.6 + - - +
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Residues in contact with LEU 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F LEU* 5.9 2.0 - - + -
60F SER* 3.6 21.1 - - - -
63F TYR* 3.6 32.9 + - + -
83F LEU* 3.9 23.8 - - + +
85F LEU* 4.2 6.1 - - + -
88F MET* 4.0 25.8 - - - -
177F VAL* 3.4 17.6 - - + +
196F VAL* 3.3 20.9 - - + +
197F TRP* 3.1 42.5 + - + +
199F ARG* 1.3 77.4 - - - +
201F GLY* 1.3 57.5 + - - +
202F ALA 3.7 0.2 - - - -
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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