Contacts of the helix formed by residues 187 - 200 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185G GLY 3.4 4.0 + - - -
186G ALA* 1.3 82.2 - - - +
188G VAL* 1.3 66.2 + - - -
189G ILE 3.3 2.5 - - - -
190G GLY 3.2 4.0 + - - +
191G VAL* 2.9 22.4 + - - +
214G GLY 4.5 1.6 - - - -
215G GLY* 4.2 11.0 - - - -
277G CYS 5.3 1.0 + - - -
481G NAD 3.7 31.2 - - - -
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Residues in contact with VAL 188 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187G GLY* 1.3 71.0 - - - +
189G ILE* 1.3 68.0 + - + +
191G VAL* 3.4 5.9 + - - +
192G GLU* 3.1 39.4 + - - +
214G GLY 3.6 20.9 + - - +
215G GLY* 5.2 0.6 - - - -
356G SER* 6.4 1.3 - - - -
357G VAL 3.9 21.1 - - - +
358G ILE* 4.1 24.0 - - + +
366G TRP* 5.1 5.6 - - + -
480G FAD 6.4 2.5 - - + +
481G NAD 4.9 7.5 + - - +
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Residues in contact with ILE 189 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168G SER* 4.1 4.5 - - - -
187G GLY 3.3 0.6 - - - -
188G VAL* 1.3 81.7 - - + +
190G GLY* 1.3 62.6 + - - +
192G GLU* 3.5 7.4 + - - +
193G LEU* 3.1 39.9 + - + +
277G CYS* 3.6 22.7 - - - -
279G GLY* 6.4 0.4 - - - -
280G ARG* 4.2 16.4 - - + -
480G FAD 3.6 60.1 - - + +
481G NAD 4.9 13.6 + - - +
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Residues in contact with GLY 190 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183G VAL* 4.0 22.6 - - - +
185G GLY 4.4 5.8 - - - -
186G ALA* 5.5 0.2 - - - -
187G GLY* 3.2 8.0 + - - +
189G ILE* 1.3 76.9 - - - +
191G VAL* 1.3 65.1 + - - +
193G LEU* 3.4 3.2 + - - +
194G GLY* 2.9 23.4 + - - -
206G ALA* 6.1 0.7 - - - -
235G PHE* 4.3 2.7 - - - -
275G LEU* 5.2 0.2 - - - -
277G CYS* 3.8 20.1 + - - -
481G NAD 5.7 0.4 + - - -
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Residues in contact with VAL 191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186G ALA* 3.6 20.2 - - + +
187G GLY 2.9 21.2 + - - +
188G VAL* 3.9 5.8 - - - +
190G GLY* 1.3 74.7 - - - +
192G GLU* 1.3 65.2 + - - +
195G SER* 2.9 24.3 + - - -
213G VAL* 4.6 10.5 - - + -
214G GLY* 4.5 8.7 - - - +
226G PHE* 3.8 19.7 - - + -
230G LEU* 3.6 28.5 - - + -
235G PHE* 3.2 16.3 - - + -
237G PHE* 4.7 7.0 - - + -
358G ILE* 4.8 2.9 - - + -
360G THR* 3.9 8.1 - - + -
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Residues in contact with GLU 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G SER* 4.3 5.2 + - - -
54G LYS* 2.6 28.3 + - - -
57G LEU* 3.6 22.8 - - + +
188G VAL* 3.1 25.2 + - - +
189G ILE* 3.8 7.5 - - - +
191G VAL* 1.3 77.8 - - - +
193G LEU* 1.3 60.7 + - + +
195G SER* 3.5 2.4 - - - -
196G VAL* 2.9 32.3 + - - +
357G VAL 4.2 0.2 - - - +
358G ILE* 3.6 18.2 - - + -
359G TYR* 2.7 35.8 + - - +
360G THR* 4.1 10.3 - - + -
480G FAD 4.7 4.2 + - - +
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Residues in contact with LEU 193 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G SER* 4.7 9.0 - - - -
56G LEU* 5.8 0.4 - - + -
168G SER* 3.8 36.8 - - - +
171G ALA* 4.0 17.0 - - + +
172G LEU* 3.6 33.0 - - + -
189G ILE* 3.1 26.9 + - + +
190G GLY 4.1 0.4 - - - +
192G GLU* 1.3 77.0 - - + +
194G GLY* 1.3 65.9 + - - +
196G VAL* 3.4 10.9 + - + +
197G TRP* 3.2 34.9 + - + +
275G LEU* 3.9 21.3 - - + -
277G CYS* 4.8 0.2 - - - -
480G FAD 4.6 3.1 - - + -
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Residues in contact with GLY 194 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G MET* 5.1 3.4 - - - -
183G VAL* 4.3 8.4 - - - +
190G GLY 2.9 16.5 + - - -
191G VAL 3.9 0.7 - - - -
193G LEU* 1.3 76.3 - - - +
195G SER* 1.3 57.6 + - - +
197G TRP* 3.3 3.0 + - - -
198G GLN* 2.8 30.7 + - - +
204G VAL* 3.7 17.0 - - - +
235G PHE* 3.8 17.0 - - - -
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Residues in contact with SER 195 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G LEU* 5.0 0.7 - - - -
191G VAL 2.9 18.4 + - - -
192G GLU 3.2 4.9 + - - -
194G GLY* 1.3 73.6 - - - +
196G VAL* 1.3 66.6 + - - +
198G GLN* 3.6 6.8 + - - +
199G ARG* 3.0 48.2 + - - +
230G LEU* 4.7 2.9 - - - +
233G GLN* 4.2 12.3 + - - -
235G PHE* 3.4 16.6 - - - -
360G THR* 4.3 16.2 - - - +
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Residues in contact with VAL 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G SER 4.6 1.3 - - - +
56G LEU* 3.9 23.1 - - + -
57G LEU* 3.5 41.7 - - + +
60G SER* 3.7 15.9 - - - +
192G GLU 2.9 18.7 + - - +
193G LEU* 3.5 17.3 - - + +
195G SER* 1.3 79.5 - - - +
197G TRP* 1.3 80.7 + - + +
199G ARG* 3.3 10.6 + - - +
200G LEU* 3.3 26.8 + - + +
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Residues in contact with TRP 197 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G LEU* 5.3 2.6 - - + +
85G LEU* 4.0 9.9 - - + -
89G MET* 3.7 26.2 - - + -
171G ALA* 3.1 33.1 + - + +
172G LEU 5.1 0.2 - - - -
174G LEU* 3.4 32.0 - - + +
176G LYS 4.2 1.3 - - - -
177G VAL* 3.8 34.6 - - + +
178G PRO* 4.0 11.7 - - + -
181G MET* 3.4 30.7 - - + -
193G LEU* 3.2 30.8 + - + +
194G GLY 4.0 2.5 - - - +
196G VAL* 1.3 85.7 - - + +
198G GLN* 1.3 66.4 + - - +
200G LEU* 2.9 29.6 + - + +
201G GLY 3.2 0.7 + - - -
202G ALA* 3.0 23.1 + - + +
204G VAL* 4.7 0.7 - - + -
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Residues in contact with GLN 198 (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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194G GLY 2.8 22.0 + - - +
195G SER* 3.6 9.6 + - - +
197G TRP* 1.3 70.7 - - - +
199G ARG* 1.3 74.8 + - - +
201G GLY* 3.0 14.9 + - - -
202G ALA 3.3 19.9 + - - +
204G VAL* 3.8 12.2 - - + +
233G GLN* 3.0 38.0 + - - +
234G GLY* 3.8 23.8 - - - +
235G PHE* 4.2 11.2 - - + +
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Residues in contact with ARG 199 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G LEU* 2.9 39.8 + - - +
60G SER* 2.9 38.9 + - - +
61G HIS* 3.4 15.9 - - - +
63G TYR* 3.5 17.8 - - - -
64G HIS* 4.3 24.7 + - + +
67G HIS* 5.8 0.2 + - - -
195G SER* 3.0 33.8 + - - +
196G VAL* 3.4 5.8 - - - +
197G TRP 3.2 0.2 - - - -
198G GLN* 1.3 87.8 - - - +
200G LEU* 1.3 61.2 + - - +
201G GLY 3.2 0.9 + - - -
233G GLN* 5.3 4.9 + - - +
359G TYR 4.9 0.4 + - - -
360G THR* 3.7 6.1 - - - +
361G HIS* 3.2 44.2 + - - +
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Residues in contact with LEU 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G LEU* 6.1 1.1 - - + -
60G SER* 3.8 21.8 - - - -
63G TYR* 3.7 32.3 + - + -
83G LEU* 4.1 14.5 - - + +
85G LEU* 4.4 9.0 - - + -
88G MET* 4.1 24.7 - - + -
177G VAL* 3.5 25.2 - - + +
196G VAL* 3.3 23.6 - - + +
197G TRP* 2.9 38.5 + - + +
199G ARG* 1.3 77.5 - - - +
201G GLY* 1.3 55.8 + - - +
202G ALA 3.8 0.4 - - - -
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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