Contacts of the helix formed by residues 187 - 201 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185C GLY 3.4 4.6 + - - -
186C ALA* 1.3 77.5 - - - +
188C VAL* 1.3 66.0 + - - -
189C ILE 3.4 2.7 - - - -
190C GLY 3.2 3.4 + - - +
191C VAL* 3.0 24.7 + - - +
214C GLY 4.5 2.0 - - - -
215C GLY* 3.8 13.2 - - - -
277C CYS 5.4 0.4 + - - -
481C NAD 3.3 28.8 + - - -
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Residues in contact with VAL 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C GLY* 1.3 71.7 - - - +
189C ILE* 1.3 68.0 + - + +
191C VAL* 3.3 3.4 + - - +
192C GLU* 3.0 45.4 + - - +
214C GLY 3.6 20.1 - - - +
356C SER* 6.2 1.6 - - - -
357C VAL 3.9 14.1 - - - +
358C ILE* 3.7 36.8 - - + -
366C TRP* 5.0 5.6 - - + -
480C FAD 6.1 3.4 - - + +
481C NAD 3.5 13.1 + - - +
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Residues in contact with ILE 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C SER* 4.1 4.0 - - - -
187C GLY 3.4 0.4 - - - -
188C VAL* 1.3 79.3 - - + +
190C GLY* 1.3 59.2 + - - +
192C GLU* 3.8 8.7 - - - +
193C LEU* 3.0 46.3 + - + +
277C CYS* 3.5 22.4 - - - -
279C GLY* 6.5 0.2 - - - -
280C ARG* 4.3 15.3 - - + -
480C FAD 3.5 58.3 - - + -
481C NAD 4.5 15.4 + - - +
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Residues in contact with GLY 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C VAL* 4.0 16.1 - - - +
185C GLY 4.0 15.3 - - - -
187C GLY* 3.2 7.8 + - - +
189C ILE* 1.3 81.2 - - - +
191C VAL* 1.3 56.3 + - - +
193C LEU* 4.2 2.0 - - - +
194C GLY* 2.8 27.0 + - - -
206C ALA* 6.0 0.9 - - - -
235C PHE* 4.3 2.4 - - - -
275C LEU* 5.0 0.2 - - - -
277C CYS* 3.7 19.2 - - - -
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Residues in contact with VAL 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C ALA* 3.6 21.8 - - + +
187C GLY 3.0 18.9 + - - +
188C VAL* 3.8 5.2 - - - +
190C GLY* 1.3 73.0 - - - +
192C GLU* 1.3 61.3 + - - +
195C SER* 2.8 29.3 + - - -
213C VAL* 4.7 3.8 - - + -
214C GLY* 4.5 7.2 - - - +
226C PHE* 3.7 17.9 - - + -
230C LEU* 3.4 32.8 - - + -
235C PHE* 3.4 10.9 - - + -
237C PHE* 4.6 11.4 - - + -
358C ILE* 5.0 2.7 - - + -
360C THR* 4.0 7.4 - - + -
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Residues in contact with GLU 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C SER* 4.0 7.1 + - - +
54C LYS* 2.9 24.0 + - - -
57C LEU* 3.8 23.8 - - + +
188C VAL* 3.0 31.3 + - - +
189C ILE* 3.8 8.2 - - - +
191C VAL* 1.3 76.5 - - - +
193C LEU* 1.3 65.5 + - + +
195C SER* 3.1 4.2 + - - -
196C VAL* 3.0 27.9 + - - +
357C VAL 4.2 0.2 - - - +
358C ILE* 3.7 18.8 - - + -
359C TYR* 2.8 40.0 + - - +
360C THR* 4.3 4.9 - - + -
480C FAD 4.4 6.5 + - - +
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Residues in contact with LEU 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C SER* 4.6 8.5 - - - -
56C LEU* 5.5 1.1 - - + -
168C SER* 3.8 27.8 - - - +
171C ALA* 4.1 16.6 - - + +
172C LEU* 3.6 34.5 - - + -
189C ILE* 3.0 39.4 + - + +
190C GLY 4.2 0.2 - - - +
192C GLU* 1.3 78.0 - - + +
194C GLY* 1.3 63.3 + - - +
196C VAL* 3.3 10.2 + - + +
197C TRP* 3.2 33.9 + - + +
275C LEU* 3.9 21.8 - - + -
277C CYS* 4.6 0.2 - - - -
480C FAD 4.4 3.6 - - + -
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Residues in contact with GLY 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C MET* 4.3 6.7 - - - -
183C VAL* 4.4 4.6 - - - +
190C GLY 2.8 19.9 + - - -
193C LEU* 1.3 79.0 - - - +
195C SER* 1.3 56.2 + - - +
197C TRP* 3.6 0.3 + - - -
198C GLN* 2.9 29.6 + - - +
204C VAL* 3.8 15.6 - - - +
235C PHE* 3.5 17.9 - - - -
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Residues in contact with SER 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C LEU* 4.9 1.1 - - - -
191C VAL 2.8 19.2 + - - -
192C GLU 3.6 4.0 - - - -
194C GLY* 1.3 77.8 - - - +
196C VAL* 1.3 62.7 + - - +
198C GLN* 3.5 5.1 + - - +
199C ARG* 3.0 55.6 + - - +
230C LEU* 4.3 9.3 - - - +
233C GLN* 4.4 5.5 + - - -
235C PHE* 3.4 14.2 - - - -
360C THR* 3.9 18.1 - - - +
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Residues in contact with VAL 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C SER* 4.7 1.8 - - - +
56C LEU* 4.0 26.9 - - + +
57C LEU* 3.6 38.8 - - + +
60C SER* 3.9 12.4 - - - +
88C MET* 6.5 0.2 - - - -
192C GLU 3.0 20.2 + - - +
193C LEU* 3.3 16.1 + - + +
195C SER* 1.3 78.4 - - - +
197C TRP* 1.3 76.7 + - + +
199C ARG* 3.5 3.9 + - - +
200C LEU* 3.2 39.2 + - + +
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Residues in contact with TRP 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU* 5.0 5.1 - - + +
85C LEU* 3.7 16.8 - - + -
89C MET* 3.7 25.6 - - + -
171C ALA* 3.0 27.8 + - + +
174C LEU* 3.4 40.8 - - + +
176C LYS 4.2 0.9 - - - -
177C VAL* 4.0 21.4 - - + +
178C PRO* 4.0 11.9 - - + -
181C MET* 3.3 32.3 - - + -
193C LEU* 3.2 28.3 + - + +
196C VAL* 1.3 82.9 - - + +
198C GLN* 1.3 65.5 + - - +
200C LEU* 3.2 37.2 + - + +
201C GLY 3.4 0.5 + - - -
202C ALA* 3.0 27.3 + - + +
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Residues in contact with GLN 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C GLY 2.9 20.5 + - - +
195C SER* 3.5 9.2 + - - +
196C VAL 3.3 0.2 - - - -
197C TRP* 1.3 79.0 - - - +
199C ARG* 1.3 78.7 + - - +
201C GLY* 3.1 9.9 + - - -
202C ALA 3.5 22.3 + - - +
204C VAL* 3.7 12.0 - - + +
233C GLN* 2.9 39.9 + - - +
234C GLY* 3.7 10.6 - - - +
235C PHE* 4.0 24.1 - - + +
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Residues in contact with ARG 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C LEU* 3.0 30.6 + - - +
60C SER* 2.9 45.1 + - - +
61C HIS* 3.7 12.7 - - - +
63C TYR* 3.5 17.4 - - - -
64C HIS* 4.6 22.8 + - + +
195C SER* 3.0 32.7 + - - +
196C VAL* 3.7 3.8 - - - +
197C TRP 3.3 0.2 - - - -
198C GLN* 1.3 88.4 + - - +
200C LEU* 1.3 60.9 + - - +
201C GLY* 3.2 2.2 + - - -
233C GLN* 5.4 4.4 + - - +
359C TYR 5.4 0.2 + - - -
360C THR* 3.9 4.2 - - - +
361C HIS* 3.2 46.3 + - - +
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Residues in contact with LEU 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU* 6.3 1.3 - - + -
60C SER* 4.1 10.3 - - - -
63C TYR* 3.8 30.8 + - + -
83C LEU* 4.0 17.4 - - + +
85C LEU* 4.2 13.2 - - + -
88C MET* 4.0 27.6 - - + -
177C VAL* 3.5 24.8 - - + +
196C VAL* 3.2 24.4 + - + +
197C TRP* 3.2 39.0 + - + +
199C ARG* 1.3 74.7 - - - +
201C GLY* 1.3 56.8 + - - +
202C ALA 3.8 0.9 - - - -
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Residues in contact with GLY 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C VAL* 4.0 6.5 - - - -
178C PRO 4.7 0.4 - - - +
179C GLU* 4.7 2.9 - - - +
198C GLN 3.1 7.2 + - - -
199C ARG 3.2 2.2 + - - -
200C LEU* 1.3 80.9 - - - +
202C ALA* 1.3 64.8 + - - +
203C ASP 3.9 0.5 + - - -
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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