Contacts of the helix formed by residues 187 - 200 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A GLY 3.4 4.4 + - - -
186A ALA* 1.3 82.6 - - - +
188A VAL* 1.3 65.6 + - - -
189A ILE 3.3 2.9 - - - -
190A GLY 3.2 4.7 + - - +
191A VAL* 2.9 19.2 + - - +
208A GLU* 4.3 0.4 + - - -
214A GLY 4.4 1.1 - - - -
215A GLY* 4.0 11.9 - - - -
277A CYS 5.3 0.6 + - - -
481A NAD 3.1 30.5 + - - -
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Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLY* 1.3 71.5 - - - -
189A ILE* 1.3 67.8 + - + +
191A VAL* 3.3 7.6 + - - +
192A GLU* 3.0 39.9 + - - +
214A GLY* 3.5 21.8 + - - +
215A GLY* 5.6 0.2 - - - -
356A SER* 6.4 0.7 - - - -
357A VAL 4.0 14.4 - - - +
358A ILE* 3.9 38.8 - - + -
366A TRP* 4.8 6.3 - - + -
480A FAD 6.5 0.7 - - + -
481A NAD 3.7 7.7 + - - +
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Residues in contact with ILE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A SER* 4.1 3.4 - - - +
187A GLY 3.3 0.8 - - - -
188A VAL* 1.3 79.9 - - + +
190A GLY* 1.3 63.1 + - - +
192A GLU* 3.8 6.5 - - - +
193A LEU* 3.1 33.9 + - + +
277A CYS* 3.5 23.1 - - - -
279A GLY 6.2 0.4 - - - -
280A ARG* 4.5 14.8 - - + -
480A FAD 3.7 64.2 - - + +
481A NAD 4.6 17.2 + - - +
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Residues in contact with GLY 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A VAL* 3.9 28.5 - - - +
185A GLY 4.2 7.4 - - - -
186A ALA* 5.4 0.2 - - - -
187A GLY 3.2 7.6 + - - +
189A ILE* 1.3 77.9 - - - +
191A VAL* 1.3 57.7 + - - +
193A LEU* 4.2 0.2 - - - +
194A GLY* 2.8 29.8 + - - -
235A PHE* 4.3 2.7 - - - -
275A LEU* 4.8 2.7 - - - -
277A CYS* 3.8 12.8 - - - +
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Residues in contact with VAL 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ALA* 3.8 10.3 - - + +
187A GLY 2.9 18.2 + - - +
188A VAL* 3.7 6.5 - - - +
190A GLY* 1.3 76.5 - - - +
192A GLU* 1.3 58.3 + - - +
195A SER* 2.9 28.1 + - - -
213A VAL* 3.6 26.9 - - + -
214A GLY* 4.4 3.1 - - - +
226A PHE* 3.8 16.6 - - + -
230A LEU* 3.7 30.1 - - + -
235A PHE* 3.3 14.5 - - + -
237A PHE* 4.9 3.4 - - + -
358A ILE* 4.7 2.7 - - + -
360A THR* 4.0 8.1 - - + -
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Residues in contact with GLU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A SER* 4.1 5.5 + - - -
54A LYS* 3.0 22.6 + - - -
57A LEU* 3.8 22.4 - - + +
188A VAL* 3.0 27.9 + - - +
189A ILE* 3.3 6.1 + - - +
191A VAL* 1.3 74.8 - - - +
193A LEU* 1.3 67.2 + - + +
195A SER* 3.1 4.3 + - - -
196A VAL* 2.9 27.6 + - - +
357A VAL 4.2 0.2 - - - +
358A ILE* 3.6 16.6 - - + -
359A TYR* 2.7 38.5 + - - +
360A THR* 4.2 11.0 - - + -
480A FAD 4.5 8.6 + - - +
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Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A SER* 4.4 12.6 - - - -
56A LEU* 6.0 0.4 - - + -
168A SER* 3.9 22.9 - - - -
171A ALA* 4.0 12.1 - - + -
172A LEU* 3.6 32.8 - - + -
181A MET* 5.8 0.2 - - - -
189A ILE* 3.1 33.0 + - + +
192A GLU* 1.3 77.0 - - + +
194A GLY* 1.3 64.5 + - - +
196A VAL* 2.9 23.0 + - + +
197A TRP* 3.2 22.7 + - + +
275A LEU* 3.8 29.8 - - + -
480A FAD 4.7 1.6 - - + -
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Residues in contact with GLY 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A MET* 5.3 4.0 - - - -
183A VAL* 4.3 9.9 - - - +
190A GLY 2.8 18.8 + - - -
191A VAL 3.7 0.9 - - - -
193A LEU* 1.3 77.2 - - - +
195A SER* 1.3 60.9 + - - +
197A TRP* 3.7 0.7 + - - +
198A GLN* 3.1 23.7 + - - +
204A VAL* 3.8 16.5 - - - +
235A PHE* 3.7 16.4 - - - -
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Residues in contact with SER 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LEU* 5.2 0.4 - - - -
191A VAL 2.9 17.9 + - - -
192A GLU 3.6 4.3 - - - -
194A GLY* 1.3 74.2 - - - +
196A VAL* 1.3 66.9 + - - +
198A GLN* 3.6 8.8 + - - +
199A ARG* 3.0 53.4 + - - +
230A LEU* 4.8 4.7 - - - +
233A GLN* 4.5 10.9 + - - -
235A PHE* 3.5 13.8 - - - -
360A THR* 4.6 13.2 - - - +
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Residues in contact with VAL 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A SER* 4.7 1.6 - - - +
56A LEU* 4.0 25.1 - - + -
57A LEU* 3.6 38.6 - - + +
60A SER* 3.8 16.2 - - - +
88A MET* 5.3 0.2 - - + -
192A GLU 2.9 20.5 + - - +
193A LEU* 2.9 17.0 + - + +
195A SER* 1.3 80.5 - - - +
197A TRP* 1.3 76.9 + - + +
199A ARG* 3.2 12.3 + - - +
200A LEU* 3.2 26.1 + - + +
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Residues in contact with TRP 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU* 5.0 5.2 - - + +
85A LEU* 4.2 8.3 - - + -
89A MET* 3.7 27.1 - - + -
171A ALA* 3.1 33.0 + - + +
174A LEU* 3.4 35.2 - - + +
177A VAL* 3.9 27.4 - - + -
178A PRO* 3.8 12.8 - - + -
181A MET* 3.4 30.1 - - + -
193A LEU* 3.2 30.4 + - + +
194A GLY 4.3 2.2 - - - +
196A VAL* 1.3 82.6 - - + +
198A GLN* 1.3 68.3 + - - +
200A LEU* 2.9 34.8 + - + +
201A GLY 3.3 0.5 + - - -
202A ALA* 3.1 24.0 + - + +
204A VAL* 4.6 1.1 - - + -
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Residues in contact with GLN 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A GLY 3.1 19.6 + - - +
195A SER* 3.6 10.1 + - - +
197A TRP* 1.3 74.6 - - - +
199A ARG* 1.3 82.6 + - - +
201A GLY* 3.0 14.9 + - - -
202A ALA 3.4 19.0 + - - +
204A VAL* 3.7 10.8 - - + +
233A GLN* 2.7 37.8 + - - +
234A GLY* 3.6 11.7 - - - +
235A PHE* 4.0 25.6 - - + +
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Residues in contact with ARG 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LEU* 2.8 43.4 + - - +
60A SER* 3.1 34.0 + - - +
61A HIS* 3.4 15.9 + - - +
63A TYR* 3.6 16.5 - - - -
64A HIS* 4.7 22.9 + - + +
67A HIS* 5.7 1.6 - - - -
195A SER* 3.0 37.5 + - - +
196A VAL 3.2 7.2 - - - +
198A GLN* 1.3 88.6 - - - +
200A LEU* 1.3 57.0 + - - +
201A GLY 3.2 3.7 + - - -
233A GLN* 5.6 3.0 + - - +
359A TYR 4.8 0.8 + - - -
360A THR* 3.6 8.9 - - - +
361A HIS* 3.1 45.4 + - - +
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Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU* 6.3 0.2 - - + -
60A SER* 3.9 11.2 - - - -
63A TYR* 3.6 32.8 + - + -
83A LEU* 4.0 15.8 - - + +
85A LEU* 4.4 9.2 - - + -
88A MET* 3.4 36.1 - - + -
89A MET* 6.2 0.2 - - + -
177A VAL* 3.3 27.1 - - + +
196A VAL* 3.3 20.4 - - + +
197A TRP* 2.9 39.8 + - + +
199A ARG* 1.3 76.3 - - - +
201A GLY* 1.3 54.4 + - - +
202A ALA 3.6 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