Contacts of the helix formed by residues 187 - 200 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185H GLY 3.4 4.6 + - - -
186H ALA* 1.3 82.9 - - - +
188H VAL* 1.3 67.7 + - - -
189H ILE 3.3 2.5 - - - -
190H GLY 3.3 3.2 + - - +
191H VAL* 3.0 18.4 + - - +
208H GLU* 4.0 0.8 + - - -
214H GLY 4.3 2.0 - - - -
215H GLY* 3.7 14.8 - - - -
277H CYS 5.3 0.4 + - - -
481H NAD 3.6 28.6 + - - -
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Residues in contact with VAL 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187H GLY* 1.3 70.6 - - - -
189H ILE* 1.3 70.1 + - + +
191H VAL* 3.3 6.3 + - - +
192H GLU* 3.1 42.2 + - + +
214H GLY 3.5 20.5 - - - +
215H GLY* 5.5 0.2 - - - -
356H SER* 6.1 2.2 - - - -
357H VAL 4.1 8.5 - - - +
358H ILE* 3.6 34.5 - - + -
366H TRP* 4.7 6.1 - - + -
480H FAD 6.1 5.4 - - + +
481H NAD 4.5 5.7 + - - +
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Residues in contact with ILE 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H SER* 4.1 4.7 - - - -
187H GLY 3.3 1.0 - - - -
188H VAL* 1.3 83.1 - - + +
190H GLY* 1.3 62.7 + - - +
192H GLU* 3.5 5.5 + - - +
193H LEU* 3.1 37.9 + - + +
277H CYS* 3.4 23.3 - - - -
279H GLY* 6.1 0.9 - - - -
280H ARG* 4.2 17.0 - - + -
480H FAD 3.8 57.7 - - + -
481H NAD 4.6 14.8 + - - +
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Residues in contact with GLY 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183H VAL* 4.0 15.8 - - - +
185H GLY 3.9 15.5 - - - -
186H ALA* 5.3 0.4 - - - -
187H GLY 3.3 7.9 + - - +
188H VAL 3.3 0.4 - - - -
189H ILE* 1.3 77.6 - - - +
191H VAL* 1.3 60.1 + - - +
193H LEU* 4.8 2.2 - - - -
194H GLY* 2.9 25.3 + - - -
206H ALA* 6.1 0.9 - - - -
235H PHE* 4.1 3.8 - - - -
277H CYS* 3.7 18.3 + - - -
481H NAD 5.5 0.4 + - - -
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Residues in contact with VAL 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186H ALA* 3.6 19.1 - - + +
187H GLY 3.0 19.9 + - - +
188H VAL* 3.9 6.1 - - - +
189H ILE 3.3 0.4 - - - -
190H GLY* 1.3 75.2 - - - +
192H GLU* 1.3 66.0 + - - +
195H SER* 2.9 22.7 + - - -
213H VAL* 4.6 9.2 - - + -
214H GLY* 4.5 7.2 - - - +
226H PHE* 3.9 17.7 - - + -
230H LEU* 3.5 30.5 - - + -
235H PHE* 3.4 12.1 - - + -
237H PHE* 4.8 5.8 - - + -
358H ILE* 4.8 3.1 - - + -
360H THR* 3.9 7.9 - - + -
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Residues in contact with GLU 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H SER* 4.4 6.2 + - - -
54H LYS* 2.8 27.1 + - - -
57H LEU* 3.7 25.7 - - + +
188H VAL* 3.1 26.1 + - - +
189H ILE* 4.0 5.1 - - - +
191H VAL* 1.3 77.3 - - - +
193H LEU* 1.3 65.9 + - + +
195H SER* 3.2 0.7 + - - -
196H VAL* 3.0 26.1 + - - +
357H VAL 4.0 0.3 - - - +
358H ILE* 3.5 19.1 - - + -
359H TYR* 2.6 37.3 + - - +
360H THR* 4.0 9.9 - - + -
480H FAD 4.5 6.6 + - - +
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Residues in contact with LEU 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H SER* 4.6 10.5 - - - -
56H LEU* 6.0 0.4 - - + -
168H SER* 3.6 37.0 - - - -
171H ALA* 4.1 13.2 - - + +
172H LEU* 3.6 33.7 - - + -
181H MET* 4.5 1.1 - - - -
189H ILE* 3.1 24.3 + - + +
190H GLY 4.3 0.4 - - - +
192H GLU* 1.3 75.5 - - + +
194H GLY* 1.3 64.3 + - - +
196H VAL* 3.3 10.4 + - + +
197H TRP* 3.2 33.3 + - + +
275H LEU* 3.8 26.9 - - + -
480H FAD 4.7 2.7 - - + -
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Residues in contact with GLY 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181H MET* 4.1 15.8 - - - +
183H VAL* 4.4 1.3 - - - -
190H GLY 2.9 20.5 + - - -
193H LEU* 1.3 79.6 - - - +
195H SER* 1.3 54.8 + - - +
197H TRP* 3.4 1.2 + - - +
198H GLN* 3.0 27.7 + - - +
204H VAL* 3.9 10.2 - - - +
235H PHE* 3.5 17.9 - - - -
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Residues in contact with SER 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H LEU* 5.0 0.4 - - - -
191H VAL 2.9 17.6 + - - -
192H GLU 3.7 3.1 - - - -
194H GLY* 1.3 72.2 - - - +
196H VAL* 1.3 67.4 + - - +
198H GLN* 3.7 7.3 + - - +
199H ARG* 2.9 49.7 + - - +
230H LEU* 4.9 4.2 - - - +
233H GLN* 4.3 11.1 + - - -
235H PHE* 3.2 18.2 - - - -
360H THR* 4.2 16.3 - - - +
361H HIS 5.4 0.2 + - - -
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Residues in contact with VAL 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H SER 4.7 0.7 - - - +
56H LEU* 3.8 25.8 - - + +
57H LEU* 3.3 52.3 - - + +
60H SER* 3.7 10.2 - - - +
88H MET* 5.5 0.2 - - + -
192H GLU 3.0 10.2 + - - +
193H LEU* 3.6 14.4 - - + +
195H SER* 1.3 78.7 - - - +
197H TRP* 1.3 84.6 + - + +
199H ARG* 3.2 4.0 + - - +
200H LEU* 3.2 33.8 + - + +
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Residues in contact with TRP 197 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H LEU* 5.0 4.8 - - + +
85H LEU* 4.0 15.3 - - + -
89H MET* 3.7 26.0 - - + -
171H ALA* 2.9 31.5 + - + +
174H LEU* 3.5 31.8 - - + +
176H LYS 4.3 1.1 - - - -
177H VAL* 4.0 24.2 - - + +
178H PRO* 4.0 11.7 - - + -
181H MET* 4.1 29.6 - - + -
193H LEU* 3.2 30.9 + - + +
194H GLY 4.1 1.8 - - - +
196H VAL* 1.3 81.9 - - + +
198H GLN* 1.3 66.2 + - - +
200H LEU* 3.2 31.1 + - + +
201H GLY 3.4 0.7 + - - -
202H ALA* 3.1 30.5 + - + +
204H VAL* 4.6 1.1 - - + -
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Residues in contact with GLN 198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194H GLY 3.0 18.8 + - - +
195H SER* 3.7 10.6 + - - +
196H VAL 3.3 0.2 - - - -
197H TRP* 1.3 75.5 - - - +
199H ARG* 1.3 77.4 + - - +
201H GLY* 3.0 12.5 + - - -
202H ALA 3.5 21.2 + - - +
204H VAL* 3.8 12.3 - - + +
233H GLN* 3.1 35.2 + - - +
234H GLY* 4.0 23.1 - - - +
235H PHE* 4.1 9.9 - - + +
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Residues in contact with ARG 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57H LEU* 2.7 42.2 + - - +
60H SER* 3.0 35.9 + - - +
61H HIS* 3.3 16.2 - - - +
63H TYR* 3.9 14.6 - - - -
64H HIS* 4.4 23.9 + - + +
67H HIS* 5.9 0.2 + - - -
195H SER* 2.9 34.1 + - - +
196H VAL 3.4 6.1 - - - +
198H GLN* 1.3 89.0 - - - +
200H LEU* 1.3 62.6 + - - +
201H GLY 3.2 1.7 + - - -
233H GLN* 5.2 4.3 + - - +
359H TYR 4.9 0.6 + - - -
360H THR* 3.8 7.9 - - - +
361H HIS* 3.2 43.0 + - - +
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Residues in contact with LEU 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H LEU* 6.3 0.4 - - + -
60H SER* 3.8 12.1 - - - -
63H TYR* 3.9 27.3 + - + -
83H LEU* 3.9 25.3 - - + +
85H LEU* 4.3 6.1 - - + -
88H MET* 3.6 34.5 - - + -
177H VAL* 3.6 24.5 - - + +
196H VAL* 3.2 19.6 + - + +
197H TRP* 3.7 36.6 - - + +
198H GLN 3.2 1.4 - - - -
199H ARG* 1.3 76.3 - - - +
201H GLY* 1.3 55.0 + - - +
202H 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
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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