Contacts of the helix formed by residues 187 - 200 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185D GLY 3.6 3.8 + - - -
186D ALA* 1.3 80.1 - - - +
188D VAL* 1.3 61.7 + - - -
189D ILE 3.4 1.6 - - - -
190D GLY* 3.9 5.0 - - - +
191D VAL* 2.9 27.3 + - - +
214D GLY 4.4 2.0 - - - -
215D GLY* 4.1 12.6 - - - -
277D CYS 5.4 0.2 + - - -
481D NAD 3.3 30.5 + - - -
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Residues in contact with VAL 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D GLY* 1.3 70.1 - - - -
189D ILE* 1.3 72.2 + - + +
191D VAL* 3.1 5.1 + - - +
192D GLU* 2.9 40.3 + - + +
214D GLY* 3.6 20.6 + - - +
356D SER* 6.2 2.0 - - - -
357D VAL 3.9 21.5 - - - +
358D ILE* 3.8 28.3 - - + -
366D TRP* 4.8 6.3 - - + -
480D FAD 6.1 2.7 - - + +
481D NAD 3.7 7.5 + - - +
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Residues in contact with ILE 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D SER* 4.2 4.0 - - - -
187D GLY 3.4 0.2 - - - -
188D VAL* 1.3 79.4 - - + +
190D GLY* 1.3 62.4 + - - +
192D GLU* 3.4 7.5 + - - +
193D LEU* 3.1 33.0 + - + +
277D CYS* 3.6 22.2 - - - -
279D GLY* 6.4 0.7 - - - -
280D ARG* 4.4 14.6 - - + -
480D FAD 3.5 69.5 - - + +
481D NAD 4.8 14.3 + - - +
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Residues in contact with GLY 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D VAL* 4.0 23.4 - - - +
185D GLY 4.3 8.3 - - - -
186D ALA* 5.2 0.2 - - - -
187D GLY* 3.4 8.9 + - - +
188D VAL 3.2 0.6 - - - -
189D ILE* 1.3 80.7 - - - +
191D VAL* 1.3 61.8 + - - +
193D LEU* 4.3 0.3 - - - +
194D GLY* 3.1 21.3 + - - -
206D ALA* 6.1 0.7 - - - -
235D PHE* 4.4 2.2 - - - -
275D LEU* 5.0 2.0 - - - -
277D CYS* 3.7 19.1 - - - -
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Residues in contact with VAL 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D ALA* 3.7 22.9 - - + +
187D GLY 2.9 23.8 + - - +
188D VAL* 3.7 4.7 - - - +
190D GLY* 1.3 77.1 - - - +
192D GLU* 1.3 62.8 + - - +
194D GLY 3.4 0.5 + - - -
195D SER* 3.0 20.8 + - - -
213D VAL* 4.5 11.9 - - + -
214D GLY* 4.5 3.8 - - - +
226D PHE* 3.9 32.5 - - + -
230D LEU* 3.9 13.0 - - + -
235D PHE* 3.4 13.6 - - + -
237D PHE* 4.7 6.7 - - + -
358D ILE* 4.6 2.9 - - + -
360D THR* 3.9 9.2 - - + -
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Residues in contact with GLU 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D SER* 4.4 6.4 + - - -
54D LYS* 2.8 25.5 + - - -
57D LEU* 3.8 20.7 - - + +
188D VAL* 2.9 34.3 + - + +
189D ILE* 3.9 6.1 - - - +
190D GLY 3.4 0.2 - - - -
191D VAL* 1.3 75.5 - - - +
193D LEU* 1.3 65.8 + - + +
195D SER* 3.2 2.6 + - - -
196D VAL* 3.0 27.3 + - - +
357D VAL 4.1 0.2 - - - +
358D ILE* 3.5 14.8 - - + -
359D TYR* 2.6 40.8 + - - +
360D THR* 4.1 9.0 - - + -
480D FAD 4.3 9.3 + - - +
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Residues in contact with LEU 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D SER* 4.9 9.0 - - - -
56D LEU* 5.8 1.6 - - + -
168D SER* 3.7 33.0 - - - -
171D ALA* 3.8 15.9 - - + +
172D LEU* 3.7 31.9 - - + -
181D MET* 4.7 0.9 - - - -
189D ILE* 3.1 26.2 + - + +
190D GLY 4.3 0.2 - - - +
192D GLU* 1.3 77.1 - - + +
194D GLY* 1.3 66.4 + - - +
196D VAL* 3.1 18.8 + - + +
197D TRP* 3.3 24.3 + - + +
275D LEU* 3.7 29.4 - - + -
277D CYS* 4.7 0.7 - - - -
480D FAD 4.7 2.2 - - + -
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Residues in contact with GLY 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D MET* 4.0 15.0 - - - +
183D VAL* 4.2 4.2 - - - +
190D GLY 3.1 18.4 + - - -
191D VAL 3.8 1.1 - - - -
193D LEU* 1.3 79.2 - - - +
195D SER* 1.3 60.5 + - - +
197D TRP* 3.6 0.7 + - - +
198D GLN* 3.1 23.0 + - - +
204D VAL* 3.8 10.8 - - - +
235D PHE* 3.9 16.8 - - - -
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Residues in contact with SER 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D LEU* 5.1 0.2 - - - -
191D VAL 3.0 17.1 + - - -
192D GLU 3.8 3.6 - - - -
194D GLY* 1.3 74.2 - - - +
196D VAL* 1.3 65.9 + - - +
198D GLN* 3.9 8.4 + - - +
199D ARG* 3.0 54.2 + - - +
230D LEU* 4.7 3.6 - - - +
233D GLN* 4.4 11.6 + - - -
235D PHE* 3.6 14.8 - - - -
360D THR* 4.3 15.3 - - - +
361D HIS 5.5 0.2 + - - -
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Residues in contact with VAL 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D SER* 4.7 1.6 - - - +
56D LEU* 4.0 24.5 - - + -
57D LEU* 3.8 37.5 - - + +
60D SER* 3.7 12.3 - - - +
192D GLU 3.0 20.1 + - - +
193D LEU* 3.1 17.0 + - + +
195D SER* 1.3 81.2 - - - +
197D TRP* 1.3 79.6 + - + +
199D ARG* 3.3 5.0 + - - +
200D LEU* 3.3 36.1 + - + +
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Residues in contact with TRP 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D LEU* 5.2 2.2 - - + +
85D LEU* 4.0 13.0 - - + -
89D MET* 3.8 26.9 - - + -
171D ALA* 3.0 30.2 + - + +
174D LEU* 3.5 33.1 - - + +
177D VAL* 3.9 30.5 - - + -
178D PRO* 3.8 12.8 - - + -
181D MET* 3.8 32.5 - - + -
193D LEU* 3.3 25.4 + - + +
195D SER 3.3 0.2 - - - -
196D VAL* 1.3 86.2 - - + +
198D GLN* 1.3 65.5 + - - +
199D ARG 3.1 1.3 - - - -
200D LEU* 2.9 32.8 + - + +
201D GLY 3.1 0.5 + - - -
202D ALA* 3.1 29.0 + - + +
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Residues in contact with GLN 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D GLY 3.1 19.1 + - - +
195D SER* 3.9 9.5 + - - +
196D VAL 3.4 0.2 - - - -
197D TRP* 1.3 76.6 - - - +
199D ARG* 1.3 77.1 + - - +
201D GLY* 3.3 9.4 + - - -
202D ALA 3.4 19.7 + - - +
204D VAL* 3.7 12.2 - - + +
233D GLN* 2.8 39.6 + - - +
234D GLY* 3.7 11.1 - - - +
235D PHE* 3.9 23.9 - - + +
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Residues in contact with ARG 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D LEU* 2.8 42.9 + - - +
60D SER* 3.1 32.4 + - - +
61D HIS* 3.3 16.0 - - - +
63D TYR* 3.6 17.5 - - - -
64D HIS* 4.6 21.9 + - + +
195D SER* 3.0 34.9 + - - +
196D VAL* 3.4 5.4 - - - +
198D GLN* 1.3 88.7 - - - +
200D LEU* 1.3 60.7 + - - +
201D GLY 3.3 1.1 + - - -
233D GLN* 5.5 3.5 + - - +
359D TYR 4.8 0.6 + - - -
360D THR* 3.6 8.7 - - - +
361D HIS* 3.1 45.4 + - - +
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Residues in contact with LEU 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D LEU* 6.2 2.0 - - + -
60D SER* 3.9 17.7 - - - -
63D TYR* 3.5 36.5 + - + -
83D LEU* 4.0 19.1 - - + +
85D LEU* 4.3 10.5 - - + -
88D MET* 4.2 20.9 - - - -
89D MET* 6.2 0.4 - - + -
177D VAL* 3.5 16.8 - - + +
196D VAL* 3.3 25.6 - - + +
197D TRP* 2.9 41.0 + - + +
199D ARG* 1.3 77.0 - - - +
201D GLY* 1.3 55.6 + - - +
202D ALA 3.7 0.7 - - - -
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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