Contacts of the helix formed by residues 187 - 200 (chain B) in PDB entry 1ZMD
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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B GLY 3.2 7.9 + - - -
186B ALA* 1.3 80.1 - - - +
188B VAL* 1.3 67.2 + - - -
189B ILE 3.5 2.0 - - - -
190B GLY 4.0 1.3 - - - +
191B VAL* 3.1 22.0 + - - +
214B GLY* 4.3 5.4 + - - -
215B GLY 3.9 9.2 - - - -
481B NAI 3.2 30.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLY* 1.3 69.9 - - - +
189B ILE* 1.3 61.0 + - - +
191B VAL* 4.0 1.7 - - - +
192B GLU* 2.9 41.7 + - + +
214B GLY 3.8 17.5 - - - +
215B GLY* 5.2 0.7 - - - -
357B VAL 5.3 0.4 - - - +
358B ILE* 4.1 25.5 - - + +
366B TRP* 5.6 2.5 - - + -
481B NAI 3.2 76.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B SER* 3.8 24.2 - - - +
188B VAL* 1.3 75.4 - - - +
190B GLY* 1.3 58.1 + - - +
192B GLU* 4.5 3.4 - - - +
193B LEU* 2.7 61.9 + - + +
275B LEU* 4.9 0.9 - - + -
277B CYS* 3.9 20.0 - - + -
280B ARG* 4.8 3.6 - - + -
480B FAD 4.0 21.1 - - + -
481B NAI 3.1 61.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B VAL* 3.8 10.6 - - - +
185B GLY 3.6 13.7 + - - -
186B ALA* 5.2 1.6 - - - -
187B GLY 3.7 4.2 + - - +
188B VAL 3.3 0.6 - - - -
189B ILE* 1.3 79.4 - - - +
191B VAL* 1.3 58.1 + - - +
194B GLY* 2.8 29.5 + - - -
206B ALA* 5.8 0.9 - - - -
235B PHE* 3.7 6.3 - - - -
275B LEU* 5.2 1.1 - - - -
277B CYS* 3.6 23.4 - - - -
481B NAI 4.4 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ALA* 3.9 14.4 - - - +
187B GLY 3.1 18.6 + - - +
188B VAL* 4.1 2.0 - - - +
190B GLY* 1.3 75.4 - - - +
192B GLU* 1.3 63.0 + - - +
195B SER* 3.0 26.7 + - - -
213B VAL* 4.4 5.2 - - + -
214B GLY 4.7 1.1 - - - +
226B PHE* 3.4 17.5 - - + -
230B LEU* 3.3 35.9 - - + -
235B PHE* 3.6 6.1 - - + -
237B PHE* 4.4 15.9 - - + -
358B ILE* 4.5 3.4 - - + -
360B THR* 3.3 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B SER* 4.3 3.8 + - - -
54B LYS* 3.0 24.2 + - - -
57B LEU* 3.6 20.1 - - + +
188B VAL* 2.9 22.2 + - - +
189B ILE* 3.8 3.1 - - - +
191B VAL* 1.3 77.5 - - - +
193B LEU* 1.3 69.4 - - + +
195B SER* 3.2 4.2 + - - -
196B VAL* 3.1 25.6 + - - +
358B ILE* 3.7 16.6 - - + -
359B TYR* 2.8 27.4 + - - +
360B THR* 4.0 6.7 - - + -
481B NAI 3.0 34.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B SER* 4.2 15.0 - - - +
56B LEU* 5.8 1.1 - - + -
57B LEU* 5.8 0.2 - - + -
168B SER* 3.7 29.6 - - - +
171B ALA* 3.8 18.8 - - + +
172B LEU* 3.8 24.2 - - + -
181B MET* 4.5 1.3 - - - -
189B ILE* 2.7 41.8 + - + +
192B GLU* 1.3 75.6 - - + +
194B GLY* 1.3 64.6 + - - +
196B VAL* 3.4 13.4 + - + +
197B TRP* 3.2 33.7 + - + +
275B LEU* 3.9 14.8 - - + -
480B FAD 4.7 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B MET* 3.8 19.0 - - - +
183B VAL* 4.6 1.1 - - - -
190B GLY 2.8 20.2 + - - -
193B LEU* 1.3 77.7 - - - +
195B SER* 1.3 57.2 + - - +
197B TRP 3.4 0.2 + - - -
198B GLN* 2.8 31.0 + - - +
204B VAL* 3.8 7.6 - - - +
235B PHE* 3.6 16.2 - - - -
275B LEU* 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 4.8 0.9 - - - -
191B VAL 3.0 20.7 + - - -
192B GLU 3.5 4.3 - - - -
194B GLY* 1.3 75.4 - - - +
196B VAL* 1.3 66.3 + - - +
198B GLN* 3.6 7.0 + - - +
199B ARG* 2.9 54.6 + - - +
230B LEU* 4.5 3.7 - - - +
233B GLN* 4.2 12.8 + - - -
235B PHE* 3.5 11.4 - - - -
360B THR* 4.1 14.1 - - - +
361B HIS 5.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 3.9 23.6 - - + -
57B LEU* 3.4 40.8 - - + +
60B SER* 3.8 12.7 - - - +
192B GLU 3.1 16.1 + - - +
193B LEU* 3.6 16.8 - - + +
195B SER* 1.3 78.5 - - - +
197B TRP* 1.3 72.4 + - + +
199B ARG* 3.3 3.9 + - - +
200B LEU* 3.1 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 5.0 4.1 - - + +
85B LEU* 4.0 17.3 - - + -
89B MET* 3.6 28.7 - - + -
171B ALA* 2.9 32.7 + - + +
174B LEU* 3.4 31.4 - - + +
177B VAL* 3.9 23.4 - - + +
178B PRO* 3.8 12.6 - - + -
181B MET* 4.1 24.7 - - + -
193B LEU* 3.2 31.2 + - + +
194B GLY 4.2 2.0 - - - +
196B VAL* 1.3 81.7 - - + +
198B GLN* 1.3 63.7 + - - +
200B LEU* 3.4 25.9 + - + +
201B GLY 3.3 5.4 + - - -
202B ALA* 2.8 36.7 + - + +
204B VAL* 4.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B GLY 2.8 20.2 + - - +
195B SER* 3.6 9.2 + - - +
197B TRP* 1.3 76.8 - - - +
199B ARG* 1.3 74.1 + - - +
201B GLY* 3.1 14.7 + - - -
202B ALA 3.6 18.6 + - - +
204B VAL* 3.8 12.0 - - + +
233B GLN* 3.2 38.1 + - - +
234B GLY* 4.2 7.8 - - - +
235B PHE* 4.3 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 2.8 40.9 + - - +
60B SER* 3.0 34.7 + - - +
61B HIS* 3.5 15.2 - - - +
63B TYR* 3.6 16.7 - - - -
64B HIS* 4.4 24.4 + - + +
195B SER* 2.9 37.6 + - - +
196B VAL 3.3 5.1 + - - +
198B GLN* 1.3 88.4 + - - +
200B LEU* 1.3 61.8 + - - +
201B GLY* 3.1 1.3 + - - -
233B GLN* 5.4 2.8 + - - +
359B TYR 4.9 0.4 + - - -
360B THR* 3.8 6.3 - - - +
361B HIS* 3.2 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 6.2 1.6 - - + -
60B SER* 3.9 20.0 - - - -
63B TYR* 3.8 29.7 + - + -
83B LEU* 3.9 28.8 - - + +
85B LEU* 4.1 15.3 - - + -
88B MET* 4.1 11.0 - - - -
89B MET* 6.1 0.2 - - + -
177B VAL* 3.6 22.5 - - + +
196B VAL* 3.1 29.2 + - + +
197B TRP* 3.7 31.6 - - + +
198B GLN 3.3 0.6 - - - -
199B ARG* 1.3 74.8 - - - +
201B GLY* 1.3 56.8 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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