Contacts of the helix formed by residues 187 - 200 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185E GLY 3.1 7.1 + - - -
186E ALA* 1.3 83.0 - - - +
188E VAL* 1.3 66.3 + - - -
189E ILE 3.5 2.0 - - - -
190E GLY 3.9 1.5 - - - +
191E VAL* 3.0 19.1 + - - +
214E GLY* 4.3 4.3 - - - -
215E GLY 3.8 10.1 - - - -
277E CYS 5.1 0.2 + - - -
481E NAI 3.2 30.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187E GLY* 1.3 68.6 - - - -
189E ILE* 1.3 66.3 + - - +
191E VAL* 3.2 7.6 - - - +
192E GLU* 3.0 29.7 + - + +
214E GLY 3.7 19.5 - - - +
215E GLY* 5.2 0.2 - - - -
357E VAL 5.3 0.7 - - - +
358E ILE* 4.1 23.6 - - + -
366E TRP* 5.4 3.1 - - + -
481E NAI 3.2 73.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 189 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168E SER* 4.0 14.1 - - - +
188E VAL* 1.3 76.7 - - - +
190E GLY* 1.3 65.3 + - - +
192E GLU* 4.6 2.9 - - - -
193E LEU* 2.9 47.6 + - + +
275E LEU* 4.8 1.6 - - + -
277E CYS* 3.7 22.2 - - + -
280E ARG* 4.7 3.6 - - + -
480E FAD 3.6 33.4 - - + -
481E NAI 3.0 62.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 190 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183E VAL* 3.7 9.4 - - - +
185E GLY 3.6 22.2 + - - -
186E ALA* 5.2 1.3 - - - -
187E GLY 3.4 4.9 + - - -
188E VAL 3.2 0.6 - - - -
189E ILE* 1.3 80.5 - - - +
191E VAL* 1.4 56.0 + - - +
194E GLY* 2.8 30.4 + - - -
206E ALA* 5.8 0.4 - - - -
235E PHE* 3.6 6.8 - - - -
275E LEU* 5.0 0.7 - - - -
277E CYS* 3.7 14.6 - - - -
481E NAI 4.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 191 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186E ALA 4.1 12.5 - - - +
187E GLY 3.0 14.7 + - - +
188E VAL* 3.2 14.1 - - - +
190E GLY* 1.4 74.9 - - - +
192E GLU* 1.3 67.3 + - - +
195E SER* 3.0 26.5 + - - -
213E VAL* 4.4 10.3 - - + -
214E GLY 4.7 0.9 - - - +
226E PHE* 4.2 11.7 - - + -
230E LEU* 4.0 22.9 - - + -
235E PHE* 3.5 7.5 - - - -
237E PHE* 4.5 9.4 - - + -
358E ILE* 3.6 29.2 - - + -
360E THR* 3.6 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 192 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E SER* 4.2 5.2 + - - -
54E LYS* 3.0 23.7 + - - -
57E LEU* 3.5 22.4 - - + +
188E VAL* 3.0 17.9 + - - +
189E ILE* 3.9 3.3 - - - +
191E VAL* 1.3 80.8 - - - +
193E LEU* 1.3 62.4 + - + +
195E SER* 3.2 3.3 + - - -
196E VAL* 3.0 27.7 + - - +
358E ILE* 3.7 11.0 - - + -
359E TYR* 2.7 34.8 + - - +
360E THR* 4.0 7.6 - - + -
480E FAD 4.8 0.2 - - - -
481E NAI 3.0 35.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E SER* 4.2 15.9 - - - -
56E LEU* 5.7 0.2 - - + -
57E LEU* 5.8 0.2 - - + -
168E SER* 3.8 26.2 - - - +
171E ALA* 3.7 25.4 - - + -
172E LEU* 3.8 25.1 - - + -
181E MET* 5.7 0.2 - - - -
189E ILE* 2.9 31.1 + - + +
192E GLU* 1.3 73.9 - - + +
194E GLY* 1.3 67.1 + - - +
196E VAL* 3.1 15.8 + - + +
197E TRP* 3.1 38.1 + - + +
275E LEU* 4.1 13.5 - - + -
480E FAD 4.8 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 194 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181E MET* 5.3 2.5 - - - -
183E VAL* 4.5 9.0 - - - +
190E GLY* 2.8 20.6 + - - -
193E LEU* 1.3 77.3 - - - +
195E SER* 1.3 56.8 + - - +
197E TRP* 4.0 1.1 - - - -
198E GLN* 2.9 30.7 + - - +
204E VAL* 3.7 17.1 - - - +
235E PHE* 3.7 16.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 195 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E LEU* 4.8 0.7 - - - -
191E VAL 3.0 21.6 + - - -
192E GLU 3.3 4.3 - - - -
194E GLY* 1.3 74.5 - - - +
196E VAL* 1.3 64.8 + - - +
198E GLN* 3.6 8.7 + - - +
199E ARG* 3.0 57.3 + - - +
230E LEU* 4.8 2.4 - - - +
233E GLN* 4.3 11.1 + - - -
235E PHE* 3.5 11.9 - - - -
360E THR* 4.1 14.0 - - - +
361E HIS 5.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 196 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E SER 4.8 0.2 - - - +
56E LEU* 4.0 25.6 - - + -
57E LEU* 3.5 39.7 - - + +
60E SER* 3.7 12.4 - - - +
192E GLU 3.0 18.9 + - - +
193E LEU* 3.1 19.5 + - + +
195E SER* 1.3 78.7 - - - +
197E TRP* 1.3 77.3 + - + +
199E ARG* 3.5 3.7 + - - +
200E LEU* 3.2 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 197 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E LEU* 5.0 4.3 - - + +
85E LEU* 3.9 22.9 - - + -
89E MET* 3.5 31.9 - - + -
171E ALA* 3.0 32.3 + - + +
174E LEU* 3.6 26.3 - - + +
176E LYS 4.0 2.2 - - - -
177E VAL* 4.0 17.4 - - + +
178E PRO* 3.8 12.6 - - + -
181E MET* 4.0 26.9 - - + -
193E LEU* 3.1 30.9 + - + +
194E GLY 4.3 1.6 - - - +
196E VAL* 1.3 83.8 - - + +
198E GLN* 1.3 65.8 + - - +
200E LEU* 3.2 30.9 + - + +
201E GLY 3.2 1.0 + - - -
202E ALA* 2.9 32.9 + - + +
204E VAL* 4.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 198 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194E GLY 2.9 19.7 + - - +
195E SER* 3.6 8.8 + - - +
197E TRP* 1.3 75.8 - - - +
199E ARG* 1.3 76.7 + - - +
201E GLY* 3.0 14.7 + - - -
202E ALA 3.6 18.8 + - - +
204E VAL* 3.8 12.2 - - + +
233E GLN* 2.9 41.2 + - - +
234E GLY* 4.1 9.0 - - - +
235E PHE* 4.3 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 199 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E LEU* 2.9 40.3 + - - +
60E SER* 3.0 36.0 + - - +
61E HIS* 3.6 14.0 + - - +
63E TYR* 3.5 17.9 - - - -
64E HIS* 4.5 24.5 + - + +
195E SER* 3.0 38.4 + - - +
196E VAL 3.6 4.3 - - - +
198E GLN* 1.3 89.0 - - - +
200E LEU* 1.3 59.0 + - - +
201E GLY* 3.1 1.7 + - - -
233E GLN* 5.3 2.8 + - - +
359E TYR 5.4 0.4 + - - -
360E THR* 3.9 6.5 - - - +
361E HIS* 3.3 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E LEU* 6.0 1.6 - - + -
60E SER* 3.8 22.4 - - - -
63E TYR* 4.0 23.7 + - + -
83E LEU* 4.0 13.7 - - + +
85E LEU* 4.1 16.4 - - + -
88E MET* 4.0 26.2 - - + -
89E MET* 6.0 0.2 - - + -
177E VAL* 3.6 26.6 - - + +
196E VAL* 3.2 26.0 - - + +
197E TRP* 3.2 34.6 + - + +
199E ARG* 1.3 76.2 - - - +
201E GLY* 1.3 56.5 + - - +
202E ALA 3.8 0.4 - - - -
----------------------------------------------------------
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