Contacts of the helix formed by residues 193 - 209 (chain A) in PDB entry 4Z30
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 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A PHE* 3.3 19.9 + - - -
192A LEU* 1.3 79.3 - - - +
194A PRO* 1.4 65.4 - - - -
195A ALA 3.3 1.6 - - - -
196A MET* 2.7 30.5 + - - +
197A GLN* 3.0 8.0 + - - +
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Residues in contact with PRO 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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191A PHE* 3.7 8.6 - - + -
193A GLY* 1.4 79.8 - - - -
195A ALA* 1.3 62.6 + - - +
197A GLN* 4.3 1.2 - - + +
198A GLU* 3.4 24.4 + - - +
277A ARG* 4.8 3.7 + - - +
302A SER 5.1 0.4 - - - +
303A LEU 4.0 8.1 - - - +
304A LEU 3.4 30.0 - - - +
305A TYR* 3.5 27.6 - - - +
306A GLY* 4.0 7.2 - - - +
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Residues in contact with ALA 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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193A GLY 3.0 2.4 + - - -
194A PRO* 1.3 79.3 - - - +
196A MET* 1.3 63.3 + - - +
198A GLU* 3.4 11.4 - - - +
199A GLU* 3.2 18.5 + - - +
231A PHE* 3.7 26.6 - - + -
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Residues in contact with MET 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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192A LEU* 3.7 43.3 - - + +
193A GLY 2.7 14.0 + - - +
195A ALA* 1.3 71.9 - - - +
197A GLN* 1.3 65.8 + - - +
199A GLU* 3.3 3.6 + - - +
200A ALA* 3.0 23.3 + - - +
227A LEU* 4.1 10.2 - - + +
231A PHE* 3.7 37.6 - - + -
233A GLN* 4.1 23.3 - - + -
234A ALA* 3.5 42.0 - - + +
238A SER* 5.3 1.6 - - - +
239A ILE* 5.0 0.2 - - + -
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Residues in contact with GLN 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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190A GLN 3.5 9.4 + - - +
191A PHE* 3.3 32.1 - - + -
192A LEU* 3.4 31.9 - - + +
193A GLY 3.0 10.7 + - - +
194A PRO 4.5 2.0 - - - +
196A MET* 1.3 74.5 - - - +
198A GLU* 1.3 53.5 - - - +
200A ALA* 3.2 4.1 + - - +
201A LEU* 2.8 44.0 + - + +
242A VAL* 3.2 39.5 - - - +
245A LEU* 4.3 0.9 - - - +
277A ARG* 5.3 3.4 - - - +
280A HIS* 2.7 35.2 + - + +
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Residues in contact with GLU 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 PRO 3.4 20.0 + - - +
195A ALA* 3.4 9.7 - - - +
196A MET 3.2 0.2 - - - -
197A GLN* 1.3 78.5 - - - +
199A GLU* 1.3 63.9 + - - +
201A LEU* 3.3 2.8 + - - +
202A LYS* 3.0 52.5 + - + +
273A TYR* 3.3 30.4 + - - +
277A ARG* 4.5 7.7 - - - +
305A TYR* 6.4 1.6 - - - -
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Residues in contact with GLU 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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195A ALA 3.2 12.4 + - - +
196A MET 3.9 2.0 - - - +
198A GLU* 1.3 78.8 - - - +
200A ALA* 1.3 57.2 + - - +
202A LYS* 3.4 10.6 + - - +
203A LEU* 2.9 34.4 + - + +
227A LEU* 3.6 23.6 - - + -
230A ARG* 6.2 0.2 - - + -
231A PHE* 4.1 12.6 - - + -
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Residues in contact with ALA 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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192A LEU* 5.1 3.8 - - + -
196A MET 3.0 16.5 + - - +
197A GLN* 3.2 8.0 + - - +
199A GLU* 1.3 74.2 - - - +
201A LEU* 1.3 60.7 + - - +
203A LEU* 3.2 7.7 + - - +
204A VAL* 2.8 33.2 + - + +
223A VAL* 4.5 11.8 - - + +
227A LEU* 4.3 15.7 - - + +
239A ILE* 4.7 9.6 - - + -
242A VAL* 4.7 14.1 - - + -
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Residues in contact with LEU 201 (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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197A GLN* 2.8 28.5 + - - +
198A GLU 3.8 2.7 - - - +
200A ALA* 1.3 71.4 - - - +
202A LYS* 1.3 56.7 + - - +
204A VAL* 3.2 6.4 + - + +
205A LEU* 2.8 29.3 + - - +
242A VAL* 4.2 15.7 - - + -
246A LEU* 3.7 36.8 - - + -
273A TYR* 4.3 10.3 - - + -
276A LEU* 3.7 14.9 - - + +
277A ARG* 3.6 38.1 - - - +
280A HIS* 3.9 27.6 - - + +
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Residues in contact with LYS 202 (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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198A GLU* 3.0 48.6 + - + +
199A GLU* 3.5 12.1 - - - +
201A LEU* 1.3 75.6 - - - +
203A LEU* 1.3 53.5 + - + +
205A LEU* 3.1 10.9 + - + +
206A LEU* 2.7 36.0 + - - +
273A TYR* 3.9 28.7 - - + -
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Residues in contact with LEU 203 (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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199A GLU* 2.9 17.4 + - + +
200A ALA 3.2 4.9 + - - +
202A LYS* 1.3 73.7 - - + +
204A VAL* 1.3 67.3 + - - +
206A LEU* 3.3 26.6 + - + +
207A ALA* 3.2 16.5 + - - +
222A PHE* 3.7 9.9 - - + -
223A VAL* 3.6 39.5 - - + +
226A ARG* 3.8 31.2 - - + +
227A LEU* 3.8 26.7 - - + -
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Residues in contact with VAL 204 (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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200A ALA* 2.8 19.9 + - + +
201A LEU* 3.2 11.0 + - + +
203A LEU* 1.3 74.1 - - - +
205A LEU* 1.3 65.0 + - - +
207A ALA* 3.1 13.9 + - - +
208A LEU* 3.1 30.2 + - + +
219A LEU* 4.6 17.5 - - + -
223A VAL* 4.0 17.7 - - + -
239A ILE* 6.1 1.1 - - + -
242A VAL* 5.7 3.8 - - + -
243A VAL* 4.9 10.1 - - + -
246A LEU* 4.4 26.2 - - + -
252A PHE* 4.7 6.5 - - + -
266A LEU* 4.8 7.9 - - + -
276A LEU* 4.8 4.0 - - + -
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Residues in contact with LEU 205 (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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201A LEU 2.8 16.8 + - - +
202A LYS* 3.3 11.0 - - + +
204A VAL* 1.3 76.2 - - - +
206A LEU* 1.3 58.8 + - - +
208A LEU 3.0 0.7 + - - -
209A GLU* 2.7 69.7 + - + +
266A LEU* 4.0 19.3 - - + -
270A PHE 4.0 3.1 - - - +
271A ARG 3.8 3.1 - - - -
272A SER* 3.7 20.9 - - - +
273A TYR* 3.2 40.2 - - + +
276A LEU* 4.5 7.4 - - + -
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Residues in contact with LEU 206 (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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202A LYS 2.7 19.3 + - - +
203A LEU* 3.5 27.6 - - + +
204A VAL 3.2 0.2 - - - -
205A LEU* 1.3 73.1 - - - +
207A ALA* 1.3 63.1 + - - +
209A GLU* 4.1 17.7 + - - +
210A ASP* 5.2 3.3 + - - +
222A PHE* 4.3 16.5 - - + -
226A ARG* 5.0 4.5 - - - +
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Residues in contact with ALA 207 (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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203A LEU 3.2 3.8 + - - +
204A VAL 3.1 10.2 + - - +
206A LEU* 1.3 82.2 - - - +
208A LEU* 1.3 57.8 + - + +
209A GLU 3.7 0.2 - - - -
210A ASP* 3.4 6.4 - - - +
212A SER* 3.3 22.3 + - - -
214A LEU* 3.9 12.1 - - + -
219A LEU* 3.9 19.3 - - + -
222A PHE* 3.7 33.6 - - + -
1001A UNX 4.0 4.3 - - - -
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Residues in contact with LEU 208 (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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204A VAL* 3.1 13.8 + - + +
205A LEU 3.0 2.0 + - - -
207A ALA* 1.3 79.3 - - + +
209A GLU* 1.3 66.3 + - - +
210A ASP* 3.3 4.0 - - - -
211A GLY* 2.9 17.1 + - - -
212A SER 3.4 25.1 - - - +
214A LEU* 3.8 26.9 - - + -
219A LEU* 4.0 17.7 - - + -
252A PHE* 3.9 28.7 - - + -
264A MET* 4.0 13.9 - - + +
265A GLN* 4.8 0.2 - - - -
266A LEU* 3.9 31.9 + - + +
271A ARG* 4.1 8.5 + - - +
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Residues in contact with GLU 209 (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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205A LEU* 2.7 58.8 + - + +
206A LEU* 4.1 17.8 - - - +
207A ALA 3.7 0.2 - - - -
208A LEU* 1.3 71.4 - - - +
210A ASP* 1.3 59.1 + - - +
211A GLY 3.0 4.5 + - - -
266A LEU* 4.7 0.4 - - - +
271A ARG* 3.6 39.0 + - - +
272A SER* 5.0 1.2 - - - -
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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