Contacts of the helix formed by residues 179 - 198 (chain A) in PDB entry 1Z59
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 ASP 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A PRO* 3.6 8.2 + - + -
29A ALA* 3.9 19.4 - - + +
32A LEU* 4.2 4.5 - - - +
68A GLN* 4.4 5.5 - - - +
70A TYR* 3.8 3.5 - - - -
178A GLY* 1.3 74.9 - - - +
180A TRP* 1.3 58.5 + - - +
181A PRO* 3.3 13.9 - - - +
182A LYS* 3.3 46.9 + - - +
183A ALA* 3.1 29.5 + - - +
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Residues in contact with TRP 180 (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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32A LEU* 4.0 17.5 - - + +
60A ILE* 3.9 13.2 - - + -
70A TYR* 3.2 29.4 + - + +
179A ASP* 1.3 70.2 - - - +
181A PRO* 1.3 82.4 - - + +
183A ALA 3.1 0.7 + - - +
184A LYS* 2.8 58.4 + - + +
187A ILE* 3.8 25.8 - - + -
188A TYR* 3.8 15.0 - + - -
205A PHE* 3.8 7.0 - + - -
207A ASP* 3.5 33.2 - - + -
208A PRO* 3.5 22.6 - - + +
209A GLU* 2.8 35.5 + - + +
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Residues in contact with PRO 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLN* 4.8 2.9 - - - +
70A TYR* 4.1 6.5 - - - +
179A ASP* 3.3 11.2 - - - +
180A TRP* 1.3 102.8 - - + +
182A LYS* 1.3 60.9 + - + +
184A LYS* 4.0 12.7 + - + +
185A SER 5.3 0.5 + - - -
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Residues in contact with LYS 182 (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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29A ALA* 3.7 22.7 - - + -
179A ASP* 3.3 28.1 + - - +
180A TRP 3.2 1.0 - - - -
181A PRO* 1.3 80.4 - - + +
183A ALA* 1.3 62.3 + - - +
184A LYS 3.6 0.3 + - - -
185A SER* 4.8 5.5 + - - -
186A ARG* 5.4 1.4 + - - +
381A TYR* 5.6 1.4 + - - -
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Residues in contact with ALA 183 (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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29A ALA* 3.4 26.5 - - - +
32A LEU* 4.4 5.6 - - + -
33A TYR* 4.7 3.3 - - + +
179A ASP 3.1 17.9 + - - +
180A TRP* 4.2 1.8 - - - +
182A LYS* 1.3 76.2 - - - +
184A LYS* 1.3 65.6 + - - +
185A SER 3.5 1.1 - - - -
186A ARG* 3.2 10.3 + - - +
187A ILE* 3.0 41.4 + - + +
381A TYR* 5.4 3.6 - - - -
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Residues in contact with LYS 184 (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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180A TRP* 2.8 45.6 + - + +
181A PRO* 4.1 10.8 - - + +
182A LYS 3.3 2.0 - - - -
183A ALA* 1.3 77.0 - - - +
185A SER* 1.3 65.8 + - - +
187A ILE* 3.3 2.4 + - - +
188A TYR* 3.1 45.4 + - + -
207A ASP* 4.8 2.0 - - - -
209A GLU* 3.1 33.0 + - - +
211A ASN* 4.8 5.0 - - - +
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Residues in contact with SER 185 (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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181A PRO 5.3 0.4 + - - -
182A LYS 4.8 5.1 + - - -
183A ALA 3.5 0.2 - - - -
184A LYS* 1.3 83.1 - - - +
186A ARG* 1.3 70.4 + - - +
188A TYR* 3.5 6.8 + - - +
189A GLU* 3.0 27.7 + - - +
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Residues in contact with ARG 186 (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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33A TYR* 4.4 9.2 - - + -
182A LYS 5.7 1.1 - - - +
183A ALA* 3.2 8.1 + - - +
184A LYS 3.2 0.6 - - - -
185A SER* 1.3 91.6 + - - +
187A ILE* 1.3 59.0 + - - +
189A GLU* 3.8 12.8 - - - +
190A TYR* 2.9 28.2 + - - +
193A ARG* 5.3 9.9 - - - +
380A ILE* 3.7 36.5 + - + +
381A TYR* 3.2 53.8 - - + +
383A GLU* 5.3 9.7 + - - -
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Residues in contact with ILE 187 (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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32A LEU* 4.1 15.0 - - + +
33A TYR* 4.0 33.7 - - + +
36A VAL* 4.5 15.7 - - + -
60A ILE* 4.4 5.8 - - + -
180A TRP* 3.8 21.1 - - + -
183A ALA* 3.0 35.0 + - + +
184A LYS 3.3 3.6 + - - +
186A ARG* 1.3 73.3 - - - +
188A TYR* 1.3 67.2 + - - +
190A TYR* 3.2 8.0 + - + +
191A ILE* 3.1 29.9 + - + +
205A PHE* 3.9 27.8 - - + -
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Residues in contact with TYR 188 (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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180A TRP* 3.8 18.2 - + - -
184A LYS* 3.1 40.4 + - + -
185A SER* 3.8 9.4 - - - +
187A ILE* 1.3 73.9 - - - +
189A GLU* 1.3 57.4 + - - +
191A ILE* 3.3 5.9 + - - +
192A LYS* 2.9 29.6 + - - +
205A PHE* 3.6 25.2 + + - -
207A ASP* 2.6 34.5 + - - +
211A ASN* 3.9 12.8 + - - +
213A THR* 3.7 19.5 + - + -
215A TYR* 4.0 12.8 + - - -
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Residues in contact with GLU 189 (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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185A SER 3.0 18.1 + - - +
186A ARG* 3.8 19.5 - - - +
188A TYR* 1.3 74.2 - - - +
190A TYR* 1.3 64.7 + - - +
192A LYS* 3.8 27.2 + - - +
193A ARG* 2.6 75.7 + - - +
196A ILE* 5.8 0.2 - - - +
371A LEU* 5.0 1.6 - - - +
380A ILE* 4.3 7.2 - - + -
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Residues in contact with TYR 190 (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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33A TYR* 4.4 8.5 - - + -
36A VAL* 4.6 7.0 - - + -
37A ARG* 3.4 61.4 + - + -
40A ILE* 4.0 28.7 - - + +
41A GLU* 2.6 34.2 + - - +
44A LEU* 5.8 0.2 - - - +
186A ARG 2.9 15.3 + - - +
187A ILE* 3.2 10.7 + - - +
189A GLU* 1.3 77.8 - - - +
191A ILE* 1.3 68.8 + - + +
194A THR* 3.0 43.9 + - - +
378A PRO* 3.6 28.9 - - + +
380A ILE* 3.9 11.6 - - + +
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Residues in contact with ILE 191 (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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36A VAL* 4.9 3.4 - - + -
40A ILE* 4.2 12.8 - - + -
58A ILE* 4.6 11.9 - - + -
187A ILE* 3.1 22.6 + - + +
188A TYR* 3.9 3.4 - - - +
190A TYR* 1.3 86.9 - - + +
192A LYS* 1.3 65.7 + - - +
194A THR* 3.2 6.7 + - - -
195A TYR* 3.0 22.1 + - - +
203A PHE* 4.8 16.4 - - + -
205A PHE* 3.7 44.2 - - + -
215A TYR* 3.6 33.9 - - + +
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Residues in contact with LYS 192 (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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188A TYR 2.9 17.2 + - - +
189A GLU* 3.8 30.3 + - - +
191A ILE* 1.3 76.3 - - - +
193A ARG* 1.3 58.9 + - - +
195A TYR* 3.2 11.2 + - + +
196A ILE* 3.0 38.9 + - + +
215A TYR* 4.5 11.1 - - + -
329A ILE* 3.9 28.7 - - + -
330A PHE* 4.4 16.6 - - - -
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Residues in contact with ARG 193 (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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186A ARG* 5.3 7.8 - - - +
189A GLU* 2.6 55.2 + - - +
190A TYR 4.0 0.4 - - - +
192A LYS* 1.3 74.8 - - - +
194A THR* 1.3 67.9 + - - +
196A ILE* 3.5 19.4 + - + +
197A ILE 3.7 1.7 + - - -
369A ILE* 4.9 7.1 - - - +
370A VAL 3.7 14.6 + - - -
371A LEU* 3.5 34.7 - - + +
372A ARG* 4.9 3.1 - - - +
373A TYR* 2.8 38.1 + - - +
378A PRO* 3.8 17.0 - - + -
379A LEU 4.2 15.3 + - - -
380A ILE* 4.0 16.0 + - - +
383A GLU* 5.2 7.5 + - - -
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Residues in contact with THR 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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40A ILE* 4.8 5.2 - - + -
44A LEU* 3.8 28.9 - - + -
190A TYR* 3.0 31.5 + - - +
191A ILE* 3.2 8.0 + - - -
193A ARG* 1.3 77.2 - - - +
195A TYR* 1.3 61.2 + - - +
197A ILE* 3.3 7.5 + - - +
198A THR* 2.8 34.0 + - - +
203A PHE* 3.9 17.9 - - + -
376A LYS 5.5 3.8 - - - +
378A PRO* 3.5 22.5 - - + +
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Residues in contact with TYR 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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191A ILE 3.0 12.6 + - - +
192A LYS* 3.3 11.4 - - + +
194A THR* 1.3 75.9 - - - +
196A ILE* 1.3 62.5 + - - +
198A THR 3.1 26.7 + - - +
199A PRO* 3.5 5.3 - - + +
201A ALA 4.2 7.6 - - - -
203A PHE* 4.2 20.3 - + + -
215A TYR* 3.9 45.5 - + + -
216A PRO* 2.6 41.8 + - + +
218A LEU* 3.5 23.6 - - + +
325A GLY* 5.5 0.2 - - - -
329A ILE* 3.8 31.8 - - + +
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Residues in contact with ILE 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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189A GLU* 5.8 0.2 - - - +
192A LYS* 3.0 28.9 + - + +
193A ARG* 3.6 22.0 - - + +
194A THR 3.3 0.4 - - - -
195A TYR* 1.3 74.6 - - - +
197A ILE* 1.3 65.4 + - + +
198A THR 3.7 0.2 + - - -
199A PRO* 3.9 3.6 - - - +
321A LEU 4.3 2.3 - - - +
322A ILE* 5.0 2.2 - - - +
325A GLY* 3.3 34.4 - - - -
326A LEU* 4.3 19.3 - - + -
329A ILE* 3.9 33.4 - - + -
330A PHE* 4.0 25.1 - - + -
371A LEU* 4.3 12.8 - - + -
373A TYR* 3.9 9.2 - - + +
412A MSE 6.3 0.7 - - + -
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Residues in contact with ILE 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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193A ARG 3.7 0.4 + - - +
194A THR* 3.3 11.1 + - - +
196A ILE* 1.3 82.1 - - + +
198A THR* 1.3 61.3 + - - +
199A PRO* 3.2 10.9 - - - +
200A TYR* 4.5 6.4 + - - -
317A ILE* 3.7 43.1 - - + +
321A LEU 5.4 0.9 - - - -
322A ILE* 5.3 3.8 - - + +
373A TYR* 3.4 47.3 - - + +
376A LYS* 3.4 35.4 - - + +
412A MSE 3.7 26.0 - - + -
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Residues in contact with THR 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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44A LEU* 4.4 15.0 - - + +
105A ARG* 4.7 8.6 + - - +
194A THR* 2.8 30.7 + - - +
195A TYR* 3.1 12.2 + - - +
197A ILE* 1.3 85.1 + - - +
199A PRO* 1.3 57.3 - - - +
200A TYR* 3.1 40.8 - - + +
201A ALA* 3.1 38.0 + - + +
203A PHE* 4.9 0.2 - - - -
376A LYS 5.2 1.7 + - - -
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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