Contacts of the helix formed by residues 196 - 209 (chain A) in PDB entry 1Z19
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 PRO 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A ALA 4.6 1.2 - - - +
194A SER 4.7 0.7 - - - +
195A SER* 1.3 95.8 - - - +
197A CYS* 1.3 66.0 + - - +
198A TRP* 3.1 33.3 + - + +
199A LEU* 3.3 16.6 + - + +
200A ARG* 4.2 3.1 + - - +
275A THR* 5.2 5.6 - - - +
288A TYR* 4.3 22.0 - - + -
36E A 4.5 17.9 - - - +
37E T 3.8 19.1 - - - +
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Residues in contact with CYS 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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195A SER 4.4 2.2 - - - -
196A PRO* 1.3 74.2 - - - +
198A TRP* 1.3 62.7 + - - +
199A LEU 3.3 0.7 + - - -
200A ARG* 3.4 14.9 + - - +
201A LEU* 3.5 19.4 + - + +
265A ILE* 4.2 29.8 - - + -
266A LEU* 5.2 2.2 - - + -
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Residues in contact with TRP 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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196A PRO* 3.5 16.9 - - + +
197A CYS* 1.3 77.3 - - - +
199A LEU* 1.3 99.2 + - + +
201A LEU* 3.9 4.8 - - - +
202A ALA* 2.9 31.1 + - + +
266A LEU* 3.6 29.6 - - + +
272A ILE* 4.6 5.8 - - + +
273A ALA 3.4 17.7 - - - +
274A SER* 4.1 2.9 - - - -
275A THR* 4.4 2.5 - - - -
280A LEU* 3.2 29.0 - - + +
284A THR* 3.9 13.2 - - + -
285A VAL* 3.7 25.1 - - + -
288A TYR* 3.3 38.8 - + + -
37E T 3.4 36.0 + - - -
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Residues in contact with LEU 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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192A ALA* 4.4 6.3 - - + -
195A SER* 3.5 26.5 - - - +
196A PRO* 3.3 14.6 + - + +
197A CYS 3.2 0.6 - - - -
198A TRP* 1.3 103.6 - - + +
200A ARG* 1.3 57.1 + - - +
202A ALA* 3.5 1.2 - - + +
203A MSE 2.9 41.6 + - + +
285A VAL* 4.2 12.1 - - + +
288A TYR* 3.3 28.9 - - + +
289A PHE* 4.1 22.7 - - + +
292A ALA* 4.3 9.2 - - + -
307A PHE* 5.1 0.2 - - + -
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Residues in contact with ARG 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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189A TYR* 3.0 66.0 + - + +
190A GLN* 3.4 10.5 + - - +
192A ALA* 3.7 18.6 - - + +
193A GLU* 3.3 41.0 + - - +
196A PRO 4.2 3.1 + - - +
197A CYS* 3.4 10.9 + - - +
198A TRP 3.3 0.4 - - - -
199A LEU* 1.3 74.4 - - - +
201A LEU* 1.3 68.7 + - + +
203A MSE 3.2 10.4 + - - +
204A GLU* 2.9 27.8 + - - +
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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 CYS* 3.6 16.2 - - + +
198A TRP 3.4 5.5 + - - +
200A ARG* 1.3 77.8 - - + +
202A ALA* 1.3 58.0 + - - +
204A GLU* 3.4 6.9 + - - +
205A LEU* 2.7 33.1 + - - +
258A THR* 4.1 12.8 - - + +
261A LYS* 3.8 44.4 - - + +
262A CYS* 3.9 23.1 - - - +
265A ILE* 4.5 13.2 - - + -
266A LEU* 3.7 34.3 - - + -
272A ILE* 4.2 2.2 - - + -
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Residues in contact with ALA 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 TRP* 2.9 22.4 + - + +
199A LEU* 3.5 5.8 - - - +
201A LEU* 1.3 76.2 - - - +
203A MSE 1.3 52.9 + - - +
205A LEU* 3.0 3.8 + - - +
206A ALA* 2.6 39.0 + - - +
216A LEU* 4.7 4.0 - - + +
272A ILE* 3.7 23.7 - - + +
285A VAL* 4.2 26.2 - - + -
307A PHE* 4.4 3.8 - - + -
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Residues in contact with MSE 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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185A TYR* 3.5 35.7 - - + +
188A ILE* 4.0 6.5 - - + -
189A TYR* 3.8 35.2 - - + +
192A ALA* 4.4 10.1 - - - -
199A LEU* 2.9 35.5 + - + +
200A ARG* 3.4 9.6 - - - +
202A ALA* 1.3 75.1 - - - +
204A GLU* 1.3 62.4 + - - +
206A ALA* 3.0 3.1 + - - +
207A VAL* 3.0 27.9 + - - +
289A PHE* 4.0 36.3 - - + -
307A PHE* 4.5 2.2 - - + -
310A LEU* 4.0 13.2 - - + -
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Residues in contact with GLU 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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185A TYR* 3.4 19.5 + - - +
189A TYR* 2.5 38.8 + - + -
200A ARG* 2.9 15.9 + - - +
201A LEU* 3.7 7.5 - - - +
203A MSE 1.3 75.5 - - - +
205A LEU* 1.3 64.2 + - - +
207A VAL* 3.3 2.4 + - - +
208A VAL* 3.0 28.6 + - - +
253A ILE* 4.0 22.6 - - + +
258A THR* 2.8 29.4 + - + +
261A LYS* 2.8 29.9 + - - -
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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 2.7 20.9 + - - +
202A ALA* 3.4 4.5 - - - +
204A GLU* 1.3 75.3 - - - +
206A ALA* 1.3 58.0 + - - +
208A VAL* 3.6 6.3 - - + -
209A THR* 2.8 52.6 + - + +
216A LEU* 4.5 8.5 - - + -
219A MSE 4.4 17.7 - - - -
229A LEU* 6.0 0.4 - - + -
255A MSE 5.1 2.9 - - + -
258A THR* 3.8 19.9 - - + +
259A LEU* 4.1 24.7 - - + +
262A CYS* 5.1 1.8 - - - -
271A ILE* 3.9 15.7 - - + -
272A ILE* 3.8 30.3 - - + -
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Residues in contact with ALA 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 ALA 2.6 19.9 + - - +
203A MSE 3.4 5.2 - - - +
205A LEU* 1.3 75.1 - - - +
207A VAL* 1.3 57.0 + - - +
209A THR* 4.3 2.0 - - - -
210A GLY* 3.2 24.8 + - - -
211A GLN 4.1 4.2 + - - +
216A LEU* 3.6 16.6 - - + +
307A PHE* 3.5 29.6 - - + -
310A LEU* 3.9 19.1 - - + +
311A ARG* 4.6 1.0 - - - -
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Residues in contact with VAL 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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185A TYR* 3.8 24.9 - - + -
203A MSE 3.0 15.9 + - - +
204A GLU 4.0 2.5 - - - +
206A ALA* 1.3 76.7 - - - +
208A VAL* 1.3 62.4 + - - +
248A ILE* 4.0 17.1 - - + +
251A LEU* 4.2 17.7 - - + -
253A ILE* 4.6 6.7 - - + -
310A LEU* 3.8 27.8 - - + +
313A LEU* 4.8 4.0 - - + -
314A SER* 2.9 39.6 + - - +
317A LEU* 4.3 5.6 - - + -
318A TYR* 3.8 4.5 - - - -
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Residues in contact with VAL 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 GLU 3.0 21.7 + - - +
205A LEU* 3.3 15.3 - - + +
207A VAL* 1.3 80.2 - - - +
209A THR* 1.3 69.8 + - + +
246A LEU* 3.5 17.4 - - + +
248A ILE* 4.0 8.7 - - + -
253A ILE* 4.0 17.9 - - + +
255A MSE 3.7 39.8 - - + +
258A THR* 5.3 1.3 - - + -
318A TYR* 2.6 37.9 + - - +
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Residues in contact with THR 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* 2.8 34.1 + - + +
208A VAL* 1.3 88.3 - - + +
210A GLY* 1.3 54.5 + - - +
211A GLN* 2.6 47.9 + - - +
216A LEU* 3.6 13.9 - - - +
219A MSE 4.8 2.2 - - + -
229A LEU* 4.8 4.9 - - + -
242A ILE* 4.3 9.9 - - - -
255A MSE 4.0 27.6 - - + -
330A LEU* 3.6 17.7 - - - +
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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