Contacts of the helix formed by residues 189 - 203 (chain A) in PDB entry 2PY5
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 THR 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A TYR* 4.1 5.6 - - + -
124A LYS* 3.4 24.7 - - + -
125A LYS* 4.2 2.5 - - - +
187A ARG 3.2 0.2 - - - -
188A MET* 1.3 88.8 - - + +
190A ALA* 1.3 63.8 + - - +
191A GLY 3.5 2.6 + - - -
192A SER* 2.9 15.5 + - - -
193A ASP* 3.0 26.8 + - - +
3D A 3.7 19.1 - - - +
4D C 2.5 41.3 + - - +
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Residues in contact with ALA 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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124A LYS 2.9 17.9 + - - +
125A LYS* 3.9 11.9 - - - +
127A PRO* 4.7 4.5 - - + -
180A GLN* 5.3 0.2 - - - +
189A THR* 1.3 71.6 - - - +
191A GLY* 1.3 57.5 + - - +
193A ASP* 3.2 11.6 + - - +
194A SER* 3.0 29.5 + - - -
384A LEU* 3.8 26.7 - - + +
385A MET* 5.1 0.9 - - - +
388A SER* 3.7 19.1 - - - +
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Residues in contact with GLY 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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189A THR* 3.3 5.1 + - - -
190A ALA* 1.3 75.8 - - - +
192A SER* 1.3 61.2 + - - +
194A SER* 3.3 1.4 + - - -
195A LEU* 2.9 24.9 + - - +
388A SER* 3.6 23.4 - - - -
392A LYS* 3.3 25.6 - - - +
4D C 4.7 7.7 + - - -
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Residues in contact with SER 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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187A ARG* 2.7 38.4 + - - +
189A THR* 2.9 23.8 + - - -
191A GLY* 1.3 74.6 - - - +
193A ASP* 1.3 63.6 + - - +
195A LEU* 3.4 3.0 + - - +
196A LYS* 3.0 24.8 + - - +
392A LYS* 3.9 10.5 - - - +
3D A 2.7 27.0 + - - -
4D C 3.8 4.8 + - - -
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Residues in contact with ASP 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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125A LYS* 2.7 26.4 + - - -
180A GLN* 4.1 3.5 + - - -
184A GLY 4.9 0.3 - - - +
185A LEU* 3.4 23.7 - - + +
186A ASP 3.3 5.4 + - - -
187A ARG* 2.9 34.6 + - - +
189A THR 3.0 16.2 + - - +
190A ALA* 3.5 10.7 - - - +
191A GLY 3.2 0.2 - - - -
192A SER* 1.3 77.0 - - - +
194A SER* 1.3 63.6 + - - +
196A LYS* 3.4 3.7 + - - +
197A GLY* 2.9 19.1 + - - -
385A MET* 3.6 21.3 - - - +
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Residues in contact with SER 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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190A ALA 3.0 9.3 + - - -
191A GLY 3.3 8.0 + - - -
193A ASP* 1.3 77.8 - - - +
195A LEU* 1.3 61.7 + - - +
197A GLY* 3.3 1.6 + - - -
198A PHE* 3.0 23.7 + - - +
363A PHE* 3.8 5.4 - - - -
385A MET* 2.8 43.0 + - - -
388A SER* 3.3 32.0 - - - -
389A LEU* 3.7 8.9 - - - +
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Residues in contact with LEU 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 GLY 2.9 16.7 + - - +
192A SER* 4.0 3.8 - - - +
193A ASP 3.3 0.2 - - - -
194A SER* 1.3 76.7 - - - +
196A LYS* 1.3 62.9 + - - +
198A PHE* 3.3 6.1 + - + +
199A LYS* 3.0 41.2 + - - +
207A PHE* 4.0 26.9 - - + -
389A LEU* 3.8 19.7 - - + +
392A LYS* 4.1 28.5 - - + -
393A PHE* 4.7 5.4 - - + -
425A VAL* 4.3 27.1 - - + -
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Residues in contact with LYS 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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184A GLY 5.1 10.2 + - - +
187A ARG* 3.6 32.8 - - - +
192A SER 3.0 17.7 + - - +
193A ASP* 3.8 3.8 - - - +
195A LEU* 1.3 76.2 - - - +
197A GLY* 1.3 60.0 + - - +
199A LYS* 3.2 10.9 + - + +
200A ASP* 2.7 62.4 + - - +
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Residues in contact with GLY 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 ASP 2.9 14.3 + - - -
194A SER 3.7 2.7 - - - -
196A LYS* 1.3 79.4 - - - +
198A PHE* 1.3 61.4 + - - +
200A ASP* 3.3 15.0 + - - +
201A ILE* 3.2 25.5 + - - +
363A PHE* 3.8 7.0 - - - -
367A TRP* 5.4 1.8 - - - -
385A MET* 4.2 13.0 - - - -
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Residues in contact with PHE 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 SER 3.0 14.0 + - - +
195A LEU* 3.5 10.8 - - + +
197A GLY* 1.3 75.4 - - - +
199A LYS* 1.3 63.9 + - - +
201A ILE* 3.0 3.6 + - - +
202A ILE* 3.0 66.2 + - + +
207A PHE* 3.8 24.9 - + - -
211A PHE* 3.9 9.4 - + - -
359A LEU* 3.5 13.0 - - + -
360A PHE* 3.5 35.2 - + - -
363A PHE* 3.6 27.4 - - + -
389A LEU* 3.9 12.6 - - + -
393A PHE* 3.8 18.2 - + - -
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Residues in contact with LYS 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 LEU* 3.0 35.8 + - + +
196A LYS* 3.2 11.6 + - - +
198A PHE* 1.3 75.7 - - - +
200A ASP* 1.3 55.6 + - - +
202A ILE* 4.4 6.5 - - - -
203A THR* 2.7 36.5 + - - -
204A THR* 3.6 22.0 + - + +
207A PHE* 3.7 52.7 - - + -
425A VAL* 6.2 0.2 - - - +
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Residues in contact with ASP 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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196A LYS* 2.7 58.7 + - - +
197A GLY* 3.4 12.2 - - - +
199A LYS* 1.3 77.2 - - - +
201A ILE* 1.3 69.7 + - + +
203A THR* 3.9 9.4 + - - +
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Residues in contact with ILE 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 GLY 3.2 13.4 + - - +
198A PHE* 3.0 9.2 + - - +
200A ASP* 1.3 85.9 - - + +
202A ILE* 1.3 68.2 + - + +
203A THR* 4.5 3.8 - - - +
362A ASP* 3.5 35.9 - - + +
363A PHE* 3.9 19.7 - - + +
366A LYS* 4.1 31.2 - - + +
367A TRP* 5.8 0.2 - - - +
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Residues in contact with ILE 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 PHE* 3.0 61.5 + - + +
199A LYS* 4.3 4.5 - - - +
201A ILE* 1.3 82.8 - - + +
203A THR* 1.3 81.3 + - - +
206A LYS* 3.3 33.1 - - + +
207A PHE* 3.7 32.5 - - + +
210A VAL* 4.8 2.0 - - + -
211A PHE* 4.3 7.2 - - + -
359A LEU* 3.8 14.4 - - + +
362A ASP* 6.0 1.3 - - + -
363A PHE* 5.8 0.7 - - + +
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Residues in contact with THR 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 LYS 2.7 16.8 + - - -
200A ASP* 3.9 6.7 + - - +
201A ILE 3.3 6.6 - - - +
202A ILE* 1.3 87.0 + - - +
204A THR* 1.3 59.3 + - - +
205A LYS* 3.8 9.5 + - - +
206A LYS* 3.2 16.3 + - - +
207A PHE* 2.9 26.2 + - - +
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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