Contacts of the helix formed by residues 197 - 214 (chain A) in PDB entry 3H5O
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 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A TYR* 3.7 29.7 + - + -
195A GLN* 3.3 22.1 + - + +
196A LEU* 1.3 83.9 - - - +
198A GLU* 1.3 65.9 + - - +
199A ARG* 3.3 31.6 + - - +
200A VAL* 3.3 25.4 + - - +
201A MSE 3.3 18.1 + - - +
203A ARG* 5.1 0.9 + - - -
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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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134A GLY* 5.0 0.3 - - - -
135A LEU* 3.9 16.2 + - - +
136A SER* 3.5 34.5 + - - -
157A ASP* 4.0 9.3 - - - +
197A ASP* 1.3 76.8 - - - +
199A ARG* 1.3 64.7 + - + +
201A MSE 3.4 7.4 + - - +
202A LYS* 3.1 58.6 + - + +
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Residues in contact with ARG 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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78A PRO* 3.9 14.8 - - - +
85A PHE* 4.0 10.3 - - - -
110A TYR* 4.1 8.3 + - - -
133A THR* 3.9 20.4 + - - +
134A GLY* 3.5 30.7 - - - +
156A MSE 3.8 19.6 - - - +
157A ASP* 3.2 25.6 + - - +
170A GLN* 3.4 33.7 - - + +
197A ASP* 3.3 19.4 + - - +
198A GLU* 1.3 79.8 + - + +
200A VAL* 1.3 59.9 + - - +
202A LYS* 3.3 4.6 + - - +
203A ARG* 2.9 49.9 + - - +
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Residues in contact with VAL 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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191A PHE* 4.0 11.2 - - + -
194A ALA 3.8 19.5 - - - +
195A GLN* 5.1 0.4 - - + -
196A LEU* 4.2 19.7 - - + +
197A ASP* 3.3 33.3 + - - +
199A ARG* 1.3 75.9 - - - +
201A MSE 1.3 61.6 + - - +
203A ARG* 3.0 29.9 - - - +
204A LEU* 2.9 24.9 + - - +
254A CYS* 4.0 23.1 - - + -
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Residues in contact with MSE 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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196A LEU* 3.9 36.8 - - - +
197A ASP 3.3 15.7 + - - +
198A GLU* 3.4 7.4 + - - +
199A ARG 3.2 0.4 - - - -
200A VAL* 1.3 77.9 - - - +
202A LYS* 1.3 59.3 + - - +
204A LEU* 3.2 33.3 + - + +
205A ASP* 2.9 35.4 + - - +
208A ARG* 5.6 4.0 - - - +
224A LEU* 4.1 14.1 - - + -
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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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135A LEU* 4.7 6.9 - - - +
157A ASP* 3.2 27.1 + - - +
158A LEU 5.3 2.6 + - - -
170A GLN* 3.5 18.6 - - + -
171A GLU* 3.4 40.9 + - - +
198A GLU* 3.1 46.2 + - + +
199A ARG* 3.3 4.2 + - - +
201A MSE 1.3 73.7 - - - +
203A ARG* 1.3 64.6 + - - +
205A ASP* 3.1 21.7 + - - +
206A GLY 3.2 8.8 + - - -
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Residues in contact with ARG 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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170A GLN* 3.0 42.4 + - - +
174A GLY* 3.8 7.4 - - - -
191A PHE* 4.4 8.1 - - + -
197A ASP* 5.1 1.2 + - - -
199A ARG* 2.9 39.4 + - - +
200A VAL* 3.0 28.7 - - - +
202A LYS* 1.3 74.1 - - - +
204A LEU* 1.3 61.4 + - - +
206A GLY* 3.3 3.3 + - - -
207A TYR* 3.1 21.3 + - - +
252A PHE* 4.0 10.1 - - + -
254A CYS* 2.7 43.1 + - - +
255A ASN* 5.1 1.6 - - - +
282A PHE* 3.3 43.6 - - + -
283A ASN* 4.7 6.9 + - - +
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Residues in contact with LEU 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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191A PHE* 3.6 39.7 - - + -
200A VAL 2.9 13.1 + - - +
201A MSE 3.2 27.1 - - + +
202A LYS 3.1 0.2 - - - -
203A ARG* 1.3 74.5 - - - +
205A ASP* 1.3 59.6 + - - +
207A TYR* 3.4 15.2 + - + +
208A ARG* 2.9 69.9 + - - +
222A GLU* 4.3 7.0 - - + +
224A LEU* 3.9 28.0 - - + -
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Residues in contact with ASP 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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171A GLU* 4.9 8.1 - - + +
201A MSE 2.9 21.9 + - - +
202A LYS* 3.1 18.6 + - - +
204A LEU* 1.3 77.2 - - - +
206A GLY* 1.3 58.1 + - - +
208A ARG* 3.4 24.1 + - - +
209A ALA* 2.9 30.0 + - - +
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Residues in contact with GLY 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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171A GLU* 3.3 29.7 - - - +
175A ALA* 3.4 21.0 - - - +
202A LYS 3.2 9.7 + - - -
203A ARG 3.3 1.8 + - - -
205A ASP* 1.3 74.3 - - - +
207A TYR* 1.3 65.9 + - - +
209A ALA* 3.1 5.2 + - - -
210A ALA 2.9 21.0 + - - -
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Residues in contact with TYR 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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174A GLY 3.7 2.6 + - - -
178A THR* 3.3 31.5 - - + +
189A ILE* 2.6 34.3 + - + -
190A GLY 3.7 13.2 - - - -
191A PHE* 3.6 19.5 - + + -
203A ARG 3.1 13.0 + - - +
204A LEU* 3.6 19.7 - - + +
206A GLY* 1.3 75.0 - - - +
208A ARG* 1.3 62.1 + - + +
210A ALA* 3.5 2.1 + - - +
211A LEU* 3.1 54.7 + - + +
217A ARG* 5.8 0.9 - - + -
218A ASP 4.7 2.1 + - - -
221A LEU* 3.5 17.5 + - - +
222A GLU* 3.8 24.6 + - + +
252A PHE* 3.9 21.5 - + + -
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Residues in contact with ARG 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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201A MSE 5.6 3.6 - - - +
204A LEU* 2.9 45.9 + - - +
205A ASP* 3.5 19.4 + - - +
207A TYR* 1.3 82.9 - - + +
209A ALA* 1.3 59.5 + - - +
211A LEU* 3.7 3.6 - - - +
212A ASP* 2.8 36.1 + - - +
217A ARG* 3.9 41.4 - - - +
222A GLU* 2.8 43.6 + - - +
224A LEU* 5.0 4.4 - - - +
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Residues in contact with ALA 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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175A ALA* 5.3 3.8 - - + -
179A ARG* 4.5 7.6 + - - +
205A ASP 2.9 18.2 + - - +
206A GLY* 3.6 6.5 - - - +
208A ARG* 1.3 75.8 - - - +
210A ALA* 1.3 62.2 + - - +
212A ASP* 3.8 8.7 - - - +
213A ALA* 3.3 21.5 + - - +
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Residues in contact with ALA 210 (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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175A ALA* 3.8 25.1 - - + +
178A THR* 3.8 14.8 - - + -
179A ARG* 3.9 26.5 + - + +
182A LEU* 4.0 10.9 - - + +
206A GLY 2.9 16.1 + - - +
207A TYR 3.7 5.2 - - - +
209A ALA* 1.3 78.1 - - - +
211A LEU* 1.3 63.0 + - - +
213A ALA* 3.5 12.6 + - - +
214A ALA 3.5 7.4 + - - -
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Residues in contact with LEU 211 (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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178A THR* 3.6 20.2 - - + -
182A LEU* 4.3 7.4 - - + -
189A ILE* 3.9 26.9 - - + +
207A TYR* 3.1 59.6 + - + +
208A ARG 3.2 4.2 + - - +
210A ALA* 1.3 75.5 - - - +
212A ASP* 1.3 63.8 + - - +
214A ALA* 3.0 4.0 + - - -
215A ASP 3.0 4.0 + - - -
216A CYS* 2.8 51.5 + - + +
217A ARG* 3.8 22.9 - - + +
218A ASP 5.2 1.1 - - - +
221A LEU* 6.1 0.4 - - + -
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Residues in contact with ASP 212 (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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208A ARG 2.8 21.2 + - - +
209A ALA* 3.8 8.8 - - - +
210A ALA 3.4 0.2 - - - -
211A LEU* 1.3 77.8 - - - +
213A ALA* 1.3 63.8 + - - +
215A ASP* 3.0 14.7 + - - +
217A ARG* 3.0 46.4 + - - +
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Residues in contact with ALA 213 (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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179A ARG* 4.1 18.2 - - - +
209A ALA 3.3 11.4 + - - +
210A ALA 3.7 9.6 - - - +
211A LEU 3.3 0.8 - - - -
212A ASP* 1.3 78.3 - - - +
214A ALA* 1.3 57.4 + - + +
215A ASP* 3.3 1.1 + - - +
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Residues in contact with ALA 214 (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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182A LEU* 4.1 20.9 - - + -
187A ARG* 6.1 0.4 - - - -
210A ALA 3.5 8.6 + - - +
211A LEU 3.0 6.9 + - - +
213A ALA* 1.3 78.1 - - + +
215A ASP* 1.3 72.0 + - - +
216A CYS* 3.2 20.5 + - + -
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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