Contacts of the helix formed by residues 194 - 209 (chain A) in PDB entry 3P3W
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 GLU 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A PHE* 6.0 1.2 - - - -
114A ARG* 3.5 28.1 + - - -
138A ASP* 3.4 10.0 + - - +
140A GLU* 4.5 21.8 - - + -
141A ARG* 4.1 11.8 + - - +
193A CYS* 1.3 74.9 - - - +
195A VAL* 1.3 81.2 + - - +
196A GLU* 3.2 6.5 + - + +
197A ARG* 2.8 17.6 + - + +
198A ILE* 2.9 11.8 + - - +
221A ASN* 3.6 5.8 + - - +
277A TYR* 3.9 7.3 + - - -
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Residues in contact with VAL 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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194A GLU* 1.3 81.1 + - - +
196A GLU* 1.3 63.9 + - - +
197A ARG 3.3 0.3 + - - -
198A ILE* 3.4 2.8 + - - +
199A ASN* 3.1 29.7 + - - +
221A ASN* 3.3 28.9 - - - +
223A GLY* 3.9 4.5 - - - +
226A ASP* 3.5 42.6 - - + +
227A ILE* 3.7 17.9 - - + +
277A TYR* 4.2 16.2 - - + -
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Residues in contact with GLU 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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15A ASN* 5.6 7.9 - - - +
194A GLU* 3.1 5.6 + - + +
195A VAL* 1.3 79.0 - - - +
197A ARG* 1.3 59.9 + - - +
199A ASN* 4.1 9.0 + - - +
200A THR* 3.7 21.1 + - - +
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Residues in contact with ARG 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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138A ASP* 3.5 25.7 + - - +
140A GLU* 5.5 6.3 - - - +
165A VAL* 2.9 38.3 + - + +
166A GLY* 3.3 24.4 + - - -
168A ILE 3.5 14.6 + - - -
174A PHE* 4.7 11.2 - - + -
193A CYS* 3.9 14.4 - - + -
194A GLU* 2.8 13.9 + - + +
196A GLU* 1.3 76.9 - - - +
198A ILE* 1.3 64.9 + - - +
199A ASN 3.2 1.6 - - - -
200A THR* 2.5 29.4 + - - +
201A ILE* 3.6 7.3 + - + +
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Residues in contact with ILE 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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191A ILE* 3.8 16.8 - - + +
193A CYS* 3.3 42.6 - - + +
194A GLU 2.9 7.4 + - - +
195A VAL 3.8 6.7 - - - +
197A ARG* 1.3 76.7 - - - +
199A ASN* 1.3 62.3 + - - +
200A THR 3.3 0.7 + - - -
201A ILE* 3.4 22.6 - - - +
202A LEU* 3.4 18.7 + - + +
219A LEU* 3.7 35.9 - - + -
221A ASN* 3.7 22.7 - - + -
227A ILE* 4.0 19.5 - - + -
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Residues in contact with ASN 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 VAL* 3.1 23.4 + - - +
196A GLU* 4.1 8.9 - - - +
197A ARG 3.2 0.8 - - - -
198A ILE* 1.3 78.2 - - - +
200A THR* 1.3 58.2 + - + +
202A LEU* 3.4 7.2 + - - +
203A GLU* 3.2 35.2 + - - +
226A ASP 3.4 18.8 + - - -
227A ILE* 3.3 12.8 - - - +
228A LEU* 2.9 48.2 + - + +
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Residues in contact with THR 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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171A VAL* 4.8 6.1 - - - +
174A PHE* 5.1 8.9 - - - -
196A GLU 3.7 13.5 - - - +
197A ARG* 2.5 30.3 + - - +
199A ASN* 1.3 78.6 - - + +
201A ILE* 1.3 60.7 + - - +
203A GLU* 3.5 19.7 - - - +
204A GLN* 3.1 27.7 + - - +
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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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136A LEU* 4.1 15.0 - - + -
165A VAL* 6.4 0.2 - - + -
174A PHE* 3.3 47.1 - - + +
178A ILE* 4.9 6.9 - - + +
191A ILE* 3.8 42.0 - - + -
193A CYS* 5.4 4.9 - - - -
197A ARG* 3.6 6.7 + - + +
198A ILE* 3.4 14.8 + - + +
200A THR* 1.3 74.3 + - - +
202A LEU* 1.3 69.5 + - + +
203A GLU 3.2 1.6 - - - -
204A GLN* 3.1 19.7 + - + +
205A VAL* 3.2 17.7 + - + +
217A TYR* 6.4 0.4 - - + -
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Residues in contact with LEU 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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191A ILE* 5.9 0.7 - - + -
198A ILE* 3.4 22.5 + - + +
199A ASN* 3.4 9.2 + - - +
201A ILE* 1.3 82.1 - - + +
203A GLU* 1.3 62.2 + - - +
205A VAL* 3.2 28.3 + - + +
206A VAL* 3.4 12.9 + - - +
217A TYR* 4.7 20.0 - - + -
219A LEU* 4.7 11.2 - - + -
227A ILE* 3.8 22.7 - - + -
228A LEU 3.6 23.1 - - - +
229A LEU* 4.4 8.5 - - + -
232A VAL* 4.2 25.7 - - + +
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Residues in contact with GLU 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 ASN* 3.2 19.9 + - - +
200A THR* 3.5 24.5 - - - +
201A ILE 3.2 0.2 - - - -
202A LEU* 1.3 77.8 - - - +
204A GLN* 1.3 67.2 + - - +
206A VAL* 3.5 17.0 + - - +
207A ILE* 3.6 18.5 + - - +
228A LEU* 4.7 16.9 - - + +
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Residues in contact with GLN 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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171A VAL* 3.4 30.6 - - + +
174A PHE* 4.1 18.2 - - + +
175A ARG* 3.7 38.9 + - + +
178A ILE* 4.7 15.3 - - + +
200A THR 3.1 24.5 + - - +
201A ILE* 3.1 14.7 + - - +
203A GLU* 1.3 86.1 + - - +
205A VAL* 1.3 63.8 + - - +
206A VAL 3.2 0.4 - - - -
207A ILE* 3.5 6.3 + - - +
208A LEU* 3.2 26.7 + - - +
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Residues in contact with VAL 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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178A ILE* 5.0 12.1 - - + -
201A ILE* 3.2 16.8 + - + +
202A LEU* 3.2 21.7 + - + +
204A GLN* 1.3 76.9 - - - +
206A VAL* 1.3 63.5 + - - +
208A LEU* 5.2 2.0 - - - -
209A GLY* 3.3 20.9 + - - +
211A HIS* 3.8 32.5 + - + +
212A SER 5.3 0.9 - - - +
217A TYR* 3.9 28.7 - - + +
232A VAL* 5.0 15.3 - - + -
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Residues in contact with VAL 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 LEU 3.4 13.9 + - - +
203A GLU* 3.6 12.3 - - - +
204A GLN 3.2 0.4 - - - -
205A VAL* 1.3 77.6 - - - +
207A ILE* 1.3 70.0 + - + +
209A GLY* 3.5 12.0 + - - -
231A ARG* 3.7 38.8 - - + +
232A VAL* 5.1 4.7 - - + -
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Residues in contact with ILE 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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175A ARG* 3.7 31.2 - - - +
203A GLU 3.6 14.4 - - - +
204A GLN* 3.5 9.9 + - - +
205A VAL 3.4 0.4 - - - -
206A VAL* 1.3 83.8 - - + +
208A LEU* 1.3 65.5 + - - +
209A GLY* 4.5 0.2 - - - -
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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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175A ARG* 4.9 24.1 - - + +
178A ILE* 4.8 15.3 - - + -
179A GLU* 5.6 4.0 - - + +
182A ASP* 4.7 7.0 - - - +
204A GLN 3.2 14.7 + - - +
205A VAL* 4.8 1.1 - - - +
207A ILE* 1.3 80.8 - - - +
209A GLY* 1.3 61.9 + - - +
210A LYS* 5.2 0.9 - - - +
211A HIS* 3.0 36.8 - - + +
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Residues in contact with GLY 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 VAL 3.3 16.4 + - - -
206A VAL* 3.7 9.9 - - - -
207A ILE 3.2 1.8 - - - -
208A LEU* 1.3 81.5 - - - +
210A LYS* 1.3 61.7 + - - +
211A HIS* 2.3 37.0 + - - -
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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