Contacts of the helix formed by residues 205 - 219 (chain A) in PDB entry 3CUQ
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 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A LYS* 4.7 0.2 - - - -
203A LYS 5.1 2.6 - - - +
204A TRP* 1.3 79.0 - - - +
206A THR* 1.3 70.5 + - + +
207A GLU* 3.2 5.2 - - + +
208A ARG* 3.0 27.2 + - + +
209A ALA* 3.2 10.2 + - - +
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Residues in contact with THR 206 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A VAL* 4.7 6.2 - - - +
199A LYS* 2.9 40.1 - - - +
204A TRP 3.8 1.2 + - - -
205A GLU* 1.3 76.8 - - + +
207A GLU* 1.3 64.4 + - + +
209A ALA* 3.3 3.9 + - - +
210A ARG* 3.0 28.8 + - - +
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Residues in contact with GLU 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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205A GLU* 3.2 4.5 - - + +
206A THR* 1.3 83.3 + - + +
208A ARG* 1.3 57.7 + - - +
210A ARG* 2.7 41.8 + - - +
211A GLN* 2.8 54.5 + - - +
72D GLU* 6.0 6.3 - - + +
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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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178A MET* 5.9 0.8 - - - +
179A ASP* 2.7 40.9 + - - +
203A LYS 5.3 0.8 + - - -
204A TRP* 3.1 50.0 - - + +
205A GLU* 3.0 21.5 + - + +
207A GLU* 1.3 77.9 - - - +
209A ALA* 1.3 63.7 + - - +
211A GLN* 3.7 11.4 - - - +
212A VAL* 3.4 27.6 + - + +
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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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195A VAL* 4.2 14.6 - - + -
198A ILE* 3.5 35.6 - - + +
199A LYS* 4.6 4.9 - - + -
204A TRP* 4.0 11.4 - - + -
205A GLU 3.2 9.9 + - - +
206A THR 3.3 8.0 + - - +
208A ARG* 1.3 72.9 - - - +
210A ARG* 1.3 67.1 + - - +
212A VAL* 3.3 5.4 + - - +
213A LEU* 3.0 28.4 + - + +
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Residues in contact with ARG 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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195A VAL* 5.1 8.3 - - + -
206A THR* 3.0 18.9 + - - +
207A GLU* 2.7 45.1 + - - +
209A ALA* 1.3 79.8 - - - +
211A GLN* 1.3 51.6 + - - +
213A LEU* 3.2 15.3 + - + +
214A GLU* 2.8 55.3 + - - +
372B VAL* 5.8 3.6 - - - +
68D LYS* 4.9 13.3 - - - +
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Residues in contact with GLN 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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207A GLU* 2.8 42.5 + - - +
208A ARG* 3.7 11.9 - - + +
209A ALA 3.2 0.2 - - - -
210A ARG* 1.3 74.3 - - - +
212A VAL* 1.3 66.6 + - + +
214A GLU* 3.3 13.7 + - - +
215A HIS* 3.1 18.7 + - - +
72D GLU* 4.8 18.0 + - - -
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Residues in contact with VAL 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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177A ASN* 4.8 5.8 - - - +
179A ASP* 3.8 35.2 - - + +
180A HIS* 4.1 16.4 - - + -
183A VAL* 3.9 19.7 - - + -
204A TRP* 3.8 17.5 - - + -
208A ARG* 3.4 15.2 + - + +
209A ALA 3.3 6.1 + - - +
211A GLN* 1.3 73.2 - - + +
213A LEU* 1.3 63.2 + - + +
215A HIS* 2.8 21.5 + - + +
216A LEU* 3.0 20.7 + - + +
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Residues in contact with LEU 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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183A VAL* 4.8 3.8 - - + -
193A VAL* 3.6 27.8 - - + -
195A VAL* 3.4 40.2 - - + +
198A ILE* 4.7 8.1 - - + -
209A ALA 3.0 25.3 + - - +
210A ARG* 3.2 9.9 - - - +
212A VAL* 1.3 75.2 - - + +
214A GLU* 1.3 65.1 + - - +
215A HIS 3.0 0.7 + - - -
216A LEU* 3.0 17.7 + - + +
217A LEU* 3.0 27.0 + - - +
234A TYR* 3.8 37.0 - - + +
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Residues in contact with GLU 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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210A ARG* 2.8 44.8 + - - +
211A GLN* 3.3 15.2 - - - +
212A VAL 3.2 0.2 - - - -
213A LEU* 1.3 72.5 - - - +
215A HIS* 1.3 56.6 + - - +
217A LEU* 3.4 10.6 + - + +
218A LYS* 2.8 38.8 + - + +
370B ASP* 4.8 4.3 - - - +
371B SER* 4.1 14.8 - - - +
372B VAL* 3.9 35.8 - - + +
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Residues in contact with HIS 215 (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 ALA* 5.2 7.1 - - + +
175A GLU* 4.1 19.6 + - - -
177A ASN* 4.6 18.2 + - - +
180A HIS* 4.4 19.5 - + + -
211A GLN 3.1 10.4 + - - +
212A VAL* 2.8 14.6 + - - +
214A GLU* 1.3 78.4 - - - +
216A LEU* 1.3 50.9 + - - +
218A LYS* 3.1 26.1 + - - +
219A GLU* 2.5 88.1 + - + +
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Residues in contact with LEU 216 (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 HIS* 3.7 36.8 - - + +
183A VAL* 4.2 25.1 - - + -
184A LEU* 4.5 9.4 - - + -
187A ALA* 6.2 0.2 - - + -
193A VAL* 5.1 2.9 - - + -
212A VAL* 3.0 17.9 + - + +
213A LEU* 3.3 20.2 - - + +
215A HIS* 1.3 76.0 - - - +
217A LEU* 1.3 63.4 + - - +
219A GLU* 3.3 1.2 + - - -
220A GLY 3.2 2.8 + - - -
221A LEU* 2.9 42.2 + - + +
222A ALA* 3.7 24.9 - - + +
234A TYR* 5.7 1.3 - - + -
236A LEU* 4.7 15.5 - - + -
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Residues in contact with LEU 217 (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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213A LEU 3.0 17.3 + - - +
214A GLU* 3.9 10.1 - - + +
216A LEU* 1.3 73.9 - - - +
218A LYS* 1.3 63.8 + - + +
219A GLU 3.0 1.0 + - - -
220A GLY* 3.0 12.5 + - - -
222A ALA* 3.2 34.3 - - + +
223A TRP* 3.8 16.4 - - - +
224A LEU* 3.9 8.5 - - + +
234A TYR* 3.8 27.1 - - + +
372B VAL* 5.2 8.3 - - + +
20C GLN* 4.6 3.4 - - - +
21C PRO* 4.4 20.6 - - + -
22C ASN* 3.7 27.1 + - + +
25C THR* 4.5 1.0 + - - -
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Residues in contact with LYS 218 (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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214A GLU* 2.8 31.1 + - + +
215A HIS* 3.1 29.5 + - - +
217A LEU* 1.3 72.3 - - - +
219A GLU* 1.3 70.4 + - - +
220A GLY 3.6 0.2 + - - -
370B ASP* 2.7 33.3 + - - +
371B SER 3.7 24.7 - - - +
372B VAL 4.8 3.6 - - - +
374B GLY* 4.1 17.7 - - - +
375B LEU* 4.3 14.8 - - + +
22C ASN* 4.1 13.8 + - - +
24C ASP* 5.4 3.5 - - - +
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Residues in contact with GLU 219 (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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116A GLY* 4.3 13.0 - - - +
172A VAL* 6.5 1.6 - - + -
173A PRO 5.7 2.7 - - - -
174A ALA* 5.4 10.7 - - + +
175A GLU* 5.1 1.2 - - - +
180A HIS* 5.9 0.4 - - - +
215A HIS* 2.5 60.1 + - + +
216A LEU 3.3 2.9 + - - +
218A LYS* 1.3 88.4 - - - +
220A GLY* 1.3 60.0 + - - +
221A LEU* 3.8 17.7 + - + -
354B LYS* 5.1 13.1 + - - -
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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