Contacts of the helix formed by residues 202 - 218 (chain A) in PDB entry 4RTL
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 202 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ASN 5.3 7.2 - - - +
200A SER 3.4 13.5 - - - +
201A PHE* 1.3 76.1 - - - +
203A LEU* 1.3 64.8 + - - +
204A GLU* 3.6 10.7 + - - +
205A GLN* 3.1 43.9 + - - +
206A GLN* 3.1 16.6 + - - +
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Residues in contact with LEU 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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186A PRO* 4.2 27.4 - - + -
202A THR* 1.3 74.1 - - - +
204A GLU* 1.3 62.3 + - - +
206A GLN* 3.2 17.8 + - + +
207A ALA* 3.4 14.0 + - - +
232A LEU* 4.5 11.0 - - + -
236A TRP* 4.2 27.7 - - + -
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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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202A THR* 3.2 11.1 + - - +
203A LEU* 1.3 79.7 - - - +
205A GLN* 1.3 60.7 + - + +
207A ALA* 3.6 5.3 + - - +
208A HIS* 3.3 21.9 + - + +
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Residues in contact with GLN 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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164A SER* 5.6 0.6 + - - -
165A TYR* 3.9 25.8 + - - +
200A SER 4.1 2.6 - - - +
201A PHE* 3.4 39.1 - - + -
202A THR* 3.1 40.1 + - - +
204A GLU* 1.3 78.5 - - + +
206A GLN* 1.3 64.4 + - - +
208A HIS* 3.4 3.3 + - - +
209A LEU* 3.2 22.5 + - - +
301A SFG 4.6 6.9 + - - -
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Residues in contact with GLN 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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182A PRO* 4.3 7.4 - - - +
183A PRO 3.1 24.4 + - - +
184A TYR 3.9 10.9 + - - -
185A ALA* 4.0 9.3 - - - +
186A PRO* 5.2 1.6 - - - +
201A PHE* 3.6 28.5 + - + +
202A THR 3.1 16.8 + - - +
203A LEU* 3.2 7.3 + - + +
205A GLN* 1.3 76.3 - - - +
207A ALA* 1.3 61.1 + - - +
209A LEU* 3.7 16.6 + - - +
210A ALA* 3.8 7.3 + - - +
227A ASN* 3.7 16.4 + - - -
236A TRP* 3.6 41.0 - - + +
237A TYR* 4.6 9.2 + - - -
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Residues in contact with ALA 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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203A LEU 3.4 9.1 + - - +
204A GLU* 4.0 8.1 - - - +
205A GLN 3.2 0.6 - - - -
206A GLN* 1.3 78.5 - - - +
208A HIS* 1.3 63.9 + - - +
210A ALA* 3.3 14.6 + - - +
211A GLU* 3.3 11.7 + - - +
236A TRP* 4.1 27.3 - - + +
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Residues in contact with HIS 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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165A TYR* 3.1 24.8 + + - +
166A ALA* 4.9 7.6 - - + -
204A GLU* 3.3 15.7 + - + +
205A GLN* 3.4 5.6 + - - +
207A ALA* 1.3 76.2 - - - +
209A LEU* 1.3 65.3 + - - +
211A GLU* 3.1 35.7 + - + +
212A ILE* 3.2 37.8 + - + +
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Residues in contact with LEU 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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35A PHE* 4.5 14.8 - - + -
165A TYR* 4.1 21.9 - - + -
169A MET* 3.8 31.1 - - + +
180A CYS* 4.3 15.5 - - + -
182A PRO* 4.1 33.0 - - + -
201A PHE* 5.3 6.1 - - + -
205A GLN 3.2 10.3 + - - +
206A GLN* 3.7 12.3 - - - +
207A ALA 3.3 0.2 - - - -
208A HIS* 1.3 78.6 + - - +
210A ALA* 1.3 62.4 + - - +
212A ILE* 3.3 5.6 + - + +
213A ALA* 3.3 19.5 + - + +
225A ILE* 4.7 14.8 - - + -
237A TYR* 5.3 5.2 - - + +
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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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206A GLN 3.8 5.3 + - - +
207A ALA* 3.3 10.8 + - - +
208A HIS 3.3 0.6 - - - -
209A LEU* 1.3 79.3 - - - +
211A GLU* 1.3 61.4 + - - +
213A ALA* 3.5 8.7 + - - +
214A GLU* 3.3 28.7 + - - +
225A ILE* 5.2 2.7 - - - -
236A TRP* 3.6 28.3 - - + +
237A TYR* 4.2 20.8 - - + -
268A TYR* 4.4 5.8 + - - +
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Residues in contact with GLU 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 ALA 3.3 9.2 + - - +
208A HIS* 3.1 28.5 + - + +
210A ALA* 1.3 76.7 - - - +
212A ILE* 1.3 64.0 + - + +
214A GLU* 3.3 21.5 + - - +
215A GLY* 3.4 9.0 + - - -
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Residues in contact with ILE 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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165A TYR* 4.3 13.0 - - + -
166A ALA* 4.2 27.4 - - + +
169A MET* 3.6 31.9 - - + -
208A HIS* 3.2 38.0 + - + +
209A LEU 3.3 6.9 + - - +
211A GLU* 1.3 75.6 - - + +
213A ALA* 1.3 64.1 + - - +
215A GLY* 3.1 11.7 + - - -
216A LEU* 3.2 18.1 + - + +
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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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169A MET* 4.7 4.2 - - + +
209A LEU* 3.3 10.0 + - + +
210A ALA* 3.7 10.8 - - - +
211A GLU 3.3 0.2 - - - -
212A ILE* 1.3 80.1 - - - +
214A GLU* 1.3 61.7 + - - +
215A GLY 3.2 0.9 + - - -
216A LEU* 3.2 17.5 + - - +
217A VAL* 3.3 15.4 + - - +
223A VAL* 4.4 22.2 - - + +
225A ILE* 4.6 6.1 - - + -
268A TYR* 4.1 29.4 - - + -
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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 ALA* 3.3 18.3 + - - +
211A GLU* 3.7 12.9 - - - +
212A ILE 3.3 0.4 - - - -
213A ALA* 1.3 76.4 - - - +
215A GLY* 1.3 56.5 + - - +
216A LEU 3.5 0.2 - - - -
217A VAL* 3.3 17.4 - - + +
218A GLU* 3.2 26.4 - - - +
236A TRP 4.7 8.5 - - - +
238A GLN* 5.5 2.8 - - - +
239A ARG* 3.9 22.3 + - + +
268A TYR* 4.0 21.6 + - + -
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Residues in contact with GLY 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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211A GLU 3.4 6.4 + - - -
212A ILE* 3.1 7.4 + - - -
213A ALA 3.1 1.0 - - - -
214A GLU* 1.3 80.2 - - - +
216A LEU* 1.3 61.6 + - - +
218A GLU* 3.6 24.4 + - - +
219A ARG* 3.9 16.5 + - - +
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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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169A MET* 4.1 43.5 - - + +
170A ALA* 6.3 0.2 - - - -
172A ALA* 4.9 3.8 - - + +
178A VAL* 4.6 13.9 - - + -
212A ILE* 3.2 17.8 + - + +
213A ALA* 3.2 8.1 + - - +
215A GLY* 1.3 74.6 - - - +
217A VAL* 1.3 60.3 + - - +
218A GLU 3.1 0.4 - - - -
219A ARG* 2.9 51.7 + - - +
221A ILE* 3.3 43.5 + - + +
223A VAL* 4.2 15.5 - - + -
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Residues in contact with VAL 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 ALA 3.3 10.8 + - - +
214A GLU* 3.3 20.9 - - - +
216A LEU* 1.3 78.4 - - - +
218A GLU* 1.3 66.2 + - + +
220A HIS* 3.2 8.9 + - - -
221A ILE 3.5 12.0 + - - +
223A VAL* 5.6 0.2 - - + -
268A TYR* 4.0 30.1 - - + +
269A LYS 3.8 9.2 - - - +
270A PRO* 3.7 40.1 - - + +
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Residues in contact with GLU 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* 3.2 21.4 - - - +
215A GLY* 3.7 16.5 - - - +
216A LEU 3.1 0.8 - - - -
217A VAL* 1.3 79.5 - - + +
219A ARG* 1.3 57.8 + - + +
220A HIS* 3.2 16.7 + - - -
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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