Contacts of the helix formed by residues 202 - 218 (chain A) in PDB entry 4UN0
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 202 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A TYR* 3.5 25.8 - - + +
201A TRP* 1.3 75.8 - - - +
203A PRO* 1.3 72.9 - - + +
204A GLU* 3.2 17.3 - - + +
205A ILE* 2.9 39.4 + - + +
206A ILE* 3.2 9.6 + - - +
239A VAL* 5.8 1.0 - - - +
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Residues in contact with PRO 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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25A TYR* 3.5 13.0 - - - +
76A ILE* 6.1 1.8 - - + -
158A GLU* 3.2 26.2 - - + +
159A HIS* 3.8 5.2 - - - -
160A PRO* 3.7 36.0 - - + +
163A PHE* 3.8 14.6 - - + -
201A TRP 3.8 1.8 - - - +
202A GLU* 1.3 86.6 - - + +
204A GLU* 1.3 64.8 + - - +
206A ILE* 3.3 2.8 + - + -
207A ALA* 2.9 30.7 + - - +
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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
----------------------------------------------------------
158A GLU* 5.3 1.0 - - - +
163A PHE* 3.5 43.1 - - + -
167A TYR* 3.6 19.3 - - - +
202A GLU* 3.4 12.5 - - + +
203A PRO* 1.3 90.1 - - - +
205A ILE* 1.3 61.8 + - + +
207A ALA* 3.5 3.4 + - - +
208A VAL* 3.2 27.0 + - - +
238A PHE 5.6 0.4 - - - +
239A VAL* 3.5 16.3 - - + +
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Residues in contact with ILE 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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201A TRP* 3.6 30.7 - - + -
202A GLU* 2.9 37.6 + - + +
204A GLU* 1.3 75.6 - - + +
206A ILE* 1.3 60.0 + - - +
208A VAL* 3.2 5.3 + - - +
209A ALA* 2.9 26.3 + - - +
239A VAL* 3.8 25.1 - - + -
242A VAL* 4.3 21.1 - - + -
246A VAL* 4.2 13.9 - - + -
247A LEU* 4.2 4.4 - - + +
250A ILE* 3.9 20.6 - - + -
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Residues in contact with ILE 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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160A PRO* 3.7 26.2 - - + -
189A VAL* 5.1 0.7 - - + -
192A SER* 4.0 22.7 - - - +
197A LEU* 4.2 22.2 - - + +
198A SER* 5.6 2.5 - - - +
201A TRP* 3.9 20.4 - - + +
202A GLU 3.2 13.8 + - - +
203A PRO* 3.7 2.9 - - + +
205A ILE* 1.3 74.5 - - - +
207A ALA* 1.3 63.0 + - - +
209A ALA* 3.1 4.4 + - - +
210A VAL* 3.0 35.8 + - + +
250A ILE* 3.9 32.8 - - + -
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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
----------------------------------------------------------
160A PRO* 3.5 27.8 - - + +
163A PHE* 3.7 17.7 - - + -
164A LEU* 3.8 9.6 - - - +
167A TYR* 4.4 3.1 - - + -
203A PRO 2.9 17.9 + - - +
204A GLU 3.6 5.8 - - - +
206A ILE* 1.3 75.9 - - - +
208A VAL* 1.3 61.7 + - - +
210A VAL* 3.1 21.2 - - - +
211A MET* 3.2 17.6 - - - +
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Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A TYR* 4.0 15.9 - - + -
204A GLU 3.2 12.9 + - - +
205A ILE* 3.2 11.3 + - + +
207A ALA* 1.3 77.3 - - - +
209A ALA* 1.3 53.0 + - - +
211A MET* 3.0 11.2 + - - +
212A TYR* 2.8 30.8 + - - +
234A TRP* 3.9 6.4 - - + -
235A TRP* 3.5 31.6 - - + -
238A PHE* 4.3 11.0 - - + -
239A VAL* 3.6 20.2 - - + -
242A VAL* 6.1 0.2 - - + -
247A LEU* 3.7 22.0 - - + -
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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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205A ILE 2.9 16.1 + - - +
206A ILE 3.1 5.4 + - - +
208A VAL* 1.3 77.2 - - - +
210A VAL* 1.3 57.5 + - + +
212A TYR* 3.2 6.5 + - - +
213A LEU* 2.8 29.0 + - - +
247A LEU* 3.9 18.4 - - + +
250A ILE* 3.8 40.6 - - + -
251A CYS* 4.0 4.0 - - - -
254A ILE* 5.8 1.6 - - + -
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Residues in contact with VAL 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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164A LEU* 4.4 2.7 - - + -
185A ALA* 3.6 33.8 - - + +
188A PHE* 3.6 26.8 - - + +
189A VAL* 3.8 24.9 - - + +
206A ILE* 3.0 18.3 + - + +
207A ALA* 3.1 20.2 - - - +
209A ALA* 1.3 75.2 - - + +
211A MET* 1.3 60.1 + - - +
213A LEU* 3.9 6.5 - - - -
214A ALA* 3.1 28.2 + - - +
254A ILE* 4.2 13.2 - - + -
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Residues in contact with MET 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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164A LEU* 3.6 27.1 - - + +
167A TYR* 4.0 31.6 - - + +
168A ALA* 4.6 6.1 - - + +
171A LEU* 4.1 26.7 - - + -
181A LEU* 3.6 23.9 - - + +
185A ALA* 4.4 4.0 - - + -
207A ALA 3.2 19.1 - - - +
208A VAL* 3.0 7.9 + - - +
210A VAL* 1.3 76.5 - - - +
212A TYR* 1.3 59.7 + - - +
215A GLY* 2.9 27.0 + - - -
222A ILE* 4.4 5.1 - - + +
234A TRP* 3.6 29.6 - - + -
238A PHE* 5.2 1.3 - - + -
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Residues in contact with TYR 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 VAL 2.8 12.5 + - - +
209A ALA* 3.3 12.1 - - - +
211A MET* 1.3 77.4 - - - +
213A LEU* 1.3 59.7 + - - +
215A GLY* 3.5 0.9 + - - -
216A ARG* 3.1 42.3 + - + +
222A ILE* 5.1 4.0 - - + +
234A TRP* 3.9 17.0 - + + -
235A TRP* 4.2 22.2 - + - -
244A VAL* 3.8 21.7 - - + +
247A LEU* 4.0 27.6 - - + -
248A GLU* 3.2 27.9 + - - -
251A CYS* 3.6 23.3 - - - -
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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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188A PHE* 3.6 39.9 - - + -
209A ALA 2.8 16.3 + - - +
210A VAL* 4.0 4.9 - - - +
211A MET 3.3 0.2 - - - -
212A TYR* 1.3 77.8 - - - +
214A ALA* 1.3 62.8 + - - +
216A ARG* 3.2 15.0 + - - +
217A LEU* 3.0 42.5 + - + +
251A CYS* 3.6 28.9 - - + -
254A ILE* 4.3 23.1 - - + -
255A LEU* 4.2 25.4 - - + -
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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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181A LEU* 3.7 23.8 - - + +
184A MET* 3.8 29.6 - - + -
185A ALA 4.1 1.1 - - - +
188A PHE* 3.9 10.3 - - + -
210A VAL 3.1 17.8 + - - +
213A LEU* 1.3 79.8 - - - +
215A GLY* 1.3 62.8 + - - +
217A LEU* 3.5 4.1 + - - +
218A CYS* 3.1 30.5 + - - +
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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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181A LEU* 3.5 12.7 - - - +
211A MET 2.9 18.3 + - - -
212A TYR 3.8 1.3 - - - -
214A ALA* 1.3 77.7 - - - +
216A ARG* 1.3 57.6 + - - +
218A CYS 3.5 0.5 + - - -
219A LYS* 3.0 7.4 + - - -
220A PHE* 2.8 38.3 + - - +
222A ILE* 3.9 14.6 - - - -
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Residues in contact with ARG 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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212A TYR* 3.1 37.6 + - + +
213A LEU* 3.7 16.9 - - - +
215A GLY* 1.3 76.8 - - - +
217A LEU* 1.3 67.9 + - - +
219A LYS* 3.6 9.8 + - - +
222A ILE* 5.1 0.4 - - - +
248A GLU* 2.7 43.5 + - - -
251A CYS* 4.5 4.2 - - - +
252A HIS* 4.9 2.4 + - - -
255A LEU* 4.4 20.6 - - - +
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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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184A MET* 4.0 16.6 - - + -
188A PHE* 3.6 31.6 - - + -
213A LEU* 3.0 35.7 + - + +
214A ALA* 3.9 4.7 - - - +
216A ARG* 1.3 84.7 - - + +
218A CYS* 1.3 60.1 + - - +
219A LYS* 3.3 1.7 + - - +
255A LEU* 5.4 9.0 - - + -
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Residues in contact with CYS 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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180A LYS* 4.9 13.0 - - - -
181A LEU* 5.9 0.4 - - - -
184A MET* 3.4 33.2 - - - -
214A ALA* 3.1 18.2 + - - +
217A LEU* 1.3 77.3 - - - +
219A LYS* 1.3 67.8 + - - +
220A PHE* 3.0 49.1 + - + -
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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