Contacts of the helix formed by residues 205 - 219 (chain B) in PDB entry 4CQM
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B VAL* 4.7 2.0 - - - -
182B HIS* 3.3 30.0 + - - +
202B ARG* 4.5 7.7 + - - +
203B PHE 4.8 1.6 - - - +
204B GLY* 1.3 76.9 - - - +
206B THR* 1.3 67.2 + - - +
207B ILE* 3.2 19.3 - - + -
208B GLU* 3.0 33.8 + - + +
209B VAL* 3.2 15.3 + - - +
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Residues in contact with THR 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLY* 3.8 34.5 + - - -
14B ILE* 3.9 22.5 - - + +
17B ALA* 3.8 11.1 - - - +
181B VAL* 4.9 2.0 - - + +
182B HIS* 4.1 26.9 - - + +
205B GLU* 1.3 76.4 + - - +
207B ILE* 1.3 59.7 + - - +
209B VAL* 3.3 5.0 + - - +
210B ALA* 2.8 27.5 + - - +
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Residues in contact with ILE 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ALA* 4.1 11.7 - - + +
20B GLN* 5.9 3.4 - - + +
21B LEU* 4.3 17.3 - - + +
205B GLU* 4.0 16.8 - - + -
206B THR* 1.3 79.5 + - - +
208B GLU* 1.3 68.8 + - + +
210B ALA* 3.2 12.9 + - + +
211B HIS* 3.0 49.9 + - + +
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Residues in contact with GLU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A GLU 5.6 2.1 - - - +
244A ASP 4.1 11.7 - - - +
246A GLY* 4.2 5.1 - - - +
247A TYR* 3.4 30.4 + - + +
248A ILE* 5.9 1.0 - - - +
202B ARG* 2.8 44.4 + - - -
205B GLU* 3.0 34.6 + - + +
207B ILE* 1.3 81.0 - - + +
209B VAL* 1.3 64.8 + - + +
211B HIS* 3.5 10.1 + - - +
212B ALA* 3.4 17.7 + - - +
229B VAL* 4.6 4.5 - - + +
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A TYR* 5.9 1.3 - - + -
14B ILE* 3.9 33.9 - - + -
133B VAL* 5.4 1.8 - - + -
176B VAL* 3.8 24.2 - - + -
178B PRO* 4.1 21.3 - - + -
181B VAL* 4.8 7.9 - - + -
204B GLY* 5.7 0.7 - - - -
205B GLU 3.2 16.9 + - - +
206B THR* 3.7 6.7 - - - +
208B GLU* 1.3 73.9 - - + +
210B ALA* 1.3 59.8 + - - +
212B ALA* 3.0 8.4 + - - +
213B VAL* 2.9 28.4 + - + +
229B VAL* 4.2 15.3 - - + +
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Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE* 4.6 0.6 - - - +
17B ALA* 3.8 9.4 - - + +
18B VAL* 3.7 40.6 - - + +
21B LEU* 3.7 9.0 - - + -
206B THR 2.8 15.2 + - - +
207B ILE* 3.2 13.2 + - + +
209B VAL* 1.3 77.0 - - - +
211B HIS* 1.3 57.0 + - - +
213B VAL* 3.1 3.3 + - - +
214B VAL* 3.0 32.6 + - - +
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Residues in contact with HIS 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A PHE* 3.7 5.4 - - - -
244A ASP* 3.2 62.5 + - + +
21B LEU* 3.5 37.0 - - + +
25B LYS* 5.5 5.3 - - - -
207B ILE* 3.0 38.2 + - + +
208B GLU* 3.7 5.2 - - - +
209B VAL 3.3 0.4 - - - -
210B ALA* 1.3 76.1 - - - +
212B ALA* 1.3 58.5 + - - +
214B VAL* 4.1 2.1 - - - +
215B PHE* 3.2 27.9 + - - +
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Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A PHE* 4.2 14.5 - - + -
248A ILE* 5.1 2.2 - - + -
176B VAL* 3.7 8.6 - - + +
208B GLU 3.4 7.4 + - - +
209B VAL 3.0 11.5 + - - +
211B HIS* 1.3 76.7 - - - +
213B VAL* 1.3 63.0 + - - +
215B PHE* 3.9 1.4 + - - +
216B LEU* 3.6 25.3 + - - +
227B LEU* 3.8 16.1 - - + +
229B VAL* 3.6 29.8 - - + -
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Residues in contact with VAL 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE* 4.9 0.9 - - + -
18B VAL* 4.0 24.9 - - + -
81B VAL* 3.9 30.5 - - + -
131B VAL* 4.0 16.8 - - + +
133B VAL* 4.6 11.9 - - + -
176B VAL* 3.9 24.2 - - + -
209B VAL* 2.9 22.2 + - + +
210B ALA 3.1 7.8 + - - +
212B ALA* 1.3 77.1 - - - +
214B VAL* 1.3 65.1 + - - +
215B PHE 3.2 0.4 + - - -
216B LEU 3.5 2.1 + - - -
217B LEU* 3.3 26.1 + - + +
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Residues in contact with VAL 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 4.8 4.3 - - + -
21B LEU* 3.7 20.9 - - + -
22B MET* 3.7 31.9 - - + -
25B LYS* 3.9 19.7 - - + -
27B TYR* 5.1 2.5 - - + -
210B ALA 3.0 16.0 + - - +
211B HIS* 4.2 4.3 - - - +
213B VAL* 1.3 76.5 - - - +
215B PHE* 1.3 62.0 + - - +
217B LEU* 3.2 9.9 + - + +
218B GLU* 3.0 50.6 + - + +
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Residues in contact with PHE 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ASP* 3.5 24.0 - - - -
236A VAL* 3.6 33.7 - - + -
239A PHE* 3.5 51.1 - + + -
253A VAL* 4.5 7.9 - - + -
211B HIS 3.2 19.5 + - - +
212B ALA 3.9 3.4 - - - +
213B VAL 3.2 0.2 - - - -
214B VAL* 1.3 76.3 - - - +
216B LEU* 1.3 79.8 + - + +
218B GLU* 3.1 8.3 + - - +
219B SER* 2.8 29.3 + - - -
222B ILE* 3.9 10.5 - - + -
227B LEU* 3.9 18.2 - - + -
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B SER* 4.0 0.2 + - - -
131B VAL* 3.8 16.6 - - + -
172B ARG* 2.6 34.5 + - - -
174B ASN* 3.7 23.7 + - + +
175B VAL 4.1 4.9 - - - +
176B VAL* 3.7 28.3 - - + -
212B ALA 3.6 8.0 + - - +
213B VAL 3.5 3.6 + - - +
214B VAL 3.4 0.2 - - - -
215B PHE* 1.3 96.8 - - + +
217B LEU* 1.3 55.5 + - - +
218B GLU 3.3 0.3 + - - -
219B SER* 3.5 5.8 + - - +
222B ILE* 3.7 29.3 - - + +
225B HIS* 4.3 9.6 - - + +
227B LEU* 3.8 22.0 - - + -
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Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B CYS* 4.9 0.7 - - - -
22B MET* 3.9 24.7 - - + -
27B TYR* 6.2 0.2 - - + -
79B PHE* 3.3 31.2 - - + -
80B LEU 4.3 4.3 - - - +
81B VAL* 3.8 25.8 - - + -
129B SER* 3.3 39.3 - - - +
131B VAL* 3.7 21.5 - - + +
172B ARG* 2.7 16.6 + - - -
213B VAL* 3.3 22.4 + - + +
214B VAL* 3.2 9.4 + - - +
215B PHE 3.2 0.6 - - - -
216B LEU* 1.3 77.3 - - - +
218B GLU* 1.3 58.8 + - + +
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Residues in contact with GLU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ASP* 4.8 7.1 - - - +
25B LYS* 3.8 14.7 + - - +
27B TYR* 2.9 38.0 + - - +
172B ARG* 4.2 1.3 - - - -
214B VAL* 3.0 37.1 + - + +
215B PHE* 3.8 5.2 - - - +
217B LEU* 1.3 82.5 - - + +
219B SER* 1.3 57.5 + - - +
220B PRO* 3.2 14.0 - - - +
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Residues in contact with SER 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ASP 4.5 4.0 + - - -
235A ASP* 3.6 17.9 + - - -
236A VAL* 4.0 6.9 - - - +
255A VAL* 4.9 0.3 - - - +
172B ARG* 2.7 28.9 + - - -
215B PHE* 2.8 20.8 + - - -
216B LEU 3.5 3.3 + - - -
218B GLU* 1.3 76.4 - - - +
220B PRO* 1.3 65.2 - - - +
221B TYR 3.3 2.3 + - - -
222B ILE* 3.2 37.9 + - - +
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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
------------------------------------------------------------
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