Contacts of the helix formed by residues 206 - 218 (chain F) in PDB entry 2CEA
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 GLY 206 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163F VAL* 4.9 1.9 - - - +
205F THR* 1.3 80.0 - - - +
207F LYS* 1.3 67.0 + - - +
208F THR 3.4 1.1 - - - -
209F LEU* 3.6 10.1 - - - +
210F LEU* 3.0 27.7 + - - +
328F VAL* 4.9 2.7 - - - -
1607F ADP 2.7 36.6 + - - -
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Residues in contact with LYS 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F LEU* 3.8 42.1 - - + +
201F GLY 2.7 35.9 + - - +
202F PRO 3.2 23.0 + - - -
203F PRO* 3.8 4.2 - - - +
205F THR* 3.3 7.7 + - - +
206F GLY* 1.3 73.2 - - - +
208F THR* 1.3 64.2 + - - +
210F LEU* 3.1 11.5 + - - +
211F ALA* 3.3 9.2 + - - +
258F PHE* 4.3 2.0 - - - -
305F ALA* 3.9 18.3 - - + +
306F THR* 4.1 3.4 - - - +
307F ASN* 4.0 12.7 - - - +
328F VAL* 4.2 13.9 - - + +
1607F ADP 2.5 41.7 + - - +
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Residues in contact with THR 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206F GLY 3.4 0.2 - - - -
207F LYS* 1.3 73.7 - - - +
209F LEU* 1.3 58.1 + - - +
211F ALA* 3.1 11.8 + - - +
212F ARG* 2.8 44.0 + - + +
222F PHE* 4.6 0.2 - - - -
224F HIS* 3.7 27.2 - - + +
258F PHE* 3.5 26.4 - - + -
260F ASP* 3.8 12.5 + - - -
1607F ADP 3.0 34.1 + - - +
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Residues in contact with LEU 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F VAL* 4.6 24.7 - - + -
162F ASP* 3.5 16.2 - - + +
163F VAL* 3.2 40.6 - - + -
206F GLY* 3.6 12.1 - - - +
207F LYS 3.3 0.4 - - - -
208F THR* 1.3 80.1 - - - +
210F LEU* 1.3 48.9 + - - +
212F ARG* 3.1 14.7 + - - +
213F ALA* 2.8 33.1 + - - +
1607F ADP 3.5 50.4 + - + +
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Residues in contact with LEU 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160F PHE* 3.8 28.5 - - + -
163F VAL* 4.6 13.7 - - + -
166F ALA* 5.0 8.3 - - + -
169F ALA* 3.8 32.5 - - + +
170F ILE* 4.8 6.7 - - + -
173F LEU* 3.9 20.9 - - + -
199F LEU* 4.3 10.5 - - + -
206F GLY 3.0 14.4 + - - +
207F LYS 3.1 9.1 + - - +
209F LEU* 1.3 75.1 - - - +
211F ALA* 1.3 63.1 + - - +
213F ALA* 3.2 5.0 + - + +
214F VAL* 3.0 31.7 + - - +
328F VAL* 4.2 18.2 - - + -
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Residues in contact with ALA 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F LEU* 4.7 2.1 - - + +
207F LYS 3.3 2.0 + - - +
208F THR 3.1 5.2 + - - +
210F LEU* 1.3 78.0 - - - +
212F ARG* 1.3 62.3 + - - +
215F ALA* 3.2 16.5 + - - +
222F PHE* 3.4 9.2 - - + -
256F ILE* 3.5 14.6 - - + +
258F PHE* 3.1 46.2 - - + -
303F MET* 4.4 22.0 - - + -
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Residues in contact with ARG 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F SER* 3.2 13.7 + - - -
155F ASN* 2.7 50.2 - - - +
156F LYS 5.3 1.2 + - - -
158F VAL* 3.4 25.0 + - + +
208F THR* 2.8 42.1 - - - +
209F LEU* 3.1 14.1 + - - +
211F ALA* 1.3 74.6 - - - +
213F ALA* 1.3 53.6 + - - +
215F ALA* 3.1 3.5 + - - +
216F GLY* 2.7 31.4 + - - -
222F PHE* 3.2 37.3 - - + -
224F HIS* 4.3 14.9 + - - -
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Residues in contact with ALA 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F VAL* 3.2 15.4 - - + +
159F THR* 3.6 25.7 - - - +
160F PHE* 3.9 12.6 - - + -
163F VAL* 3.8 14.4 - - + -
209F LEU 2.8 18.8 + - - +
210F LEU* 3.2 6.5 + - - +
212F ARG* 1.3 74.6 - - - +
214F VAL* 1.3 52.7 + - - +
216F GLY 3.2 0.2 + - - -
217F GLU* 2.6 39.1 + - - +
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Residues in contact with VAL 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F PHE* 3.8 17.5 - - + -
173F LEU* 3.6 27.1 - - + -
176F VAL* 3.9 17.5 - - + -
177F VAL* 3.6 23.2 - - + +
180F LEU* 3.8 19.2 - - + +
210F LEU 3.0 18.5 + - - +
211F ALA* 3.8 5.6 - - - +
213F ALA* 1.3 74.6 - - - +
215F ALA* 1.3 57.7 + - - +
217F GLU* 3.7 1.4 - - - +
218F ALA* 3.0 28.6 + - - +
256F ILE* 4.0 8.1 - - + -
303F MET* 4.7 2.2 - - + -
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Residues in contact with ALA 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180F LEU* 5.3 0.7 - - - -
211F ALA 3.2 4.2 + - - +
212F ARG 3.1 9.0 + - - +
214F VAL* 1.3 78.9 - - - +
216F GLY* 1.3 56.3 + - - +
218F ALA* 3.4 3.1 + - - -
219F ASN 3.0 6.9 + - - -
220F VAL* 2.9 41.2 + - - +
221F PRO 4.2 4.7 - - - +
222F PHE* 3.5 39.9 - - + -
256F ILE* 4.2 11.1 - - + +
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Residues in contact with GLY 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157F ARG* 2.9 42.1 + - - -
158F VAL 3.4 21.1 - - - -
159F THR* 4.0 4.9 - - - +
212F ARG 2.7 14.7 + - - -
213F ALA 3.5 0.2 - - - -
215F ALA* 1.3 72.5 - - - +
217F GLU* 1.3 61.2 + - - +
219F ASN* 3.3 6.1 + - - +
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Residues in contact with GLU 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F THR* 2.9 26.7 - - - +
160F PHE* 3.0 50.4 + - + +
161F LYS 4.4 1.2 + - - -
177F VAL* 3.8 19.8 - - + +
181F LYS* 3.7 14.9 + - - +
213F ALA 2.6 20.2 + - - +
214F VAL 3.7 4.7 - - - +
215F ALA 3.3 0.2 - - - -
216F GLY* 1.3 73.3 - - - +
218F ALA* 1.3 58.6 + - - +
219F ASN* 3.4 1.7 - - - +
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Residues in contact with ALA 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177F VAL* 4.0 6.5 - - - +
180F LEU* 3.5 24.9 - - + -
181F LYS* 3.5 27.5 - - + +
214F VAL 3.0 17.6 + - - +
215F ALA 4.1 0.2 - - - +
216F GLY 3.2 0.2 - - - -
217F GLU* 1.3 75.0 - - - +
219F ASN* 1.3 72.2 + - - +
220F VAL* 2.8 27.2 - - + +
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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