Contacts of the helix formed by residues 206 - 218 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163B VAL* 5.5 0.6 - - - +
204B GLY 3.4 1.4 - - - -
205B THR* 1.3 81.1 - - - +
207B LYS* 1.3 62.0 + - - +
208B THR 3.3 1.3 - - - -
209B LEU* 3.6 9.1 - - - +
210B LEU* 2.9 37.8 + - - +
328B VAL* 4.7 0.4 - - - -
1607B ADP 3.1 34.3 + - - -
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Residues in contact with LYS 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LEU* 3.4 43.1 - - + +
201B GLY 2.8 35.2 - - - +
202B PRO 3.4 10.5 + - - -
203B PRO* 4.2 2.5 - - - +
205B THR* 4.0 7.4 - - - +
206B GLY* 1.3 80.0 - - - +
208B THR* 1.3 63.5 + - - +
210B LEU 3.4 0.3 + - - -
211B ALA* 3.2 16.3 + - - +
258B PHE* 4.6 2.2 - - - -
260B ASP* 5.3 0.8 + - - -
305B ALA* 3.9 21.2 - - + +
306B THR 4.0 8.7 - - - +
307B ASN* 4.8 2.2 - - - +
328B VAL* 4.0 20.6 - - + -
1607B ADP 2.1 53.6 + - - +
1608B MG 3.9 4.8 - - - -
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Residues in contact with THR 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B LYS* 1.3 74.8 - - - +
209B LEU* 1.3 59.3 + - - +
211B ALA* 3.2 2.9 + - - +
212B ARG* 2.9 44.8 + - + +
224B HIS* 3.5 31.3 - - + +
258B PHE* 3.8 25.6 - - + -
260B ASP* 4.4 9.5 + - - -
1607B ADP 2.9 35.5 + - - -
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Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B VAL* 4.7 16.8 - - + -
162B ASP* 3.6 20.2 - - + +
163B VAL* 3.6 17.3 - - + -
206B GLY* 3.6 9.0 - - - +
207B LYS 3.2 0.2 - - - -
208B THR* 1.3 79.7 - - - +
210B LEU* 1.3 51.4 + - - +
212B ARG* 3.2 21.9 + - - +
213B ALA* 2.7 36.4 + - + +
1607B ADP 3.1 74.0 + - + +
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Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B PHE* 4.4 6.9 - - + -
163B VAL* 4.1 27.1 - - + +
166B ALA* 4.8 4.0 - - + -
169B ALA* 3.9 17.7 - - + -
170B ILE* 4.1 18.4 - - + -
173B LEU* 4.0 24.9 - - + -
199B LEU* 4.4 7.0 - - + -
205B THR 5.7 0.2 - - - +
206B GLY 2.9 21.7 + - - +
207B LYS* 3.7 4.9 - - - +
208B THR 3.4 0.2 - - - -
209B LEU* 1.3 75.6 - - - +
211B ALA* 1.3 58.4 + - - +
213B ALA* 2.9 5.7 + - - +
214B VAL* 2.8 33.6 + - - +
328B VAL* 3.8 32.3 - - + -
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Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LEU* 4.5 0.2 - - - +
207B LYS 3.2 7.6 + - - +
208B THR 3.2 9.0 + - - +
210B LEU* 1.3 77.6 - - - +
212B ARG* 1.3 65.3 + - - +
214B VAL* 3.1 12.1 + - - +
215B ALA* 3.1 13.5 + - - +
222B PHE* 3.8 15.0 - - + -
256B ILE* 4.5 3.0 - - + +
258B PHE* 3.7 30.7 - - + -
303B MET* 4.3 25.1 - - + -
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Residues in contact with ARG 212 (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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155B ASN* 4.4 9.3 - - - +
156B LYS* 2.9 47.6 + - - +
158B VAL* 3.5 33.0 + - + +
208B THR* 2.9 36.0 + - + +
209B LEU* 3.5 20.2 - - - +
211B ALA* 1.3 76.1 - - - +
213B ALA* 1.3 57.1 + - - +
215B ALA* 3.2 2.9 + - - +
216B GLY* 2.9 27.2 + - - -
222B PHE* 3.6 35.3 - - + -
224B HIS* 5.2 2.7 - - - -
1607B ADP 4.5 8.7 + - - -
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Residues in contact with ALA 213 (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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158B VAL* 3.8 14.1 - - + +
159B THR* 3.9 16.0 - - - +
160B PHE* 3.5 27.8 - - + -
163B VAL* 4.2 5.4 - - + -
209B LEU* 2.7 22.9 + - + +
210B LEU* 2.9 9.1 + - - +
212B ARG* 1.3 74.1 - - - +
214B VAL* 1.3 56.6 + - - +
217B GLU* 2.8 32.7 + - - +
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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
----------------------------------------------------------
160B PHE* 4.0 17.7 - - + -
173B LEU* 4.0 30.5 - - + -
176B VAL* 4.0 22.2 - - + -
177B VAL* 3.8 18.6 - - + +
180B LEU* 4.1 4.7 - - + -
210B LEU 2.8 17.2 + - - +
211B ALA* 3.1 9.2 + - - +
213B ALA* 1.3 74.5 - - - +
215B ALA* 1.3 66.8 + - - +
217B GLU* 3.3 2.6 + - - +
218B ALA* 3.0 23.0 + - - +
256B ILE* 3.8 15.5 - - + -
303B MET* 4.8 5.2 - - - -
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Residues in contact with ALA 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ARG* 4.4 1.7 + - - +
211B ALA 3.1 9.4 + - - +
212B ARG 3.5 7.6 - - - +
214B VAL* 1.3 75.4 - - - +
216B GLY* 1.3 58.4 + - - +
218B ALA* 3.2 1.4 + - - -
219B ASN 2.9 22.7 + - - -
220B VAL* 3.0 31.2 + - + +
222B PHE* 3.8 24.5 - - + -
256B ILE* 3.4 23.6 - - + +
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Residues in contact with GLY 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ARG* 3.4 23.5 - - - +
158B VAL 3.0 23.1 - - - -
159B THR* 4.1 7.2 - - - +
212B ARG 2.9 11.0 + - - -
215B ALA* 1.3 75.0 - - - +
217B GLU* 1.3 64.8 + - - +
219B ASN* 3.2 21.7 + - - +
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Residues in contact with GLU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B VAL 3.8 1.2 + - - -
159B THR* 3.3 16.0 - - - +
160B PHE* 3.0 47.4 + - + +
161B LYS* 6.1 1.0 - - - +
177B VAL* 3.8 26.7 - - + -
181B LYS* 3.5 21.5 - - - +
213B ALA 2.8 15.0 + - - +
214B VAL 3.7 4.3 - - - +
216B GLY* 1.3 79.7 - - - +
218B ALA* 1.3 57.0 + - - +
219B ASN* 3.3 6.6 + - - -
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Residues in contact with ALA 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B VAL* 3.8 13.0 - - + +
180B LEU* 3.6 32.1 - - + -
181B LYS* 4.0 19.9 - - - +
214B VAL 3.0 16.9 + - - +
215B ALA 3.9 1.8 - - - +
217B GLU* 1.3 76.3 - - - +
219B ASN* 1.3 72.0 + - - +
220B VAL* 3.2 14.1 - - + +
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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