Contacts of the helix formed by residues 166 - 182 (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 ALA 166 (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* 3.8 18.6 - - + +
164B GLY 3.1 9.2 + - - +
165B GLY* 1.3 78.4 - - - +
167B GLU* 1.3 65.1 + - - +
168B GLU* 3.4 2.5 - - - -
169B ALA* 3.4 14.0 + - + +
170B ILE* 3.0 28.6 + - + +
205B THR 5.8 1.3 - - - +
210B LEU* 4.8 7.9 - - + -
328B VAL* 5.4 8.3 - - + -
329B ASP 6.1 0.9 - - - +
1607B ADP 5.0 2.0 - - - +
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Residues in contact with GLU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLY* 3.1 15.4 - - - +
166B ALA* 1.3 80.8 + - - +
168B GLU* 1.3 75.0 + - - +
170B ILE* 3.0 11.7 + - + +
171B GLU* 3.0 24.0 + - - +
174B LYS* 5.6 0.3 + - - -
338B LYS* 5.8 1.7 + - - -
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Residues in contact with GLU 168 (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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166B ALA* 3.4 0.7 - - - -
167B GLU* 1.3 87.1 - - - +
169B ALA* 1.3 63.8 + - - +
171B GLU* 3.3 7.8 + - - +
172B GLU* 3.3 24.1 + - - +
327B VAL 6.0 1.3 - - - +
442B ARG* 5.0 9.0 + - - -
593B GLU* 5.5 0.7 - - - +
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ALA* 3.4 13.1 + - + +
167B GLU 3.2 0.6 - - - -
168B GLU* 1.3 78.9 - - - +
170B ILE* 1.3 63.0 + - - +
172B GLU* 3.4 3.3 + - - +
173B LEU* 3.1 29.7 + - + +
210B LEU* 3.9 25.4 - - + -
326B ILE* 3.8 26.9 - - + +
327B VAL 4.6 8.9 + - - +
328B VAL* 4.9 3.4 - - + -
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Residues in contact with ILE 170 (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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160B PHE* 3.7 48.6 - - + +
163B VAL* 4.2 21.3 - - + +
166B ALA 3.0 24.0 + - - +
167B GLU* 3.0 12.5 + - + +
169B ALA* 1.3 76.4 - - - +
171B GLU* 1.3 57.6 + - - +
173B LEU* 3.2 8.8 + - - +
174B LYS* 2.9 43.0 + - - +
210B LEU* 4.1 16.4 - - + -
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Residues in contact with GLU 171 (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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167B GLU 3.0 11.7 + - - +
168B GLU* 3.7 10.8 - - - +
170B ILE* 1.3 78.6 - - - +
172B GLU* 1.3 63.7 + - + +
173B LEU 3.4 0.2 + - - -
174B LYS* 3.2 42.7 + - - +
175B GLU* 4.5 0.5 + - - +
383C ARG* 3.3 34.0 + - - -
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Residues in contact with GLU 172 (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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168B GLU 3.3 11.9 + - - +
169B ALA* 3.9 3.6 - - - +
170B ILE 3.3 0.2 - - - -
171B GLU* 1.3 82.7 - - + +
173B LEU* 1.3 61.7 + - - +
174B LYS 3.6 0.3 + - - -
175B GLU* 4.0 18.0 + - - +
176B VAL* 4.3 4.9 - - - +
324B LYS* 4.2 25.0 + - + +
326B ILE* 3.5 27.6 - - + +
383C ARG* 5.9 0.2 + - - -
400C ARG* 2.7 42.0 + - - -
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Residues in contact with LEU 173 (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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160B PHE* 4.4 4.3 - - + -
169B ALA* 3.1 20.5 + - + +
170B ILE* 3.2 6.9 + - - +
172B GLU* 1.3 75.8 - - - +
174B LYS* 1.3 65.6 + - - +
175B GLU 3.2 2.7 - - - -
176B VAL* 2.9 30.4 + - + +
177B VAL* 3.1 13.9 + - - +
197B ILE* 4.4 4.0 - - + -
199B LEU* 4.7 5.4 - - + -
210B LEU* 4.0 39.0 - - + -
214B VAL* 4.0 23.6 - - + -
303B MET* 3.9 23.8 - - + -
326B ILE* 3.7 22.2 - - + -
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Residues in contact with LYS 174 (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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160B PHE* 4.8 6.7 - - + -
167B GLU 5.6 0.2 + - - -
170B ILE* 2.9 33.9 + - + +
171B GLU* 3.2 50.5 + - - +
172B GLU 3.4 1.2 - - - -
173B LEU* 1.3 75.9 - - - +
175B GLU* 1.3 62.6 + - - +
177B VAL* 3.0 11.0 + - - +
178B GLU* 3.0 29.0 + - + +
383C ARG* 3.9 12.1 - - + +
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Residues in contact with GLU 175 (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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171B GLU 5.7 0.4 - - - +
172B GLU* 4.0 13.9 + - - +
174B LYS* 1.3 78.4 - - - +
176B VAL* 1.3 66.3 + - + +
178B GLU* 3.4 0.7 + - - +
179B PHE* 3.0 22.7 + - - +
186B PHE* 3.7 9.2 - - + -
193B MET* 4.2 11.2 - - - +
376C GLU* 4.6 1.2 - - - +
379C LEU* 4.0 38.2 - - - +
380C LEU* 4.0 4.5 - - - +
383C ARG* 4.0 37.9 - - + +
400C ARG* 2.7 35.6 + - - -
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Residues in contact with VAL 176 (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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172B GLU 4.3 5.2 - - - +
173B LEU* 2.9 24.1 + - + +
175B GLU* 1.3 75.3 - - + +
177B VAL* 1.3 64.0 + - - +
179B PHE* 3.2 3.3 + - + +
180B LEU* 3.0 31.7 + - + +
193B MET* 3.9 18.2 - - + -
194B PRO* 6.1 0.2 - - + -
197B ILE* 3.5 30.1 - - + -
214B VAL* 4.0 19.1 - - + -
301B ILE* 4.2 21.3 - - + -
303B MET* 5.4 2.7 - - - -
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Residues in contact with VAL 177 (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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160B PHE* 4.0 16.2 - - + -
173B LEU 3.1 12.4 + - - +
174B LYS* 3.0 10.6 + - - +
176B VAL* 1.3 75.4 - - - +
178B GLU* 1.3 67.6 + - - +
180B LEU* 3.1 4.3 + - - +
181B LYS* 2.9 51.9 + - - +
214B VAL* 3.8 27.6 - - + +
217B GLU* 3.8 37.7 - - + +
218B ALA* 3.8 4.5 - - - +
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Residues in contact with GLU 178 (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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174B LYS* 3.0 17.4 + - + +
175B GLU 3.8 6.5 - - - +
177B VAL* 1.3 79.5 - - - +
179B PHE* 1.3 65.2 + - - +
181B LYS* 3.2 38.0 + - - +
182B ASP* 3.2 20.4 + - - +
185B LYS* 5.6 0.7 - - - +
186B PHE* 4.1 12.5 - - + -
382C ALA 4.9 0.9 - - - +
383C ARG* 3.4 31.9 - - + +
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Residues in contact with PHE 179 (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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175B GLU 3.0 14.3 + - - +
176B VAL* 3.3 10.1 - - - +
177B VAL 3.1 0.2 - - - -
178B GLU* 1.3 76.1 - - - +
180B LEU* 1.3 70.1 + - + +
182B ASP 2.9 2.9 + - - -
183B PRO* 2.7 58.7 - - + +
186B PHE* 3.7 39.4 - + + -
187B ASN* 4.7 7.2 - - - -
191B ALA 5.3 0.9 - - - -
193B MET* 3.7 37.9 - - + -
296B SER* 3.6 28.7 - - - -
297B LYS* 5.0 1.6 - - - -
299B GLY* 4.2 12.3 - - - -
300B ILE 5.0 0.9 - - - -
301B ILE* 4.4 15.0 - - + -
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Residues in contact with LEU 180 (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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176B VAL* 3.0 27.6 + - + +
177B VAL 3.7 1.3 - - - +
179B PHE* 1.3 86.6 - - + +
181B LYS* 1.3 61.7 + - - +
182B ASP 3.4 0.2 + - - -
183B PRO* 3.8 4.6 - - - +
214B VAL* 4.1 6.5 - - + -
218B ALA* 3.6 17.3 - - + -
220B VAL* 3.9 14.7 - - + +
254B PRO* 3.8 25.0 - - + +
255B CYS 4.4 6.1 - - - +
256B ILE* 3.4 37.0 - - + -
299B GLY* 3.2 31.6 - - - +
301B ILE* 4.2 9.2 - - + -
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Residues in contact with LYS 181 (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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177B VAL* 2.9 24.1 + - - +
178B GLU* 3.2 44.3 + - - +
179B PHE 3.2 0.2 - - - -
180B LEU* 1.3 77.4 - - - +
182B ASP* 1.3 64.9 + - + +
183B PRO* 4.0 0.8 - - - +
217B GLU* 3.5 23.8 + - - +
218B ALA* 4.0 19.9 - - - +
219B ASN* 6.1 0.7 - - - +
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Residues in contact with ASP 182 (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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178B GLU 3.2 8.7 + - - +
179B PHE 2.9 6.3 + - - +
181B LYS* 1.3 85.1 - - + +
183B PRO* 1.3 67.1 - - - +
184B SER* 2.5 30.8 + - - -
185B LYS* 3.1 45.6 + - + +
186B PHE* 4.3 2.3 + - - -
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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