Contacts of the helix formed by residues 182 - 197 (chain B) in PDB entry 3CEI
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 ASN 182 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ASP* 3.0 28.2 + - - +
79B CYS 2.7 15.8 + - - +
80B LEU 3.9 7.6 + - - +
81B SER* 3.8 19.5 - - - -
85B THR* 3.6 8.9 + - - +
180B HIS 3.3 1.0 + - - -
181B ILE* 1.3 71.5 - - - +
183B TRP* 1.3 62.5 + - - +
184B HIS* 3.4 14.3 + - - +
185B PHE* 2.9 33.3 + - - +
186B VAL* 3.0 12.0 + - - +
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Residues in contact with TRP 183 (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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84B ALA* 6.0 2.5 - - + -
85B THR* 3.0 27.5 + - - +
86B ALA 3.9 5.6 - - - +
87B LEU* 3.4 45.9 - - + +
91B LEU* 4.0 8.0 - - + +
95B LEU* 4.3 11.4 - - + -
105B PHE* 4.1 14.4 - + - -
153B LEU* 4.4 3.1 - - + -
178B TYR* 3.4 39.0 + + - -
181B ILE* 3.0 53.7 + - + +
182B ASN* 1.3 72.3 - - - +
184B HIS* 1.3 57.8 + - - +
186B VAL* 3.2 18.9 + - + +
187B SER* 2.8 34.7 + - - -
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Residues in contact with HIS 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B THR* 3.1 24.4 + - + +
86B ALA 3.8 10.9 + - - +
182B ASN* 3.0 11.4 + - - +
183B TRP* 1.3 76.3 - - - +
185B PHE* 1.3 59.5 + - + +
187B SER* 3.3 8.8 + - - -
188B GLN* 3.1 44.2 + - + +
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Residues in contact with PHE 185 (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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75B PHE* 3.6 25.6 - + - -
78B ASP* 3.4 39.5 - - + -
79B CYS* 3.9 16.4 - - - -
182B ASN* 2.9 27.3 + - - +
184B HIS* 1.3 80.0 - - + +
186B VAL* 1.3 68.9 + - + +
187B SER 3.1 0.2 - - - -
188B GLN* 3.1 24.6 + - - +
189B CYS* 3.0 47.7 + - - -
204B TYR* 3.7 27.6 - + - -
208B LEU* 5.7 1.8 - - + -
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Residues in contact with VAL 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B CYS* 5.0 1.6 - - + -
91B LEU* 3.5 26.7 - - + -
124B ALA* 6.3 0.4 - - + -
152B LEU* 3.5 35.3 - - + +
153B LEU* 3.8 26.7 - - + -
181B ILE* 3.9 12.3 - - + -
182B ASN 3.0 17.0 + - - +
183B TRP* 3.2 18.4 + - + +
185B PHE* 1.3 80.1 - - + +
187B SER* 1.3 62.9 + - - +
189B CYS* 3.4 3.0 + - - +
190B TYR* 3.1 21.1 + - - +
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Residues in contact with SER 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ALA 4.4 0.2 + - - -
87B LEU* 3.7 0.7 - - - -
88B SER* 2.8 49.2 + - - -
90B GLU* 5.3 0.5 - - - +
91B LEU* 3.4 13.1 - - - +
183B TRP 2.8 20.5 + - - -
184B HIS* 3.4 9.6 - - - -
186B VAL* 1.3 75.9 - - - +
188B GLN* 1.3 65.4 + - - +
190B TYR* 3.2 5.4 + - - +
191B GLU* 3.0 25.2 + - - +
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Residues in contact with GLN 188 (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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184B HIS* 3.1 34.8 + - + +
185B PHE* 3.1 26.4 + - + +
187B SER* 1.3 77.2 - - - +
189B CYS* 1.3 62.6 + - - +
190B TYR 3.2 0.2 + - - -
191B GLU* 3.3 9.1 + - - +
192B TRP* 3.0 70.8 + - + -
208B LEU* 4.3 8.7 - - - +
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Residues in contact with CYS 189 (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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75B PHE* 3.5 17.3 - - - -
150B VAL* 4.5 3.8 - - + +
151B PRO 3.7 14.8 - - - +
152B LEU* 3.6 10.7 - - + +
185B PHE* 3.0 49.7 + - - -
186B VAL 3.6 8.3 - - - +
188B GLN* 1.3 80.5 - - - +
190B TYR* 1.3 57.0 + - - +
192B TRP* 3.7 5.9 + - - +
193B ALA* 3.0 29.5 + - - +
200B SER* 4.8 0.9 + - - -
204B TYR* 5.7 2.0 - - - -
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Residues in contact with TYR 190 (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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88B SER* 5.1 0.2 - - - -
90B GLU* 3.8 25.1 + - + -
91B LEU* 3.9 26.9 - - + -
94B ALA* 3.2 20.4 - - + +
97B LYS* 6.0 0.7 - - - -
126B TYR* 3.7 27.5 - + - -
131B GLN 5.5 1.0 + - - -
133B ILE* 4.0 11.9 - - + -
152B LEU* 3.5 25.1 - - + +
186B VAL 3.1 13.7 + - - +
187B SER 3.5 7.6 - - - +
188B GLN 3.2 0.2 - - - -
189B CYS* 1.3 73.6 - - - +
191B GLU* 1.3 68.0 - - - +
193B ALA* 2.9 13.4 + - - +
194B LYS* 3.0 53.7 + - + +
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Residues in contact with GLU 191 (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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90B GLU* 3.9 30.9 - - - +
187B SER 3.0 13.4 + - - +
188B GLN* 3.6 8.1 - - - +
190B TYR* 1.3 81.5 - - - +
192B TRP* 1.3 81.8 + - + +
194B LYS* 3.3 6.5 + - - +
195B LYS* 3.1 57.8 + - - +
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Residues in contact with TRP 192 (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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188B GLN* 3.0 48.0 + - + +
189B CYS* 4.3 4.0 - - - +
191B GLU* 1.3 102.2 + - + +
193B ALA* 1.3 60.7 + - - +
195B LYS* 4.2 10.5 - - + +
196B GLU* 2.7 30.5 + - + +
197B GLY 3.4 0.5 + - - -
200B SER* 3.4 29.9 - - - -
203B TYR* 3.9 28.3 - + - -
204B TYR* 6.0 1.8 - - + -
208B LEU* 3.5 32.1 - - + -
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Residues in contact with ALA 193 (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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126B TYR* 4.0 19.7 - - + -
128B LEU* 3.8 9.5 - - - +
150B VAL* 3.6 28.0 - - + -
152B LEU* 4.3 0.4 - - + -
189B CYS 3.0 20.0 + - - +
190B TYR* 2.9 8.1 + - - +
192B TRP* 1.3 77.6 - - - +
194B LYS* 1.3 59.1 + - - +
197B GLY* 2.9 27.8 + - - -
200B SER* 3.8 8.9 + - - -
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Residues in contact with LYS 194 (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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90B GLU* 3.0 33.5 + - - +
126B TYR* 3.8 27.8 - - + +
128B LEU* 5.6 0.7 - - - +
190B TYR* 3.0 50.8 + - + +
191B GLU* 3.5 8.7 - - - +
193B ALA* 1.3 80.4 - - - +
195B LYS* 1.3 62.5 + - + +
197B GLY 4.6 0.5 + - - -
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Residues in contact with LYS 195 (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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191B GLU* 3.1 50.0 + - + +
192B TRP* 4.2 9.0 - - + +
194B LYS* 1.3 82.6 - - + +
196B GLU* 1.3 76.9 + - + +
197B GLY 3.6 0.2 - - - -
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Residues in contact with GLU 196 (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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192B TRP* 2.7 18.3 + - + +
195B LYS* 1.3 90.4 - - + +
197B GLY* 1.3 65.4 + - - +
198B LEU 3.4 0.2 + - - -
199B GLY* 2.9 17.2 + - - -
200B SER* 3.7 19.3 - - - +
203B TYR* 6.5 0.2 - - + -
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Residues in contact with GLY 197 (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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128B LEU* 3.9 15.7 - - - -
150B VAL* 3.8 7.7 - - - +
192B TRP 3.4 0.8 + - - +
193B ALA* 2.9 23.9 + - - -
194B LYS 4.5 0.6 + - - -
195B LYS 3.6 1.4 - - - -
196B GLU* 1.3 76.5 - - - +
198B LEU* 1.3 57.5 + - - -
199B GLY 2.9 4.0 + - - -
200B SER* 2.7 28.9 + - - -
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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
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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