Contacts of the helix formed by residues 187 - 204 (chain B) in PDB entry 3C2B
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 ASP 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185B ASP* 2.7 36.5 + - - +
188B PHE* 1.3 64.0 + - - +
189B SER* 3.3 12.0 + - - -
190B ALA* 3.1 32.8 + - + +
191B ARG* 3.4 17.0 + - - +
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Residues in contact with PHE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B HIS* 3.6 21.6 + - + +
99B LEU* 3.5 47.3 - - + +
100B ASP* 3.2 23.1 - - - -
103B ALA* 3.7 15.7 - - + -
174B LEU* 4.1 20.9 - - + -
178B MSE 4.7 0.2 - - - -
184B PRO* 3.6 24.0 - - + -
185B ASP* 3.5 28.9 - - + -
187B ASP* 1.3 74.0 + - - +
189B SER* 1.3 57.6 + - - +
191B ARG* 3.4 6.2 + - + +
192B ALA* 2.9 30.1 + - - +
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Residues in contact with SER 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B HIS* 3.7 25.6 - - - -
187B ASP* 3.2 8.7 + - - -
188B PHE* 1.3 75.6 - - - +
190B ALA* 1.3 66.6 + - - +
192B ALA* 3.2 5.4 + - - +
193B LYS* 3.0 40.3 + - - +
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Residues in contact with ALA 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ASP* 3.1 34.0 + - + +
189B SER* 1.3 74.4 + - - +
191B ARG* 1.3 62.8 + - - +
193B LYS* 3.1 11.9 - - - +
194B LYS* 3.0 42.4 + - - +
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Residues in contact with ARG 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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161A GLU* 2.6 44.3 + - - -
164A ARG* 3.2 48.4 - - - +
99B LEU* 3.8 16.4 - - + -
169B LEU 4.3 4.4 + - - -
170B ILE* 3.4 18.6 - - - +
174B LEU* 6.1 1.1 - - + -
185B ASP* 5.3 10.1 + - + +
187B ASP 3.4 10.6 + - - +
188B PHE* 3.6 11.0 - - + +
189B SER 3.3 0.4 - - - -
190B ALA* 1.3 78.9 - - - +
192B ALA* 1.3 57.4 + - - +
194B LYS* 3.2 31.9 + - - +
195B ALA* 3.0 27.9 + - - +
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Residues in contact with ALA 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B GLU* 3.4 29.4 - - + +
95B ALA* 3.7 11.4 - - + -
96B HIS* 3.7 18.2 - - + +
99B LEU* 4.6 1.3 - - - +
170B ILE* 5.7 0.2 - - - -
188B PHE 2.9 20.0 + - - +
189B SER* 3.2 5.8 + - - +
191B ARG* 1.3 74.0 - - - +
193B LYS* 1.3 63.2 + - + +
195B ALA* 3.5 2.1 + - - +
196B VAL* 3.1 32.0 + - - +
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Residues in contact with LYS 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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92B GLU* 3.3 39.3 + - + +
189B SER* 3.0 29.0 + - - +
190B ALA* 3.1 14.6 - - - +
192B ALA* 1.3 72.1 - - - +
194B LYS* 1.3 65.9 - - + +
196B VAL* 3.3 3.1 + - - +
197B VAL* 3.1 30.8 + - + +
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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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161A GLU* 4.0 14.5 + - - +
190B ALA* 3.0 28.9 + - - +
191B ARG* 3.6 41.6 - - - +
193B LYS* 1.3 80.0 - - + +
195B ALA* 1.3 57.8 + - - +
197B VAL* 3.4 9.4 + - - +
198B ALA* 3.1 27.2 + - - +
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Residues in contact with ALA 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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166B PHE* 4.1 2.7 - - + -
169B LEU* 3.8 15.3 - - + +
170B ILE* 3.7 44.6 - - + +
191B ARG* 3.0 17.9 + - - +
192B ALA* 3.8 4.5 - - - +
194B LYS* 1.3 78.1 - - - +
196B VAL* 1.3 57.8 + - - +
198B ALA* 3.4 4.5 + - - +
199B PHE* 2.8 30.3 + - - +
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Residues in contact with VAL 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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88B ALA* 3.9 19.1 - - + +
91B LEU* 3.6 22.4 - - + +
92B GLU* 3.6 35.0 - - + +
95B ALA* 4.9 0.4 - - + -
166B PHE* 3.9 10.3 - - + -
192B ALA 3.1 19.5 + - - +
193B LYS 3.8 3.8 - - - +
195B ALA* 1.3 75.2 - - - +
197B VAL* 1.3 60.4 + - + +
199B PHE* 3.6 4.8 - - - +
200B LEU* 2.8 50.7 + - + +
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Residues in contact with VAL 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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92B GLU* 5.9 1.6 - - - +
193B LYS* 3.1 21.2 + - + +
194B LYS* 3.6 10.1 - - - +
196B VAL* 1.3 77.9 - - + +
198B ALA* 1.3 62.9 + - - +
200B LEU* 3.4 6.4 + - - +
201B THR* 3.0 33.0 + - - +
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Residues in contact with ALA 198 (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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165A SER* 5.3 3.6 - - - +
202A LEU* 3.5 22.6 - - + +
203A TYR* 5.8 1.3 - - - +
169B LEU* 4.0 26.5 - - + -
194B LYS 3.1 13.7 + - - +
195B ALA* 3.8 6.7 - - - +
197B VAL* 1.3 78.7 - - - +
199B PHE* 1.3 63.1 + - - +
201B THR* 3.3 2.2 + - - -
202B LEU* 3.2 26.2 + - - +
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Residues in contact with PHE 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 4.0 30.7 - - + -
145B ILE* 4.2 20.0 - - + -
154B LEU* 4.0 28.7 - - + -
156B PHE* 5.9 0.2 - + - -
162B ALA* 3.5 22.7 - - + -
166B PHE* 3.6 37.9 - + + -
169B LEU* 3.9 7.6 - - + +
195B ALA 2.8 17.6 + - - +
196B VAL* 3.6 3.1 - - - +
198B ALA* 1.3 77.6 - - - +
200B LEU* 1.3 60.9 + - + +
202B LEU* 3.2 2.4 + - - -
203B TYR* 2.9 60.4 + + + +
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Residues in contact with LEU 200 (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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87B LEU* 4.9 2.0 - - + -
88B ALA* 4.4 11.4 - - + +
91B LEU* 4.0 16.6 - - + -
154B LEU* 3.7 28.3 - - + -
196B VAL* 2.8 36.9 + - + +
197B VAL* 4.0 5.4 - - - +
199B PHE* 1.3 74.5 - - + +
201B THR* 1.3 60.4 + - - +
204B GLY* 2.8 23.6 + - - +
208B VAL* 4.7 13.7 - - + -
209B HIS* 2.9 30.0 + - + -
212B LEU* 4.0 27.1 - - + -
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Residues in contact with THR 201 (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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201A THR* 4.3 25.4 - - + +
202A LEU* 3.8 22.1 - - + +
197B VAL* 3.0 23.4 + - - +
198B ALA* 3.3 9.3 + - - -
200B LEU* 1.3 77.7 - - - +
202B LEU* 1.3 62.0 + - - +
204B GLY 4.5 3.8 + - - +
209B HIS* 4.2 10.8 + - - -
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Residues in contact with LEU 202 (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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169A LEU* 3.9 28.0 - - + -
198A ALA* 3.6 36.6 - - + +
201A THR* 3.9 17.3 - - + +
202A LEU* 3.7 18.2 - - + -
155B ARG 5.0 0.3 - - - +
165B SER* 4.5 2.0 - - - +
169B LEU* 4.0 18.2 - - + -
198B ALA 3.2 10.3 + - - +
199B PHE 3.2 2.4 + - - +
201B THR* 1.3 79.5 - - - +
203B TYR* 1.3 89.3 + - + +
204B GLY 5.3 0.4 - - - +
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Residues in contact with TYR 203 (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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154B LEU* 3.1 13.6 - - + -
155B ARG* 2.8 52.7 + - - +
156B PHE* 3.6 21.5 - - + -
161B GLU* 3.8 12.5 + - + +
162B ALA* 3.7 18.6 + - + -
165B SER* 2.9 37.5 + - - -
199B PHE* 2.9 48.3 + + + +
202B LEU* 1.3 98.1 - - + +
204B GLY* 1.3 63.2 + - - +
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Residues in contact with GLY 204 (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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153B TYR 3.5 7.6 - - - -
154B LEU* 4.2 3.1 - - - -
155B ARG* 6.0 0.4 - - - -
200B LEU* 2.8 27.1 + - - +
201B THR 4.8 3.5 - - - +
202B LEU 3.7 0.9 - - - +
203B TYR* 1.3 79.0 - - - +
205B THR* 1.3 64.8 + - - -
206B GLU 4.1 0.2 + - - -
208B VAL* 3.7 10.5 - - - -
209B HIS* 3.5 11.4 + - - -
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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