Contacts of the helix formed by residues 189 - 211 (chain B) in PDB entry 3C98
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 LYS 189 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B MET* 3.2 49.5 - - - +
184B ASP 5.5 0.2 - - - +
185B SER 3.4 13.5 + - - +
186B SER* 3.6 8.9 + - - +
187B ILE 3.0 0.4 - - - -
188B SER* 1.3 81.1 + - - +
190B GLN* 1.3 59.5 + - - +
192B LEU* 3.5 31.2 - - + +
193B SER* 3.1 26.3 + - - -
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Residues in contact with GLN 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PRO* 3.7 26.2 + - - +
66B ASN* 3.4 25.9 + - - +
186B SER 3.1 17.5 + - - +
187B ILE* 3.3 8.7 + - + +
189B LYS* 1.3 78.0 - - - +
191B ALA* 1.3 64.0 + - - +
192B LEU 3.2 0.2 - - - -
193B SER* 3.4 6.5 + - - -
194B GLU* 3.2 22.4 + - - +
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Residues in contact with ALA 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLN* 3.2 37.0 - - + +
155B ILE* 4.3 16.8 - - + -
156B THR* 4.8 5.4 - - + -
187B ILE* 2.8 21.1 + - + +
188B SER* 4.8 3.1 - - - -
190B GLN* 1.3 77.0 - - - +
192B LEU* 1.3 57.6 + - - +
194B GLU* 3.5 3.1 + - - +
195B ILE* 2.9 35.8 + - + +
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Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B PHE* 6.6 0.2 - - + -
178B ALA* 4.0 25.1 - - + -
181B ILE* 3.8 25.9 - - + +
182B ILE 5.2 0.7 - - - +
183B MET* 5.2 2.5 - - + -
188B SER 3.1 18.7 + - - +
189B LYS* 3.5 35.4 - - + +
191B ALA* 1.3 78.3 - - - +
193B SER* 1.3 67.8 + - - +
194B GLU 3.1 0.7 + - - -
195B ILE* 3.3 11.7 + - + +
196B GLU* 3.2 25.6 + - + +
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Residues in contact with SER 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ASN* 3.6 19.6 + - - -
189B LYS 3.1 23.4 + - - -
190B GLN* 3.5 15.0 - - - -
191B ALA 3.4 0.4 - - - -
192B LEU* 1.3 82.7 - - - +
194B GLU* 1.3 57.4 + - - +
196B GLU* 4.0 4.2 + - - +
197B THR* 3.2 22.3 + - - -
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Residues in contact with GLU 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PRO* 3.8 33.0 - - + +
66B ASN* 5.8 0.2 - - - +
148B ARG* 3.3 28.6 + - - -
152B GLN* 3.6 26.1 + - + +
190B GLN* 3.2 16.0 + - - +
191B ALA* 3.9 3.5 - - - +
192B LEU 3.1 0.4 - - - -
193B SER* 1.3 75.5 - - - +
195B ILE* 1.3 60.8 + - - +
196B GLU 3.1 2.0 - - - -
197B THR* 2.9 7.0 + - - -
198B ARG* 2.8 66.5 + - + +
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Residues in contact with ILE 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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149B ILE* 4.1 20.6 - - + +
152B GLN* 3.5 33.4 - - + +
153B LEU* 4.1 22.2 - - + -
156B THR* 5.3 0.7 - - + -
177B PHE* 3.8 36.1 - - + -
181B ILE* 4.8 13.0 - - + -
191B ALA* 2.9 30.9 + - + +
192B LEU* 3.3 12.1 + - + +
194B GLU* 1.3 75.5 - - - +
196B GLU* 1.3 57.5 + - - +
198B ARG* 3.8 5.8 + - - +
199B HIS* 3.1 25.6 + - - +
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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
----------------------------------------------------------
174B PRO 4.7 8.4 - - - +
175B ALA* 5.9 0.7 - - - -
177B PHE* 5.3 4.9 - - - -
192B LEU* 3.2 17.4 + - + +
193B SER* 4.3 4.3 - - - +
194B GLU 3.1 0.8 - - - -
195B ILE* 1.3 79.8 - - + +
197B THR* 1.3 59.7 + - - +
199B HIS* 3.7 22.1 + - - +
200B SER* 2.9 35.1 + - - -
203B ILE* 5.8 1.2 - - - +
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Residues in contact with THR 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PRO 5.6 0.9 - - - -
66B ASN* 5.1 6.8 + - - -
67B PRO* 3.9 19.1 - - + -
72B LYS* 3.4 35.2 + - - +
193B SER* 3.2 14.3 + - - -
194B GLU* 2.9 13.1 + - + -
196B GLU* 1.3 79.4 - - - +
198B ARG* 1.3 73.9 + - - +
200B SER* 3.4 6.7 + - - -
201B GLU* 3.2 24.9 + - + +
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Residues in contact with ARG 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ILE* 3.0 40.4 + - - +
62B LEU* 3.5 32.0 + - - +
64B SER 2.9 26.6 + - - -
65B PRO* 4.8 0.2 - - - +
67B PRO* 4.1 8.4 - - - +
141B TYR* 5.1 1.6 + - - -
145B CYS* 4.0 14.0 - - + +
148B ARG* 3.8 26.1 - - + +
149B ILE* 4.1 21.8 - - + +
194B GLU* 2.8 47.8 + - + +
195B ILE* 5.0 0.4 - - - -
197B THR* 1.3 79.6 - - - +
199B HIS* 1.3 60.6 + - - +
201B GLU* 3.7 7.0 + - - +
202B ILE* 3.3 30.5 + - - +
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Residues in contact with HIS 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ILE* 4.5 6.3 - - + +
168B MET 5.1 3.6 + - - -
169B LEU* 3.5 34.9 + - + +
172B GLY* 5.8 5.5 - - - -
173B ASN 4.7 13.7 - - - -
174B PRO 5.0 4.6 + - - -
176B ILE* 5.5 2.2 - - + -
177B PHE* 3.7 21.9 - + + -
195B ILE 3.1 19.2 + - - +
196B GLU* 3.9 21.9 + - - +
197B THR 3.2 0.4 - - - -
198B ARG* 1.3 76.7 - - - +
200B SER* 1.3 64.7 + - - +
201B GLU 3.2 0.4 - - - -
202B ILE* 3.5 6.6 + - + +
203B ILE* 3.1 52.5 + - + +
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Residues in contact with SER 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LYS* 5.9 2.0 + - - -
196B GLU* 2.9 27.3 + - - -
197B THR* 3.6 8.1 - - - -
199B HIS* 1.3 77.5 + - - +
201B GLU* 1.3 58.4 + - - +
203B ILE* 3.4 11.9 + - - +
204B LYS* 3.1 50.3 + - - +
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Residues in contact with GLU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ILE* 4.4 12.8 - - + +
72B LYS* 3.9 28.8 - - - +
75B LEU* 3.7 21.5 - - - +
76B GLU* 5.3 0.9 - - - +
141B TYR* 3.2 37.0 + - + +
145B CYS* 4.5 4.9 - - - -
197B THR* 3.2 17.6 + - + +
198B ARG* 3.9 7.4 - - - +
199B HIS 3.2 0.6 - - - -
200B SER* 1.3 75.9 - - - +
202B ILE* 1.3 59.8 + - - +
203B ILE 3.1 1.3 - - - -
204B LYS* 3.2 25.3 + - - +
205B LEU* 2.9 31.1 + - - +
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Residues in contact with ILE 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ARG* 4.0 31.4 - - + +
145B CYS* 3.4 30.3 - - + -
146B LYS* 3.7 21.1 - - + +
149B ILE* 4.3 12.3 - - + -
169B LEU* 4.6 15.5 - - + -
198B ARG 3.3 15.7 + - - +
199B HIS* 3.5 8.5 + - + +
201B GLU* 1.3 76.3 - - - +
203B ILE* 1.3 60.6 + - + +
205B LEU* 3.8 7.5 - - - +
206B GLU* 3.2 43.6 + - - +
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Residues in contact with ILE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B GLU* 5.8 1.3 - - - +
199B HIS* 3.1 46.3 + - + +
200B SER* 3.5 11.7 - - - +
201B GLU 3.1 0.4 - - - -
202B ILE* 1.3 74.9 - - + +
204B LYS* 1.3 67.4 + - + +
205B LEU 3.1 1.3 + - - -
206B GLU* 3.3 10.7 + - - +
207B ASN* 3.0 44.6 + - - +
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Residues in contact with LYS 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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69B GLU* 5.2 5.5 + - - -
72B LYS* 4.7 13.9 - - - +
76B GLU* 2.9 32.0 + - + +
79B MET* 4.8 16.3 - - + +
200B SER* 3.1 31.7 + - - +
201B GLU* 3.2 30.8 + - - +
203B ILE* 1.3 77.9 - - + +
205B LEU* 1.3 60.9 + - - +
207B ASN* 3.4 14.1 - - - +
208B SER* 3.3 21.1 + - - -
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Residues in contact with LEU 205 (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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79B MET* 5.5 2.9 - - - -
138B GLN* 3.2 48.0 + - + +
141B TYR* 3.3 30.5 - - + -
142B ARG* 3.7 26.2 - - + +
201B GLU 2.9 16.9 + - - +
202B ILE* 3.8 6.3 - - + +
203B ILE 3.1 0.2 - - - -
204B LYS* 1.3 72.9 - - - +
206B GLU* 1.3 96.4 + - + +
207B ASN 3.1 1.1 - - - -
208B SER* 3.1 15.4 + - - -
209B ILE* 3.2 25.1 + - + +
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Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ARG* 3.3 30.9 + - - +
169B LEU* 5.8 1.0 - - - +
202B ILE* 3.2 27.4 + - + +
203B ILE* 3.9 9.0 - - - +
205B LEU* 1.3 92.5 - - + +
207B ASN* 1.3 64.3 + - - +
209B ILE* 3.9 6.3 - - - +
210B ARG* 3.1 28.8 + - - +
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Residues in contact with ASN 207 (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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203B ILE* 3.0 42.3 + - - +
204B LYS* 3.4 14.2 - - - +
205B LEU 3.1 0.2 - - - -
206B GLU* 1.3 78.8 - - - +
208B SER* 1.3 58.5 + - - +
210B ARG* 2.8 34.3 + - - +
211B GLU* 3.0 30.9 + - - +
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Residues in contact with SER 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B MET* 4.4 22.5 + - - +
83B LYS* 5.9 2.4 - - - +
134B TYR* 3.1 26.7 + - - -
138B GLN* 4.7 2.9 - - - -
204B LYS 3.3 8.8 + - - -
205B LEU 3.1 8.7 + - - -
207B ASN* 1.3 79.3 - - - +
209B ILE* 1.3 62.5 + - - +
211B GLU* 3.7 15.3 + - - +
212B LEU* 3.5 28.0 + - - +
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Residues in contact with ILE 209 (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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336A GLN* 5.2 10.1 - - - +
134B TYR* 5.5 3.8 - - + -
135B ASN* 3.9 28.3 - - - +
138B GLN* 3.7 35.4 - - + -
139B SER* 4.9 2.5 - - - +
205B LEU* 3.2 23.9 + - + +
206B GLU* 3.9 8.1 - - + +
207B ASN 3.2 0.2 - - - -
208B SER* 1.3 76.0 - - - +
210B ARG* 1.3 62.8 + - - +
211B GLU 3.1 0.9 - - - -
212B LEU* 3.0 23.4 + - - +
213B HIS* 3.4 8.7 + - - +
216B PHE* 4.7 8.0 - - + -
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Residues in contact with ARG 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLU* 3.1 17.9 + - - +
207B ASN* 2.8 37.9 + - - +
209B ILE* 1.3 78.0 - - - +
211B GLU* 1.3 62.2 + - - +
212B LEU 3.0 1.5 + - - -
213B HIS* 3.3 22.3 + - + +
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Residues in contact with GLU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LYS* 3.3 42.5 + - + +
207B ASN 3.0 17.9 + - - +
208B SER* 3.8 17.5 + - - +
209B ILE 3.1 0.6 - - - -
210B ARG* 1.3 78.5 - - - +
212B LEU* 1.3 62.4 + - - +
213B HIS 3.5 0.2 - - - -
214B ASP* 5.0 3.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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