Contacts of the helix formed by residues 196 - 214 (chain B) in PDB entry 3EGC
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 LEU 196 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLU* 3.9 23.8 - - + +
154B ARG* 3.6 48.2 - - + +
192B GLY* 5.6 0.7 - - - -
193B SER* 3.2 36.6 + - - +
195B GLY* 1.3 79.3 - - - +
197B MET* 1.3 60.3 + - - +
198B THR* 3.9 13.7 - - - +
199B SER* 3.6 10.9 - - - +
200B ARG* 3.0 31.7 + - - +
135C GLU* 3.9 5.6 - - - +
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Residues in contact with MET 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ASN 3.4 24.5 - - - +
154B ARG* 4.5 11.6 - - + +
155B GLU* 3.6 49.8 - - + +
165B LEU* 3.7 20.0 - - + -
168B ASN* 3.8 11.9 - - - +
195B GLY 3.8 0.2 + - - -
196B LEU* 1.3 73.3 - - - +
198B THR* 1.3 59.8 + - + +
200B ARG* 3.2 21.6 + - - +
201B GLU* 2.8 69.1 + - + +
325B ARG* 4.2 0.9 - - - +
135C GLU* 4.4 6.4 + - - +
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Residues in contact with THR 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ASN* 3.4 45.8 - - - +
154B ARG* 4.3 8.4 + - + +
168B ASN* 4.3 10.3 - - - +
196B LEU* 3.9 16.8 - - - +
197B MET* 1.3 81.8 - - + +
199B SER* 1.3 59.1 + - - -
201B GLU* 3.3 0.9 + - - +
202B ARG* 2.9 66.5 + - - +
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Residues in contact with SER 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B VAL* 4.1 21.7 - - - +
192B GLY* 3.5 21.4 + - - -
193B SER 2.6 30.7 + - - -
194B ALA* 4.3 5.2 - - - -
196B LEU* 3.6 13.1 + - - +
197B MET 3.5 0.6 - - - -
198B THR* 1.3 79.1 + - - +
200B ARG* 1.3 62.8 + - - +
202B ARG* 4.2 2.3 - - - +
203B LEU* 3.0 26.9 + - - +
252B SER* 5.3 4.0 + - - -
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Residues in contact with ARG 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B GLU* 5.7 1.6 + - - -
157B ARG* 4.6 0.4 - - - +
194B ALA 3.8 12.8 + - - +
195B GLY 2.9 26.8 + - - -
196B LEU 3.0 9.8 + - - +
197B MET* 3.5 23.9 - - - +
198B THR 3.2 0.2 - - - -
199B SER* 1.3 79.4 - - - +
201B GLU* 1.3 58.3 + - + +
203B LEU* 3.6 5.8 - - - +
204B LYS* 3.0 28.5 + - - +
135C GLU* 3.7 5.9 + - - -
137C ASP* 3.5 23.8 + - - +
138C TYR* 4.0 11.3 - - - +
141C THR* 2.8 43.4 + - - +
142C GLU* 3.1 35.4 - - - +
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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
----------------------------------------------------------
168B ASN* 2.9 25.6 + - + +
169B VAL* 3.5 28.0 - - + +
197B MET* 2.8 39.9 + - + +
198B THR 4.0 0.2 - - - +
200B ARG* 1.3 71.2 - - + +
202B ARG* 1.3 66.0 + - - +
204B LYS* 3.5 10.4 + - + +
205B GLY 3.1 17.3 + - - -
325B ARG* 2.7 47.8 + - - -
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Residues in contact with ARG 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ASN* 4.4 5.1 - - - +
166B SER* 5.1 0.2 - - - -
168B ASN* 2.9 32.4 + - + +
172B ALA* 3.2 17.7 - - + +
191B VAL* 5.0 1.8 - - + -
198B THR* 2.9 46.5 + - - +
199B SER 4.2 1.6 - - - +
201B GLU* 1.3 76.3 - - - +
203B LEU* 1.3 62.7 + - - +
205B GLY 3.3 0.3 + - - -
206B PHE* 3.1 20.3 + - - +
250B LEU* 3.9 7.9 - - + +
252B SER* 2.8 53.4 + - - -
253B SER* 4.6 5.1 - - - -
280B PHE* 3.5 37.1 - - + -
298B GLN* 3.4 29.5 + - - +
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Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ALA* 3.9 24.0 - - + -
191B VAL* 3.9 21.6 - - + +
199B SER 3.0 17.9 + - - +
200B ARG* 3.6 5.8 - - - +
202B ARG* 1.3 78.1 - - - +
204B LYS* 1.3 56.2 + - - +
206B PHE* 3.2 8.5 - - + +
207B ARG* 3.0 52.3 + - - +
222B ILE* 3.9 38.1 - - + -
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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
----------------------------------------------------------
169B VAL* 4.1 27.3 - - + +
200B ARG 3.0 17.3 + - - +
201B GLU* 3.5 9.4 - - + +
203B LEU* 1.3 74.0 - - - +
205B GLY* 1.3 59.7 + - - +
207B ARG* 3.3 10.1 + - - +
208B ALA* 3.0 28.9 + - + +
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Residues in contact with GLY 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B VAL* 3.4 33.2 - - - +
172B ALA* 4.1 0.2 - - - -
173B ARG* 3.4 21.9 - - - +
201B GLU 3.1 12.8 + - - -
202B ARG 3.3 3.3 + - - -
204B LYS* 1.3 72.1 - - - +
206B PHE* 1.3 65.5 + - - +
208B ALA* 3.4 2.3 + - - +
209B ALA* 3.1 18.5 + - - +
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Residues in contact with PHE 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ALA* 4.2 1.4 - - - +
176B VAL* 3.7 25.4 - - + -
187B ILE* 3.2 45.3 - - + -
188B GLY* 3.7 12.3 - - - -
189B ALA* 4.2 11.4 - - + -
202B ARG 3.1 12.3 + - - +
203B LEU* 3.2 15.9 - - + +
205B GLY* 1.3 76.6 - - - +
207B ARG* 1.3 69.8 + - + +
209B ALA* 3.3 3.3 + - - +
210B MET* 3.1 46.6 + - + +
217B VAL* 3.8 18.4 - - + -
222B ILE* 3.5 28.3 - - + -
250B LEU* 4.1 11.2 - - + -
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Residues in contact with ARG 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LEU* 3.0 37.8 + - + +
204B LYS* 3.3 11.6 + - - +
206B PHE* 1.3 86.9 - - + +
208B ALA* 1.3 59.0 + - - +
210B MET* 3.3 5.3 + - - +
211B SER* 2.8 31.7 + - - -
217B VAL* 4.2 29.3 + - + +
219B GLN* 2.7 29.5 + - - +
222B ILE* 4.7 10.1 - - - +
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Residues in contact with ALA 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B VAL* 5.6 5.2 - - + -
173B ARG* 4.4 24.3 - - - +
204B LYS* 3.0 18.0 + - + +
205B GLY* 3.8 7.0 - - - +
206B PHE 3.3 0.2 - - - -
207B ARG* 1.3 74.7 - - - +
209B ALA* 1.3 64.2 + - - +
211B SER* 3.4 6.4 + - - -
212B ALA* 3.0 25.3 + - - +
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Residues in contact with ALA 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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173B ARG* 3.7 30.7 - - + +
176B VAL* 3.5 27.8 - - + -
177B GLU* 3.9 11.6 - - + +
180B ILE* 3.9 4.8 - - + +
205B GLY 3.1 12.6 + - - +
206B PHE 3.7 3.4 - - - +
208B ALA* 1.3 76.7 - - - +
210B MET* 1.3 62.5 + - - +
212B ALA* 3.4 3.3 + - - +
213B ALA* 3.2 22.2 + - - +
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Residues in contact with MET 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B VAL* 4.1 4.3 - - + -
180B ILE* 4.1 13.9 - - - -
185B THR 3.7 23.8 - - - +
187B ILE* 3.9 43.1 - - + +
206B PHE* 3.1 36.4 + - + +
207B ARG* 3.7 5.2 - - - +
209B ALA* 1.3 79.6 - - - +
211B SER* 1.3 62.3 + - - +
213B ALA* 3.2 2.8 + - - -
214B GLY 3.0 3.1 + - - -
215B LEU* 2.9 53.4 + - + +
216B PRO 4.0 13.2 - - - +
217B VAL* 4.8 9.0 - - + -
221B TRP* 4.7 1.3 - - + -
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Residues in contact with SER 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ARG 2.8 18.3 + - - -
208B ALA* 3.6 7.9 - - - -
209B ALA 3.3 0.2 - - - -
210B MET* 1.3 77.1 - - - +
212B ALA* 1.3 57.6 + - - +
214B GLY* 3.0 19.9 + - - -
215B LEU 4.7 3.4 - - - -
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Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ARG* 3.7 22.7 - - - +
177B GLU* 5.3 3.8 - - - +
208B ALA 3.0 17.9 + - - +
209B ALA* 3.8 5.2 - - - +
210B MET 3.3 0.2 - - - -
211B SER* 1.3 76.3 - - - +
213B ALA* 1.3 59.2 + - - +
214B GLY 3.2 1.1 + - - -
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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
----------------------------------------------------------
180B ILE* 4.0 29.8 - - + -
209B ALA 3.2 15.5 + - - +
210B MET 3.8 3.6 - - - +
211B SER 3.1 1.2 - - - -
212B ALA* 1.3 76.5 - - - +
214B GLY* 1.3 62.8 + - - +
215B LEU* 3.5 12.9 + - + +
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Residues in contact with GLY 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B MET 3.0 0.2 + - - -
211B SER* 3.0 15.3 + - - -
212B ALA 3.2 0.8 + - - -
213B ALA* 1.3 80.9 - - - +
215B LEU* 1.3 63.5 + - - +
216B PRO* 3.6 8.0 - - - +
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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
------------------------------------------------------------
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