Contacts of the helix formed by residues 196 - 213 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F GLU* 6.4 0.2 - - - -
133F GLU* 4.0 22.4 + - + +
154F ARG* 3.3 50.5 - - + +
192F GLY* 5.1 1.1 - - - -
193F SER* 3.2 36.6 + - - +
195F GLY* 1.3 77.8 - - - +
197F MET* 1.3 64.5 + - - +
198F THR* 3.2 13.7 - - - +
199F SER* 3.6 12.2 - - - +
200F ARG* 3.0 25.1 + - - +
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Residues in contact with MET 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F ASN 3.4 24.0 - - - +
154F ARG* 4.4 12.9 - - + +
155F GLU* 3.5 53.4 - - + +
165F LEU* 4.0 13.0 - - + -
168F ASN* 3.8 10.8 - - - +
196F LEU* 1.3 73.1 - - - +
198F THR* 1.3 58.0 + - + +
200F ARG* 3.4 22.8 + - - +
201F GLU* 2.9 70.3 + - + +
325F ARG* 4.1 5.2 - - - +
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Residues in contact with THR 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F ASN* 3.4 44.0 - - - +
154F ARG* 3.9 14.4 + - + +
168F ASN* 4.2 13.2 - - - +
196F LEU* 3.8 16.1 - - - +
197F MET* 1.3 74.1 - - + +
199F SER* 1.3 68.3 + - - +
201F GLU* 3.5 0.5 + - - +
202F ARG* 3.0 57.7 + - - +
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Residues in contact with SER 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191F VAL* 4.2 21.6 - - - +
192F GLY* 3.2 23.5 + - - +
193F SER 2.7 27.5 + - - -
194F ALA 4.3 5.8 - - - -
196F LEU* 3.6 13.6 + - - +
198F THR* 1.3 78.4 + - - +
200F ARG* 1.3 63.6 + - - +
202F ARG* 3.9 2.7 - - - +
203F LEU* 3.0 28.7 + - - +
252F SER* 5.4 2.0 - - - -
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Residues in contact with ARG 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155F GLU* 5.5 2.6 + - - -
157F ARG* 4.7 14.8 - - - +
194F ALA 3.8 14.6 - - - +
195F GLY* 2.8 31.3 + - - -
196F LEU 3.0 6.9 + - - +
197F MET* 3.6 27.0 - - - +
199F SER* 1.3 81.6 - - - +
201F GLU* 1.3 58.3 + - + +
203F LEU* 3.8 6.3 - - - +
204F LYS* 3.0 26.4 + - - +
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Residues in contact with GLU 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155F GLU* 5.3 0.3 - - - +
168F ASN* 2.7 42.7 + - + +
169F VAL* 3.5 29.7 + - + +
197F MET* 2.9 38.4 + - + +
198F THR 4.2 0.4 - - - +
200F ARG* 1.3 76.5 - - + +
202F ARG* 1.3 61.6 + - - +
204F LYS* 3.3 5.7 + - + +
205F GLY 3.0 22.9 + - - -
325F ARG* 2.7 38.5 + - - -
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Residues in contact with ARG 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F ASN* 4.5 4.8 - - - +
168F ASN* 2.8 35.9 + - + -
172F ALA* 3.4 17.6 - - + +
191F VAL* 4.8 2.5 - - + -
198F THR* 3.0 42.3 + - - +
199F SER 4.1 2.2 - - - +
201F GLU* 1.3 74.5 - - - +
203F LEU* 1.3 64.4 + - - +
206F PHE 3.2 16.3 + - - -
250F LEU* 3.7 10.8 - - + +
252F SER* 2.6 52.3 + - - -
253F SER* 4.4 5.3 - - - -
280F PHE* 3.4 40.7 - - + +
298F GLN* 3.3 26.7 + - - +
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Residues in contact with LEU 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189F ALA* 3.7 22.7 - - + -
191F VAL* 3.9 21.5 - - + +
199F SER 3.0 19.4 + - - +
200F ARG* 3.8 5.4 - - - +
202F ARG* 1.3 77.8 - - - +
204F LYS* 1.3 61.7 + - - +
206F PHE* 3.1 8.4 + - + +
207F ARG* 3.0 45.4 + - - +
222F ILE* 3.7 39.9 - - + -
250F LEU* 5.5 0.2 - - - -
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Residues in contact with LYS 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169F VAL* 4.2 26.6 - - + +
200F ARG 3.0 19.5 + - - +
201F GLU* 3.5 9.2 - - + +
202F ARG 3.3 0.2 - - - -
203F LEU* 1.3 76.6 - - - +
205F GLY* 1.3 57.1 + - - +
207F ARG* 3.3 10.9 + - - +
208F ALA* 3.0 29.9 + - + +
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Residues in contact with GLY 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169F VAL* 3.5 32.5 - - - +
172F ALA* 4.1 0.2 - - - -
173F ARG* 3.3 23.9 - - - +
201F GLU 3.0 13.2 + - - -
202F ARG 3.9 2.7 - - - -
204F LYS* 1.3 73.0 - - - +
206F PHE* 1.3 64.4 + - - +
208F ALA* 3.4 2.8 + - - +
209F ALA 3.1 17.3 + - - -
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Residues in contact with PHE 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172F ALA* 4.3 1.4 - - - +
176F VAL* 3.6 28.3 - - + -
187F ILE* 3.3 45.3 - - + -
188F GLY* 4.0 11.9 - - - -
189F ALA* 4.1 12.8 - - + -
202F ARG 3.2 11.8 + - - +
203F LEU* 3.1 14.6 + - + +
205F GLY* 1.3 72.6 - - - +
207F ARG* 1.3 74.2 + - + +
209F ALA* 3.1 4.3 + - - +
210F MET* 3.0 43.0 + - + +
217F VAL* 3.8 18.6 - - + -
222F ILE* 3.5 31.0 - - + -
250F LEU* 4.0 11.7 - - + -
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Residues in contact with ARG 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203F LEU* 3.0 33.7 + - + +
204F LYS* 3.6 11.4 - - - +
206F PHE* 1.3 86.3 - - + +
208F ALA* 1.3 58.4 + - - +
210F MET* 3.1 6.7 + - - +
211F SER* 2.8 31.7 + - - -
217F VAL* 4.1 32.1 + - + +
219F GLN* 2.7 30.1 + - - +
222F ILE* 4.4 14.0 - - - +
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Residues in contact with ALA 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F VAL* 5.6 4.0 - - + -
173F ARG* 4.2 25.2 + - - +
204F LYS* 3.0 19.8 + - + +
205F GLY* 3.8 7.0 - - - +
207F ARG* 1.3 76.4 - - - +
209F ALA* 1.3 61.4 + - - +
211F SER* 3.7 6.4 - - - -
212F ALA* 3.0 26.9 + - - +
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Residues in contact with ALA 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173F ARG* 3.6 31.2 - - + +
176F VAL* 3.6 21.1 - - + -
177F GLU* 3.8 11.3 - - + +
180F ILE* 3.6 12.3 - - + +
205F GLY 3.1 15.2 + - - +
206F PHE 3.1 6.1 + - - +
208F ALA* 1.3 78.3 - - - +
210F MET* 1.3 60.7 - - - +
212F ALA* 3.5 2.9 + - - +
213F ALA* 3.3 16.3 + - - +
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Residues in contact with MET 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176F VAL* 4.2 4.0 - - + -
180F ILE* 4.1 18.8 - - - -
185F THR 3.7 18.2 - - - +
187F ILE* 4.1 34.3 - - + +
206F PHE* 3.0 38.0 + - + +
207F ARG* 3.6 8.1 - - - +
209F ALA* 1.3 72.9 - - - +
211F SER* 1.3 61.3 + - - +
213F ALA* 3.2 3.3 + - - +
214F GLY 3.1 3.6 + - - -
215F LEU* 2.8 59.3 + - + +
216F PRO 3.9 14.1 - - - +
217F VAL* 4.7 9.2 - - + -
221F TRP* 4.7 1.3 - - + -
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Residues in contact with SER 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207F ARG 2.8 20.7 + - - -
208F ALA* 3.7 7.9 - - - -
210F MET* 1.3 72.5 - - - +
212F ALA* 1.3 55.4 + - - +
214F GLY* 2.7 24.9 + - - -
215F LEU 4.2 2.9 + - - +
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Residues in contact with ALA 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F ARG* 3.7 22.2 - - - +
177F GLU* 5.2 3.6 - - - +
208F ALA 3.0 16.5 + - - +
209F ALA* 3.9 4.5 - - - +
210F MET 3.3 0.4 - - - -
211F SER* 1.3 79.2 - - - +
213F ALA* 1.3 58.4 + - - +
214F GLY 3.3 0.6 + - - -
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Residues in contact with ALA 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180F ILE* 3.8 30.5 - - + -
209F ALA 3.3 13.1 + - - +
210F MET 3.2 5.5 + - - +
211F SER 3.1 0.6 - - - -
212F ALA* 1.3 78.7 - - - +
214F GLY* 1.3 62.6 + - - +
215F LEU* 3.3 12.8 + - + +
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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
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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