Contacts of the helix formed by residues 198 - 214 (chain B) in PDB entry 3EBL
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 SER 198 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B GLY* 3.6 11.9 - - - -
122B GLY 3.9 0.2 - - - -
123B SER* 3.4 8.3 + - - -
197B ASP* 1.3 73.4 - - - +
199B SER* 1.3 65.6 + - - -
201B GLY* 2.8 17.0 + - - +
202B ASN 3.3 1.0 + - - -
224B LEU 3.0 12.5 + - - -
225B ASN* 3.2 17.1 + - - +
227B MET* 3.0 27.2 + - - -
251B ARG* 4.9 0.2 + - - -
401B GA4 2.8 46.4 + - - -
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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
----------------------------------------------------------
120B HIS 3.7 2.3 + - - -
121B GLY 3.7 1.4 - - - -
123B SER* 3.4 9.5 + - - -
124B PHE* 3.0 53.8 + - - -
154B TYR* 2.8 24.2 + - - -
198B SER* 1.3 79.3 + - - +
200B GLY* 1.3 56.8 + - - +
202B ASN* 3.2 4.7 + - - +
203B ILE* 2.9 32.5 + - - +
227B MET* 3.6 11.0 - - - +
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Residues in contact with GLY 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PHE* 3.3 36.1 - - - +
120B HIS 3.5 7.0 + - - -
196B GLY* 3.4 10.4 - - - -
197B ASP 2.8 9.8 + - - -
199B SER* 1.3 77.5 + - - +
201B GLY* 1.3 57.8 + - - +
203B ILE* 3.4 4.2 + - - -
204B ALA* 2.9 28.4 + - - +
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Residues in contact with GLY 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B GLY* 3.3 25.9 - - - -
198B SER 2.8 10.1 + - - -
200B GLY* 1.3 74.9 - - - +
202B ASN* 1.3 64.2 + - - +
204B ALA* 3.4 3.3 + - - +
205B HIS* 3.0 18.5 + - - +
223B LEU* 3.7 16.5 - - - +
226B ALA* 3.9 18.2 - - - -
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Residues in contact with ASN 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PHE* 3.5 11.9 - - + -
166B TYR* 2.5 30.8 + - - -
198B SER 3.3 4.4 + - - +
199B SER* 3.2 11.8 + - - +
201B GLY* 1.3 72.4 - - - +
203B ILE* 1.3 64.6 + - - +
205B HIS* 3.1 6.1 + - - +
206B HIS* 3.1 23.0 + - - -
226B ALA* 4.1 2.6 - - - +
227B MET 2.9 29.2 + - - +
228B PHE* 3.7 19.3 - - - -
255B TRP* 3.9 8.5 - - - -
269B ALA 2.9 24.2 + - - -
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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
----------------------------------------------------------
119B PHE* 3.7 28.9 - - + -
124B PHE* 4.0 8.3 - - + -
154B TYR* 3.5 50.7 - - + +
165B ALA* 3.9 21.3 - - + +
166B TYR* 3.9 26.7 - - + -
199B SER 2.9 21.9 + - - +
200B GLY* 3.7 7.4 - - - +
201B GLY 3.4 0.4 - - - -
202B ASN* 1.3 70.3 - - - +
204B ALA* 1.3 58.5 + - - +
206B HIS* 3.1 3.6 + - - +
207B VAL* 2.8 39.1 + - + +
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Residues in contact with ALA 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PHE* 4.3 10.5 - - + -
194B LEU* 3.9 12.8 - - + +
195B SER 3.9 26.2 - - - +
200B GLY 2.9 18.2 + - - +
201B GLY 3.5 5.8 - - - +
203B ILE* 1.3 76.0 - - - +
205B HIS* 1.3 62.6 + - - +
207B VAL* 3.5 1.1 + - - +
208B ALA* 3.0 26.0 + - - +
221B ASN* 5.0 1.8 - - - +
223B LEU* 3.7 18.8 - - + -
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Residues in contact with HIS 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B GLY 3.0 13.0 + - - +
202B ASN 3.1 8.3 + - - +
204B ALA* 1.3 74.7 - - - +
206B HIS* 1.3 84.5 + + - +
208B ALA* 3.1 8.1 + - - +
209B VAL* 3.0 50.3 + - + +
221B ASN* 4.7 4.0 - - - +
223B LEU* 4.6 3.7 - - + +
228B PHE* 4.2 10.1 - + + -
272B PRO* 3.8 21.9 - - + +
273B PHE* 4.4 5.8 - + - -
280B LEU* 4.0 15.9 - - + +
285B PHE* 4.0 5.9 - + - -
305B TYR* 2.8 42.7 + + - +
309B LEU* 5.0 0.2 - - + -
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Residues in contact with HIS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B TYR* 3.2 50.1 + + + -
202B ASN* 3.1 24.2 + - - -
203B ILE 3.8 4.7 - - - +
205B HIS* 1.3 99.3 + + - +
207B VAL* 1.3 60.4 + - - +
209B VAL* 3.4 9.4 + - - +
210B ARG* 3.1 23.0 + - - +
268B PRO* 3.6 20.8 + - + -
269B ALA* 3.2 25.4 + - - -
272B PRO* 4.4 5.3 - - + +
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Residues in contact with VAL 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PHE* 4.4 2.7 - - + -
166B TYR* 4.0 10.1 - - + +
169B GLY* 3.6 42.0 - - - +
170B TRP* 3.8 9.4 - - + +
173B LEU* 3.8 19.3 - - + -
194B LEU* 3.7 22.9 - - + -
203B ILE* 2.8 30.3 + - + +
204B ALA* 4.0 4.9 - - - +
206B HIS* 1.3 72.4 - - - +
208B ALA* 1.3 58.1 + - - +
210B ARG* 3.5 7.1 + - - +
211B ALA* 3.0 26.0 + - - +
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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
----------------------------------------------------------
194B LEU* 3.7 10.0 - - + +
204B ALA 3.0 18.3 + - - +
205B HIS 3.1 5.6 + - - +
207B VAL* 1.3 76.6 - - - +
209B VAL* 1.3 58.9 + - - +
211B ALA* 3.4 6.0 + - - +
212B ALA* 3.0 28.1 + - - +
218B VAL* 5.2 1.9 - - + +
221B ASN* 3.3 33.7 - - - +
285B PHE* 3.6 11.2 - - + -
286B ALA* 5.1 5.6 + - + -
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B HIS* 3.0 46.7 + - + +
206B HIS* 3.7 11.4 - - - +
208B ALA* 1.3 72.1 - - - +
210B ARG* 1.3 60.9 + - - +
212B ALA* 3.2 5.2 + - - +
213B ASP* 2.9 30.0 + - - +
278B ARG* 3.5 29.4 - - - +
280B LEU* 3.9 20.6 - - + -
283B LEU* 4.7 1.6 - - + -
285B PHE* 3.7 15.0 - - + -
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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
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166B TYR 5.1 1.2 + - - -
167B ASP* 4.4 16.0 + - - +
170B TRP* 3.2 67.0 - - + +
206B HIS 3.1 14.8 + - - +
207B VAL* 3.7 6.7 - - - +
209B VAL* 1.3 80.7 - - - +
211B ALA* 1.3 56.1 + - - +
213B ASP* 3.3 7.5 + - - +
214B GLU* 3.0 56.3 + - + +
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Residues in contact with ALA 211 (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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170B TRP* 3.5 12.5 - - - -
173B LEU* 3.9 20.9 - - + -
207B VAL 3.0 18.1 + - - +
208B ALA 3.6 6.1 - - - +
209B VAL 3.3 0.2 - - - -
210B ARG* 1.3 76.2 - - - +
212B ALA* 1.3 56.9 + - - +
214B GLU 3.2 0.9 + - - -
215B GLY 3.0 9.2 + - - -
216B VAL* 2.7 47.0 + - + +
218B VAL* 3.9 12.3 - - + -
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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
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208B ALA 3.0 14.3 + - - +
209B VAL* 3.2 11.2 + - - +
211B ALA* 1.3 75.7 - - - +
213B ASP* 1.3 62.1 + - - +
214B GLU 3.3 0.5 + - - -
215B GLY* 3.4 8.1 + - - -
216B VAL 4.2 3.1 + - - -
283B LEU* 4.1 27.6 - - + +
284B PRO* 3.6 39.9 - - - +
285B PHE* 4.1 8.7 - - + -
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Residues in contact with ASP 213 (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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209B VAL* 2.9 19.4 + - - +
210B ARG* 3.6 7.7 - - - +
212B ALA* 1.3 75.0 - - - +
214B GLU* 1.3 63.3 + - + +
215B GLY 3.5 0.7 + - - -
278B ARG* 2.6 48.1 + - - -
283B LEU* 3.1 19.3 - - - +
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Residues in contact with GLU 214 (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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170B TRP* 3.5 30.9 + - + -
210B ARG* 3.0 43.2 + - + +
211B ALA 4.2 0.2 - - - +
212B ALA 3.2 0.4 - - - -
213B ASP* 1.3 83.8 - - + +
215B GLY* 1.3 64.6 + - - +
216B VAL* 3.3 8.3 + - + +
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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