Contacts of the helix formed by residues 194 - 211 (chain B) in PDB entry 6AN8
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 GLU 194 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B LYS* 3.9 23.5 + - - +
105B SER* 5.7 0.2 - - - -
192B ASP 3.9 1.8 + - - +
193B LEU* 1.3 78.3 - - - +
195B ILE* 1.3 63.0 + - - +
196B GLY 3.2 4.7 - - - +
197B GLN* 3.0 16.5 + - + +
198B HIS* 2.5 35.6 + - - +
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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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104B LYS* 6.3 3.1 - - + -
105B SER* 5.0 11.2 - - - +
193B LEU 4.0 0.2 + - - -
194B GLU* 1.3 79.0 + - - +
196B GLY* 1.3 63.1 + - - +
198B HIS* 4.4 4.9 - - - -
199B ARG* 3.1 68.8 + - + +
233B GLU* 5.1 2.2 - - - +
235B HIS* 5.3 12.3 - - + -
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Residues in contact with GLY 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B GLU* 3.2 2.8 - - - +
195B ILE* 1.3 79.9 - - - +
197B GLN* 1.3 61.5 + - - +
199B ARG* 4.2 3.5 - - - +
200B THR* 2.9 30.1 + - - -
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Residues in contact with GLN 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 3.6 28.3 - - + +
194B GLU* 3.0 17.0 + - + +
196B GLY* 1.3 76.2 - - - +
198B HIS* 1.3 63.1 + - - +
200B THR* 3.4 7.5 + - - +
201B LYS* 3.0 43.0 + - - +
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Residues in contact with HIS 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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105B SER* 3.5 30.9 + - - -
107B THR* 2.7 32.0 + - - -
189B VAL* 3.5 23.1 - - + -
191B SER* 2.5 37.1 + - - +
193B LEU* 3.9 9.6 - - - +
194B GLU 2.5 22.5 + - - +
195B ILE* 3.9 6.1 - - - +
197B GLN* 1.3 73.4 - - - +
199B ARG* 1.3 67.4 + - + +
201B LYS* 3.0 7.4 + - - +
202B ILE* 2.9 43.4 + - + +
233B GLU* 5.1 5.4 - - + -
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Residues in contact with ARG 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ILE* 3.1 42.0 + - + +
196B GLY* 4.2 3.4 - - - +
198B HIS* 1.3 81.2 - - + +
200B THR* 1.3 61.7 + - - +
202B ILE* 3.4 10.6 + - - +
203B GLU* 3.1 22.3 + - - +
206B ARG* 4.7 2.5 + - - +
233B GLU* 2.7 41.5 + - - +
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Residues in contact with THR 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B GLY 2.9 22.1 + - - -
197B GLN* 3.6 11.7 - - - +
199B ARG* 1.3 78.1 - - - +
201B LYS* 1.3 66.8 + - + +
203B GLU* 3.2 7.9 + - - +
204B GLU* 3.1 37.7 + - + +
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Residues in contact with LYS 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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171B PHE* 3.4 14.1 - - + -
174B GLN* 5.6 4.6 - - - +
175B ASN* 3.5 27.1 + - - +
178B ILE* 4.1 17.7 - - + -
191B SER* 5.9 0.2 - - - +
193B LEU* 4.0 20.4 - - + -
197B GLN* 3.0 28.6 + - - +
198B HIS* 3.0 10.3 + - - +
200B THR* 1.3 78.8 - - + +
202B ILE* 1.3 66.0 + - + +
204B GLU* 3.3 34.9 + - - +
205B LEU* 3.1 17.2 + - - +
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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
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107B THR* 3.7 20.4 - - + +
109B LEU* 4.1 10.5 - - + -
178B ILE* 6.3 0.2 - - + -
189B VAL* 3.6 38.1 - - + -
198B HIS* 2.9 47.8 + - + +
199B ARG* 3.6 9.6 - - - +
200B THR 3.2 0.4 - - - -
201B LYS* 1.3 78.8 - - + +
203B GLU* 1.3 56.9 + - - +
205B LEU* 3.2 7.1 + - + +
206B ARG* 2.9 56.4 + - - +
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Residues in contact with GLU 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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199B ARG 3.1 13.2 + - - +
200B THR* 3.2 9.8 + - - +
202B ILE* 1.3 74.3 - - - +
204B GLU* 1.3 60.7 + - + +
206B ARG* 3.1 34.7 + - - +
207B GLN* 2.8 64.2 + - + +
210B LEU* 5.7 0.2 - - - +
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Residues in contact with GLU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B PHE* 4.1 13.2 - - + -
174B GLN* 5.4 4.2 + - - +
175B ASN* 4.8 2.3 + - - -
200B THR* 3.1 29.8 + - + +
201B LYS* 3.3 40.4 + - - +
202B ILE 3.3 0.2 - - - -
203B GLU* 1.3 76.0 - - - +
205B LEU* 1.3 56.9 + - - +
207B GLN* 3.4 9.3 + - - +
208B HIS* 2.9 28.9 + - - +
211B ARG* 4.7 1.0 + - - -
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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
----------------------------------------------------------
109B LEU* 4.3 13.2 - - + -
168B LEU* 3.7 26.5 - - + -
171B PHE* 3.7 33.1 - - + -
180B ILE* 4.2 9.6 - - + -
187B LEU* 4.3 8.1 - - + -
189B VAL* 3.6 39.7 - - + -
201B LYS 3.1 13.8 + - - +
202B ILE* 3.2 9.8 + - + +
204B GLU* 1.3 73.6 - - - +
206B ARG* 1.3 66.6 + - - +
208B HIS* 3.2 10.6 + - + +
209B LEU* 3.0 27.9 + - + +
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Residues in contact with ARG 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B THR* 4.5 0.8 - - - +
109B LEU* 3.6 15.8 - - + +
199B ARG* 4.7 2.2 + - - +
202B ILE* 2.9 47.0 + - - +
203B GLU* 3.1 42.0 + - - +
205B LEU* 1.3 76.6 - - - +
207B GLN* 1.3 58.2 + - - +
209B LEU* 3.0 10.6 + - - +
210B LEU* 2.9 35.3 + - + +
228B LEU* 3.2 38.1 + - + +
229B TRP* 4.1 12.0 + - - +
230B MET 3.6 3.4 + - - -
231B GLY* 3.6 30.5 - - - +
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Residues in contact with GLN 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B GLU* 2.8 48.3 + - + +
204B GLU* 3.8 7.6 - - - +
206B ARG* 1.3 75.1 - - - +
208B HIS* 1.3 60.8 + - - +
210B LEU* 3.4 27.1 - - - +
211B ARG* 3.0 46.1 + - - +
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Residues in contact with HIS 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ILE* 3.2 31.8 - - + +
168B LEU* 5.2 1.1 - - + -
170B PRO* 3.3 37.9 - - + +
171B PHE* 3.9 22.8 + + + +
204B GLU 2.9 14.8 + - - +
205B LEU* 3.3 19.7 - - + +
206B ARG 3.1 0.4 - - - -
207B GLN* 1.3 77.9 - - - +
209B LEU* 1.3 58.4 + - + +
211B ARG* 3.3 39.1 + - - +
212B TRP* 4.7 1.0 - - - +
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Residues in contact with LEU 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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109B LEU* 4.9 4.0 - - + -
111B VAL* 4.0 18.8 - - + -
164B MET* 4.9 9.9 - - + -
167B ILE* 3.7 27.4 - - + -
168B LEU* 4.2 17.7 - - + -
187B LEU* 4.6 8.3 - - + -
205B LEU* 3.0 22.0 + - + +
206B ARG* 3.0 6.0 + - - +
208B HIS* 1.3 76.8 - - - +
210B LEU* 1.3 64.4 + - - +
211B ARG 3.2 2.2 - - - -
212B TRP* 3.3 20.4 + - - +
228B LEU* 3.8 33.4 - - + -
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Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ARG* 2.9 19.9 + - + +
207B GLN* 3.4 37.2 + - - +
209B LEU* 1.3 71.5 - - - +
211B ARG* 1.3 56.8 + - - +
212B TRP 2.9 15.2 + - - -
228B LEU* 3.7 22.7 - - + -
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Residues in contact with ARG 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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204B GLU 4.7 1.4 + - - -
207B GLN* 3.0 45.8 + - - +
208B HIS* 3.3 42.8 + - - +
209B LEU 3.2 0.2 - - - -
210B LEU* 1.3 74.4 - - - +
212B TRP* 1.3 58.8 + - - +
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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