Contacts of the helix formed by residues 193 - 207 (chain B) in PDB entry 3E88
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 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163B PHE* 4.5 19.2 - - + -
188B ILE* 3.1 20.2 + - + +
191B LYS* 3.6 23.4 - - + +
192B ASP* 1.3 79.8 - - - +
194B VAL* 1.3 55.9 + - - +
195B ALA 3.6 1.8 - - - +
196B HIS* 2.7 39.1 + - + +
197B THR* 2.7 33.1 + - - +
296B LEU* 4.7 3.1 - - - +
11D ALA* 3.2 32.2 - - - +
12D GLU* 5.4 2.6 - - - +
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Residues in contact with VAL 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ILE* 4.1 14.1 - - + -
189B ILE* 4.4 21.3 - - + -
192B ASP* 3.5 10.3 + - - +
193B GLU* 1.3 79.8 - - - +
195B ALA* 1.3 61.8 + - - +
196B HIS 3.3 0.2 - - - -
197B THR* 3.2 2.1 + - - -
198B VAL* 2.9 40.0 + - + +
470B PHE* 3.4 32.5 - - + -
471B PRO* 5.8 3.1 - - + -
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Residues in contact with ALA 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B GLU 3.6 0.2 - - - -
194B VAL* 1.3 79.6 - - - +
196B HIS* 1.3 59.2 + - + +
198B VAL* 3.3 6.0 + - - +
199B THR* 2.7 38.5 + - - +
202B ARG* 5.1 0.5 + - - -
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Residues in contact with HIS 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B GLU* 2.7 41.3 + - - +
194B VAL 3.3 0.6 - - - -
195B ALA* 1.3 85.1 - - + +
197B THR* 1.3 61.2 + - - +
199B THR* 3.3 8.0 + - - -
200B GLU* 3.1 19.9 + - - +
274B ARG* 4.3 9.1 + - - -
295B GLY 3.3 26.9 - - - +
296B LEU* 4.2 8.0 - - + +
297B CYS 4.9 6.5 - - - -
298B LYS* 6.3 0.4 - - + -
309B TPO 3.1 39.1 + - + +
311B CYS* 5.1 0.7 - - + -
11D ALA* 3.7 20.5 - - + +
12D GLU* 6.1 0.2 - - + -
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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
----------------------------------------------------------
183B LEU* 4.0 21.4 - - + +
188B ILE* 3.7 15.5 - - + +
193B GLU* 2.7 23.6 + - - +
194B VAL* 3.2 5.4 + - - -
196B HIS* 1.3 74.5 - - - +
198B VAL* 1.3 66.5 + - - +
200B GLU* 3.4 21.8 + - - +
201B SER 3.5 4.0 + - - -
225B LEU* 3.8 28.5 - - + -
227B PHE* 4.0 12.8 - - + -
295B GLY* 5.7 0.2 - - - -
470B PHE* 5.0 2.2 - - - -
473B PHE* 3.9 8.7 - - + -
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Residues in contact with VAL 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B VAL* 2.9 27.4 + - + +
195B ALA* 3.7 6.5 - - - +
197B THR* 1.3 74.1 - - - +
199B THR* 1.3 64.8 - - - +
201B SER* 3.2 5.5 + - - -
202B ARG* 3.0 30.9 + - - +
470B PHE* 3.9 24.9 - - + -
471B PRO* 4.4 15.3 - - + -
472B GLN* 3.4 31.5 - - + +
473B PHE* 4.3 9.2 - - + -
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Residues in contact with THR 199 (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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195B ALA* 2.7 29.7 + - - +
196B HIS* 3.4 11.2 - - - -
198B VAL* 1.3 73.9 - - - +
200B GLU* 1.3 57.4 + - - +
202B ARG* 3.2 19.1 + - - +
203B VAL* 2.8 42.6 + - + +
297B CYS* 3.4 31.7 + - + +
298B LYS* 5.0 0.9 - - - -
299B GLU* 3.4 19.9 + - + +
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Residues in contact with GLU 200 (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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1B G96 2.7 28.1 + - - +
181B LYS* 2.7 32.5 + - - -
183B LEU* 5.0 1.6 - - - +
196B HIS 3.1 7.1 + - - +
197B THR* 3.4 17.3 - - - +
198B VAL 3.2 0.2 - - - -
199B THR* 1.3 79.2 - - - +
201B SER* 1.3 60.6 + - - +
203B VAL* 4.3 1.7 - - - +
204B LEU* 3.2 31.9 + - + +
227B PHE* 3.7 21.2 - - + -
294B PHE* 3.4 28.6 + - + +
295B GLY* 3.4 18.3 - - - -
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Residues in contact with SER 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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197B THR 3.5 1.4 + - - -
198B VAL 3.2 5.8 + - - -
200B GLU* 1.3 77.7 - - - +
202B ARG* 1.3 60.8 + - - +
204B LEU* 3.0 8.1 + - - +
205B GLN* 2.8 49.4 + - - +
215B LEU* 4.3 2.0 - - - +
218B ALA* 3.6 19.8 - - - +
227B PHE* 4.0 19.0 - - - -
472B GLN 3.4 15.1 + - - -
473B PHE* 4.1 13.1 - - - -
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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
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195B ALA 5.1 0.6 + - - -
198B VAL* 3.0 21.9 + - - +
199B THR* 3.7 23.8 + - - +
201B SER* 1.3 77.3 - - - +
203B VAL* 1.3 62.7 + - - +
205B GLN* 3.3 21.1 + - - +
206B ASN* 3.4 21.2 - - - +
299B GLU* 2.7 45.4 + - - +
472B GLN* 3.8 33.0 - - + +
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Residues in contact with VAL 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B THR* 2.8 31.6 + - + +
200B GLU* 4.3 3.6 - - - +
202B ARG* 1.3 71.4 - - - +
204B LEU* 1.3 64.7 + - - +
205B GLN 3.4 0.3 + - - -
206B ASN* 3.4 3.7 + - - +
207B THR* 3.1 43.5 + - + +
266B LEU* 4.9 0.9 - - + -
271B VAL* 4.5 21.1 - - + -
294B PHE* 4.5 20.4 - - + -
297B CYS* 4.3 11.2 - - + -
299B GLU* 3.7 34.1 - - + +
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Residues in contact with LEU 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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1B G96 3.8 38.4 - - + +
200B GLU* 3.2 22.4 + - + +
201B SER 3.0 5.0 + - - +
203B VAL* 1.3 78.8 - - - +
205B GLN* 1.3 61.9 + - - +
206B ASN 3.2 0.7 + - - -
207B THR* 3.6 23.0 + - - +
212B LEU* 6.1 0.4 - - + -
213B THR 3.4 25.1 - - - +
214B ALA* 5.4 0.2 - - - -
215B LEU* 3.8 40.2 + - + +
227B PHE* 4.6 1.8 - - + -
294B PHE* 3.6 29.8 - - + -
475B TYR* 5.1 1.9 + - - -
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Residues in contact with GLN 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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201B SER* 2.8 43.1 + - - +
202B ARG* 3.5 15.9 - - - +
203B VAL 3.2 0.6 - - - -
204B LEU* 1.3 73.1 - - - +
206B ASN* 1.3 68.6 + - - +
207B THR 5.2 0.2 - - - -
208B ARG* 5.8 3.6 + - - -
215B LEU* 5.0 1.1 - - + -
472B GLN* 3.2 39.0 + - - +
473B PHE 4.3 2.5 + - - -
475B TYR* 3.5 66.5 + - + +
480B ARG 5.2 2.1 - - - -
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Residues in contact with ASN 206 (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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202B ARG* 3.4 19.8 - - - +
203B VAL 3.4 4.9 + - - +
205B GLN* 1.3 89.6 + - - +
207B THR* 1.3 65.2 + - - +
208B ARG* 3.6 19.1 + - - +
265B TYR* 4.4 0.9 + - - -
269B ARG* 3.2 23.9 + - - +
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Residues in contact with THR 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B VAL* 3.1 35.2 + - + +
204B LEU* 3.6 26.5 + - - +
206B ASN* 1.3 75.9 - - - +
208B ARG* 1.3 72.4 + - - +
212B LEU* 4.0 18.1 - - + +
213B THR 5.5 0.5 + - - -
214B ALA* 6.0 1.9 - - - -
265B TYR* 3.7 10.5 - - + -
266B LEU* 4.1 19.3 - - + -
269B ARG* 3.7 11.7 - - + +
271B VAL* 5.8 3.1 - - + -
294B PHE* 5.6 1.0 - - + -
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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
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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