Contacts of the helix formed by residues 193 - 202 (chain B) in PDB entry 3K8G
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 ASN 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B ASP* 4.5 2.5 + - + +
191B ILE* 3.3 12.8 - - + +
192B LYS* 1.3 76.2 - - + +
194B GLY* 1.3 62.2 + - - +
195B GLY* 3.7 3.6 + - - -
196B HIS* 3.4 34.6 + - + +
197B PHE* 3.4 13.0 + - - +
208B ASN* 5.2 0.7 + - - -
209B LEU 5.5 2.1 - - - +
211B LEU 4.1 9.0 - - - +
212B GLY 4.3 0.2 - - - -
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Residues in contact with GLY 194 (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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191B ILE* 4.3 5.4 - - - -
192B LYS 3.5 1.8 + - - -
193B ASN* 1.3 71.8 - - - +
195B GLY* 1.3 57.2 + - - +
197B PHE* 4.4 0.4 - - - -
198B ILE* 2.7 37.6 + - - +
212B GLY 2.8 21.1 + - - -
214B MET* 3.9 17.8 - - - +
231B LEU* 3.8 16.2 - - - -
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Residues in contact with GLY 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ASN* 3.3 5.2 + - - -
194B GLY* 1.3 77.9 - - - +
196B HIS* 1.3 61.5 + - - +
197B PHE 3.2 1.0 + - - -
198B ILE* 3.4 20.5 - - - +
199B THR* 3.4 9.4 - - - +
208B ASN* 3.1 18.3 + - - -
209B LEU 6.2 0.7 - - - -
211B LEU* 3.9 29.1 + - - +
212B GLY 3.9 4.2 + - - -
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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 ASN* 3.4 34.2 + - + +
194B GLY 3.4 0.4 - - - -
195B GLY* 1.3 74.2 - - - +
197B PHE* 1.3 57.4 + - + +
199B THR* 3.3 7.0 + - - -
200B LYS* 3.2 35.6 + - + +
208B ASN* 3.2 24.9 + - - +
280B LEU* 6.2 3.1 - - + -
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Residues in contact with PHE 197 (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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46B VAL* 5.4 1.3 - - + -
189B LEU* 5.3 8.5 - - + -
191B ILE* 3.7 45.1 - - + -
193B ASN 3.4 2.1 + - - +
194B GLY* 3.1 7.0 + - - +
196B HIS* 1.3 76.8 - - + +
198B ILE* 1.3 65.5 + - - +
199B THR 3.1 2.5 - - - -
200B LYS* 3.0 28.3 + - - +
201B LEU* 3.2 23.1 + - + -
214B MET* 3.5 31.6 - - + -
216B LEU* 4.3 8.7 - - + -
276B VAL* 3.6 29.8 - - + -
277B ILE* 5.5 4.5 - - + -
280B LEU* 4.5 26.5 - - + -
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Residues in contact with ILE 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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194B GLY 2.7 19.3 + - - +
195B GLY* 3.4 17.9 - - - +
197B PHE* 1.3 76.6 - - - +
199B THR* 1.3 64.8 + - + +
201B LEU* 4.0 3.6 - - - -
202B LEU* 3.0 54.7 + - + +
204B PHE* 5.4 5.2 - - + -
211B LEU* 4.9 4.5 - - + -
214B MET* 4.4 7.6 - - - -
229B LEU* 4.1 29.8 - - + -
231B LEU* 3.6 32.1 - - + -
261B LEU* 5.3 2.5 - - + -
263B ILE* 4.6 5.4 - - + -
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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 GLY 3.4 15.7 - - - +
196B HIS* 3.3 13.9 + - - -
198B ILE* 1.3 82.3 - - + +
200B LYS* 1.3 65.7 + - - +
203B ASN 2.9 24.4 + - - -
204B PHE* 3.0 41.4 + - + +
205B PRO* 4.0 11.3 - - - +
206B GLN* 3.9 23.7 + - + +
207B LEU 5.2 1.6 - - - +
208B ASN* 4.5 8.1 + - - +
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Residues in contact with LYS 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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196B HIS* 3.2 45.3 + - + +
197B PHE* 3.0 22.5 + - - +
199B THR* 1.3 83.1 + - - +
201B LEU* 1.3 67.1 + - - +
203B ASN* 3.3 6.6 + - - +
205B PRO* 6.4 1.6 - - + -
272B ARG* 2.9 16.3 + - - -
276B VAL* 3.7 23.1 + - + +
279B SER* 3.7 26.4 + - - +
280B LEU* 4.6 14.1 - - - +
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Residues in contact with LEU 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 PHE* 3.2 20.4 + - + +
198B ILE 3.9 4.3 - - - +
200B LYS* 1.3 76.7 - - - +
202B LEU* 1.3 70.8 + - + +
214B MET* 3.6 30.5 - - + -
216B LEU* 4.0 18.4 - - + -
218B LEU* 5.9 1.3 - - + -
227B TYR* 4.6 20.2 - - + +
229B LEU* 3.7 18.6 - - + -
250B LEU* 5.6 0.5 - - - +
268B ILE* 3.9 23.1 - - + -
272B ARG* 2.8 29.8 + - - +
273B LEU* 6.4 1.6 - - + -
276B VAL* 4.3 11.7 - - + +
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Residues in contact with LEU 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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198B ILE* 3.0 46.9 + - + +
201B LEU* 1.3 98.7 - - + +
203B ASN* 1.3 64.2 + - - +
204B PHE* 3.2 50.4 + - + -
227B TYR* 4.8 2.0 - - - +
229B LEU* 4.5 6.1 - - + -
246B ILE* 4.7 5.4 - - + -
249B VAL* 5.6 2.3 - - - +
250B LEU* 3.6 45.4 - - + +
263B ILE* 4.6 6.1 - - + -
272B ARG* 5.4 0.4 - - - -
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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