Contacts of the helix formed by residues 196 - 207 (chain B) in PDB entry 4XZC
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 ARG 196 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195B SER* 1.3 75.8 + - - +
197B GLU* 1.3 62.2 + - + +
198B HIS 3.1 4.7 - - - -
199B VAL* 3.7 21.6 - - - +
200B ASN* 3.1 26.6 + - - +
203B ARG* 3.0 35.0 - - - +
238B LYS* 5.7 2.8 - - - +
242B LEU* 4.2 12.1 - - - +
476B ASN* 6.3 0.8 - - - +
479B ASN* 5.7 3.0 + - - -
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Residues in contact with GLU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B SER 2.5 31.6 + - - -
196B ARG* 1.3 86.4 + - + +
198B HIS* 1.3 70.1 + - - +
200B ASN* 3.5 13.6 + - - +
201B TRP 3.2 18.0 + - - -
217B PRO* 3.4 28.6 - - + +
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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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195B SER* 3.8 24.7 + - - +
196B ARG 3.1 0.2 - - - -
197B GLU* 1.3 97.3 + - - +
199B VAL* 1.3 60.7 + - + +
200B ASN 3.1 0.7 - - - -
201B TRP* 3.4 8.0 + - - +
202B GLY 3.4 0.3 + - - -
217B PRO* 4.4 5.6 - - + +
218B TRP* 3.4 56.0 - + + +
231B LEU* 4.2 22.0 - - + +
235B SER* 2.5 35.9 + - - -
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Residues in contact with VAL 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B SER 3.4 17.9 + - - +
196B ARG* 3.7 25.1 + - - +
198B HIS* 1.3 76.5 - - + +
200B ASN* 1.3 58.1 + - - +
202B GLY* 3.0 5.2 + - - -
203B ARG* 2.9 57.9 + - + +
235B SER* 4.2 4.9 - - - -
238B LYS* 4.4 27.6 - - + +
239B VAL* 3.6 11.0 - - + +
242B LEU* 3.9 15.3 - - + -
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Residues in contact with ASN 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 ARG* 3.1 18.3 + - - +
197B GLU* 3.5 13.9 + - - +
199B VAL* 1.3 80.3 - - - +
201B TRP* 1.3 56.9 + - - +
203B ARG* 3.3 13.1 + - - +
204B GLU* 2.9 52.4 + - - +
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Residues in contact with TRP 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 GLU 3.2 11.9 + - - +
198B HIS 3.7 7.9 - - - +
199B VAL 3.3 0.4 - - - -
200B ASN* 1.3 79.5 - - - +
202B GLY* 1.3 62.6 + - - +
204B GLU* 3.5 7.4 + - - +
205B LEU* 3.0 47.1 + - + +
212B VAL* 2.6 42.0 + - + +
213B VAL* 4.0 16.2 - - + -
215B ASN 5.1 0.2 - - - -
216B PRO* 3.5 5.6 - - + +
217B PRO* 3.4 29.6 - - + -
218B TRP* 3.5 23.1 - + + -
221B ILE* 4.0 19.5 - - + -
232B ALA* 3.9 34.1 - - + -
235B SER* 3.6 7.2 - - - -
236B MET* 4.4 7.6 - - + -
281B LEU* 4.2 9.0 - - + -
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Residues in contact with GLY 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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199B VAL 3.0 8.0 + - - -
201B TRP* 1.3 83.4 - - - +
203B ARG* 1.3 52.8 + - - +
205B LEU* 3.1 5.7 + - - +
206B ALA* 2.8 34.8 + - - +
235B SER* 3.3 19.9 + - - -
236B MET* 5.0 3.1 - - - -
239B VAL* 3.4 15.7 - - - -
251B ILE* 4.4 5.2 - - - +
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Residues in contact with ARG 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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196B ARG* 3.0 34.1 - - - +
199B VAL* 2.9 27.8 + - - +
200B ASN* 3.7 13.7 - - - +
202B GLY* 1.3 74.9 - - - +
204B GLU* 1.3 64.6 + - + +
206B ALA* 3.3 7.7 + - - +
207B ALA* 3.1 23.9 + - - +
239B VAL* 3.3 11.1 - - + +
242B LEU* 3.7 20.0 + - - +
243B ASP* 2.9 41.8 + - - +
247B ARG* 5.0 1.0 + - - -
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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
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200B ASN* 2.9 43.4 + - - +
201B TRP* 3.6 7.4 - - - +
202B GLY 3.2 0.2 - - - -
203B ARG* 1.3 77.1 - - - +
205B LEU* 1.3 62.7 + - - +
207B ALA* 3.1 14.1 + - - +
208B GLY 3.6 0.2 + - - -
209B LYS* 3.3 57.7 + - + +
212B VAL* 3.8 22.0 - - + +
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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
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201B TRP* 3.0 44.0 + - + +
202B GLY* 3.6 5.2 - - - +
204B GLU* 1.3 76.2 - - - +
206B ALA* 1.3 58.8 + - - +
207B ALA 3.2 0.9 + - - -
208B GLY 3.2 3.6 + - - -
209B LYS 4.2 4.5 - - - -
210B PHE* 3.8 21.1 - - - -
212B VAL* 4.0 6.9 - - + +
213B VAL* 3.6 27.6 - - + -
236B MET* 4.3 9.0 - - + -
251B ILE* 3.6 30.2 - - + -
254B THR* 2.9 33.3 + - + +
255B LEU* 4.5 7.0 - - + -
281B LEU* 4.5 5.6 - - + -
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Residues in contact with ALA 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 GLY 2.8 16.6 + - - +
203B ARG* 3.5 10.5 - - - +
204B GLU 3.2 0.2 - - - -
205B LEU* 1.3 77.3 - - - +
207B ALA* 1.3 57.1 + - - +
208B GLY 3.3 1.8 + - - -
239B VAL* 4.5 2.9 - - + -
247B ARG* 3.3 39.1 + - + +
250B ASP* 3.4 18.2 - - - +
251B ILE* 3.7 26.6 - - + +
254B THR* 4.3 0.8 + - - -
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Residues in contact with ALA 207 (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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203B ARG 3.1 15.5 + - - +
204B GLU* 3.1 6.9 + - - +
205B LEU 3.1 1.2 - - - -
206B ALA* 1.3 76.5 - - - +
208B GLY* 1.3 55.5 + - - +
209B LYS* 3.4 19.2 + - + +
247B ARG* 4.4 7.4 - - - +
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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