Contacts of the helix formed by residues 195 - 205 (chain B) in PDB entry 3P05
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 195 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B GLN* 2.8 36.9 + - - +
156B GLY 3.2 27.1 + - - +
157B PRO* 3.3 22.0 + - + -
158B LYS* 5.2 0.4 - - - +
159B GLU 4.2 2.2 + - - -
194B ALA* 1.3 72.7 - - - +
196B PRO* 1.3 65.7 - - + +
197B ASP* 3.4 10.5 + - - +
198B CYS* 3.0 24.8 + - - +
199B LYS* 2.7 30.3 + - - +
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Residues in contact with PRO 196 (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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157B PRO* 5.9 1.3 - - + -
194B ALA 3.8 1.3 - - - +
195B ASN* 1.3 89.5 - - + +
197B ASP* 1.3 68.4 + - - +
199B LYS* 3.7 9.5 - - + +
200B THR* 2.9 30.2 + - - +
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Residues in contact with ASP 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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157B PRO 5.2 5.7 - - - +
195B ASN* 3.4 9.9 + - - +
196B PRO* 1.3 80.6 - - - +
198B CYS* 1.3 66.3 + - - +
200B THR* 3.2 5.0 + - - -
201B ILE* 3.1 30.8 + - + +
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Residues in contact with CYS 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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155B GLN* 3.3 36.8 - - - +
159B GLU 5.3 0.2 - - - -
161B PHE* 4.3 6.3 - - + -
194B ALA* 4.3 4.7 - - + -
195B ASN* 3.0 18.3 + - - +
197B ASP* 1.3 79.3 - - - +
199B LYS* 1.3 52.6 - - - +
201B ILE* 3.1 7.3 + - - +
202B LEU* 2.7 41.2 + - + +
218B CYS* 3.6 39.0 - - - -
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Residues in contact with LYS 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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191B VAL* 3.7 13.6 - - + +
192B GLN* 2.8 50.2 + - - +
194B ALA* 3.9 22.5 + - + +
195B ASN 2.7 21.5 + - - +
196B PRO* 3.7 10.1 - - + +
198B CYS* 1.3 72.5 - - - +
200B THR* 1.3 57.8 + - - +
202B LEU* 3.8 6.6 - - - +
203B LYS* 3.1 49.9 + - + +
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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
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196B PRO* 2.9 21.8 + - - +
197B ASP* 3.4 6.3 - - - +
199B LYS* 1.3 75.0 - - - +
201B ILE* 1.3 69.3 + - + +
202B LEU 3.2 0.5 + - - -
203B LYS* 3.3 7.5 + - - +
204B ALA* 3.2 20.4 + - - +
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Residues in contact with ILE 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 ASP* 3.1 18.3 + - + +
198B CYS* 3.4 9.4 - - - +
200B THR* 1.3 77.6 - - + +
202B LEU* 1.3 63.1 + - - +
204B ALA* 3.4 9.5 + - - +
205B LEU* 3.4 19.3 + - + +
217B ALA* 3.4 48.7 - - + +
218B CYS* 4.1 13.7 - - - -
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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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161B PHE* 3.7 30.3 - - + -
191B VAL* 4.0 24.3 - - + +
194B ALA* 4.1 11.0 - - + -
198B CYS 2.7 32.1 + - - +
199B LYS* 3.8 5.2 - - - +
200B THR 3.1 0.4 - - - -
201B ILE* 1.3 72.6 - - + +
203B LYS* 1.3 65.3 + - - +
205B LEU* 3.2 24.7 + - + +
206B GLY 3.7 4.9 + - - +
209B ALA* 5.5 0.3 - - - +
214B MET* 3.4 50.7 - - + +
218B CYS* 3.7 15.9 - - - -
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Residues in contact with LYS 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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191B VAL* 4.4 19.4 - - + +
192B GLN* 5.7 5.2 - - - +
199B LYS* 3.1 34.4 + - + +
200B THR* 3.3 6.9 + - - +
202B LEU* 1.3 76.4 - - - +
204B ALA* 1.3 57.3 + - - +
206B GLY* 2.8 24.2 + - - -
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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
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200B THR* 3.2 10.5 + - + +
201B ILE* 3.5 12.6 - - - +
203B LYS* 1.3 73.6 - - - +
205B LEU* 1.3 61.6 + - - +
206B GLY* 2.9 7.3 + - - -
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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 ILE 3.4 9.3 + - - +
202B LEU* 3.2 17.8 + - + +
204B ALA* 1.3 77.3 - - - +
206B GLY* 1.3 67.0 + - - +
207B PRO 4.2 4.0 - - - +
209B ALA* 3.9 13.6 - - + +
213B GLU* 4.0 14.6 - - + +
214B MET* 3.7 44.6 - - + +
217B ALA* 4.1 15.9 - - + -
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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