Contacts of the helix formed by residues 198 - 207 (chain B) in PDB entry 2OUC
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 ASP 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195B ASN* 3.1 23.1 - - - +
197B ALA* 1.3 77.7 - - - +
199B LYS* 1.3 61.2 + - - +
200B ILE* 2.8 47.7 + - - +
201B SER* 3.3 6.8 + - - +
202B ARG* 3.0 29.8 + - - +
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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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197B ALA 3.2 7.5 + - - +
198B ASP* 1.3 73.4 + - - +
200B ILE* 1.3 59.7 + - + +
202B ARG* 4.3 23.8 - - - +
203B ARG* 2.9 73.3 + - - +
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Residues in contact with ILE 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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198B ASP* 2.8 22.6 + - - +
199B LYS* 1.3 79.7 - - + +
201B SER* 1.3 59.5 + - - +
203B ARG* 3.8 3.8 - - - +
204B ARG* 2.9 48.2 + - + +
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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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195B ASN* 2.9 44.4 + - - -
198B ASP* 3.3 10.8 + - - +
200B ILE* 1.3 75.7 - - - +
202B ARG* 1.3 69.4 + - - +
203B ARG 3.0 1.6 - - - -
204B ARG* 3.0 6.8 + - - +
205B LEU* 2.8 32.4 + - - +
210B ILE* 4.4 4.0 - - - +
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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 ASN 3.9 6.0 + - - -
196B CYS* 2.8 31.0 + - - +
197B ALA 4.8 1.9 + - - -
198B ASP 3.0 19.0 + - - +
199B LYS* 4.2 26.5 - - - +
201B SER* 1.3 76.5 + - - +
203B ARG* 1.3 59.9 + - + +
205B LEU* 3.6 6.7 - - - +
206B GLN* 2.9 59.5 + - - +
249B SER* 2.8 38.1 + - - +
251B PRO* 4.5 11.7 - - - +
254B ILE* 3.6 18.7 - - + +
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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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199B LYS* 2.9 60.6 + - + +
200B ILE* 3.8 3.8 - - - +
201B SER 3.0 0.4 - - - -
202B ARG* 1.3 76.6 - - + +
204B ARG* 1.3 60.2 + - + +
205B LEU 3.0 5.8 - - - -
206B GLN* 3.9 14.2 - - - +
207B GLN* 2.9 42.2 + - + +
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Residues in contact with ARG 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 ILE* 2.9 41.2 + - + +
201B SER* 3.0 4.5 + - - +
203B ARG* 1.3 76.4 - - + +
205B LEU* 1.3 56.6 + - - +
207B GLN* 3.9 6.1 - - - -
208B GLY 3.2 5.9 + - - -
209B LYS* 3.0 82.5 + - + +
210B ILE* 3.2 22.7 + - + +
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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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194B ILE* 3.7 26.9 - - + -
195B ASN 4.1 12.1 - - - +
196B CYS* 4.4 1.3 - - - -
201B SER* 2.8 18.9 + - - +
202B ARG* 3.6 4.3 - - - +
204B ARG* 1.3 75.7 - - - +
206B GLN* 1.3 64.8 + - - +
207B GLN 2.9 16.6 + - - +
208B GLY* 4.3 0.2 - - - -
210B ILE* 3.3 33.9 - - + +
211B THR* 4.0 4.7 - - - -
212B VAL* 4.0 11.7 - - + +
215B LEU* 4.7 8.1 - - + -
254B ILE* 4.3 22.2 - - + -
255B VAL* 5.5 0.7 - - + -
258B SER* 3.8 25.2 + - - +
261B ARG* 3.9 8.5 + - - -
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Residues in contact with GLN 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* 2.9 53.5 + - + +
203B ARG* 3.4 14.2 + - - +
205B LEU* 1.3 74.8 - - - +
207B GLN* 1.3 62.8 + - + +
248B PRO 5.1 4.0 + - - -
249B SER* 5.7 1.4 - - - +
254B ILE* 4.1 31.4 - - + +
261B ARG* 3.9 14.6 + - - +
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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
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203B ARG* 2.9 32.1 - - - +
204B ARG* 3.9 2.8 - - - +
205B LEU 2.9 9.3 - - - +
206B GLN* 1.3 82.3 - - + +
208B GLY* 1.3 60.8 + - - +
209B LYS* 3.5 40.4 + - - +
261B ARG* 3.7 18.9 + - - -
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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