Contacts of the helix formed by residues 197 - 206 (chain B) in PDB entry 1B0P
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 GLN 197 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B PHE* 5.7 1.0 - - - -
192B ALA 3.9 9.3 + - - -
195B VAL* 3.2 35.6 + - - +
196B ASN* 1.3 69.1 - - - +
198B LYS* 1.3 80.1 + - + +
199B ALA 3.3 0.2 - - - -
200B LEU* 3.7 18.7 - - - +
201B ALA* 2.9 28.2 + - - +
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Residues in contact with LYS 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 VAL 5.2 0.4 + - - -
196B ASN* 3.6 19.5 - - - +
197B GLN* 1.3 110.4 - - - +
199B ALA* 1.3 58.0 + - - +
201B ALA* 3.4 6.4 + - - +
202B GLU* 3.0 38.5 + - - +
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Residues in contact with ALA 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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161B ILE 3.5 24.5 - - - +
162B GLU* 3.9 12.6 - - + +
164B ASN* 5.7 1.2 + - - -
196B ASN* 2.8 32.7 + - + +
198B LYS* 1.3 76.5 - - - +
200B LEU* 1.3 57.8 + - - +
202B GLU* 3.3 14.9 + - - +
203B PHE* 2.9 28.4 + - - +
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Residues in contact with LEU 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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52B PHE* 3.8 28.7 - - + -
80B LEU* 4.0 33.7 - - + -
161B ILE* 4.2 14.1 - - + +
195B VAL* 3.8 20.0 - - + -
196B ASN 3.0 15.3 + - - +
197B GLN* 3.7 18.4 - - - +
198B LYS 3.3 0.2 - - - -
199B ALA* 1.3 77.4 - - - +
201B ALA* 1.3 61.4 + - - +
203B PHE* 3.4 11.9 + - + +
204B ARG* 3.2 42.5 + - - +
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Residues in contact with ALA 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 GLN 2.9 18.7 + - - +
198B LYS* 3.9 7.4 - - - +
199B ALA 3.3 0.2 - - - -
200B LEU* 1.3 74.7 - - - +
202B GLU* 1.3 57.1 + - - +
204B ARG* 3.4 8.5 + - - +
205B ALA* 3.1 27.5 + - - +
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Residues in contact with GLU 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 LYS* 3.0 24.3 + - - +
199B ALA* 3.5 15.0 - - - +
200B LEU 3.3 0.2 - - - -
201B ALA* 1.3 75.6 - - + +
203B PHE* 1.3 62.5 + - - +
205B ALA* 3.7 7.0 - - - +
206B LYS* 3.1 28.4 + - - +
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Residues in contact with PHE 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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75B LEU* 3.5 29.6 - - + -
78B GLY 3.5 28.3 - - - -
79B ALA 3.8 10.5 - - - -
80B LEU* 3.6 30.7 - - + -
105B LEU* 4.7 4.9 - - + -
106B PRO* 3.6 34.5 - - + -
161B ILE* 5.5 3.8 - - + +
164B ASN* 5.1 5.6 - - - +
199B ALA 2.9 13.8 + - - +
200B LEU* 3.5 19.7 - - + +
201B ALA 3.3 0.2 - - - -
202B GLU* 1.3 76.1 - - - +
204B ARG* 1.3 62.9 + - - +
205B ALA 3.3 0.3 + - - -
206B LYS* 3.4 20.1 - - - +
207B SER* 2.7 36.4 + - - -
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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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886A ARG* 3.4 38.2 + - - +
889A HIS* 5.8 3.8 + - - -
950A ASP* 4.8 4.0 - - - +
23B GLU* 2.4 46.4 + - - -
52B PHE* 4.3 14.8 - - - -
78B GLY 3.2 19.0 + - - +
79B ALA* 4.4 0.2 - - - +
80B LEU* 4.4 3.2 - - - +
200B LEU* 3.2 40.9 + - - +
201B ALA* 3.6 11.2 - - - +
202B GLU 3.3 0.2 - - - -
203B PHE* 1.3 85.3 - - - +
205B ALA* 1.3 60.7 + - - +
207B SER* 3.2 23.1 + - - +
212B HIS* 4.7 3.6 + - - -
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Residues in contact with ALA 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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950A ASP* 5.5 1.3 - - - -
201B ALA 3.1 16.4 + - - +
202B GLU* 4.0 7.4 - - - +
203B PHE 3.3 0.4 - - - -
204B ARG* 1.3 77.0 - - - +
206B LYS* 1.3 58.5 - - - +
207B SER 3.2 1.6 + - - -
212B HIS* 3.5 25.5 + - - -
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Residues in contact with LYS 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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662A ASP* 4.7 5.2 + - - +
664A ARG* 2.9 54.2 + - - +
103B GLU 4.3 3.6 + - - -
104B LEU* 2.8 33.8 + - - +
105B LEU* 4.8 8.1 - - - -
164B ASN* 3.3 27.6 + - - +
202B GLU 3.1 19.1 + - - +
203B PHE* 3.4 24.5 - - - +
205B ALA* 1.3 75.2 - - - +
207B SER* 1.3 64.5 + - - +
212B HIS* 5.6 0.2 - - - -
214B HIS* 3.5 2.1 - - - -
216B ARG* 4.5 0.5 + - - -
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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