Contacts of the helix formed by residues 294 - 301 (chain B) in PDB entry 3BWB
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 PRO 294 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A HIS* 5.1 2.0 - - + +
281A TYR* 3.6 42.8 - - + +
286A MSE 3.6 9.2 - - + -
213B ILE* 3.9 20.9 - - + -
214B TRP* 5.7 0.2 - - + -
239B LEU* 3.9 20.2 - - + -
293B LEU* 1.3 89.7 - - + +
295B ARG* 1.3 65.8 + - - +
296B PHE* 3.2 26.5 - - + -
297B ALA* 3.0 14.2 + - + +
298B ARG* 3.0 8.0 + - - -
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Residues in contact with ARG 295 (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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276A ALA 3.6 15.6 + - - -
277A LYS* 2.7 44.4 + - - +
279A LEU 3.0 20.0 + - - +
280A LYS* 3.4 9.2 + - - +
281A TYR 3.2 18.2 + - - +
282A TYR 3.6 17.0 - - - +
283A ASP* 3.7 26.0 - - - +
293B LEU 3.6 0.2 + - - -
294B PRO* 1.3 71.6 - - - +
296B PHE* 1.3 62.8 + - - +
297B ALA 3.1 0.9 + - - -
298B ARG* 3.2 73.4 + - - +
299B HIS* 4.7 1.4 + - - -
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Residues in contact with PHE 296 (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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76A TYR* 5.6 2.0 - - - -
79A PHE* 3.8 15.9 - + + -
280A LYS* 2.8 36.7 + - + +
281A TYR* 4.6 0.7 - + - -
213B ILE* 3.4 45.1 - - + -
214B TRP* 3.8 36.8 - + - -
217B LEU* 3.7 11.8 - - + +
294B PRO* 3.5 22.4 - - + -
295B ARG* 1.3 73.2 - - - +
297B ALA* 1.3 66.5 + - + +
298B ARG 3.7 0.2 - - - -
299B HIS* 3.2 20.8 + - - -
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Residues in contact with ALA 297 (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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213B ILE* 4.2 14.6 - - + -
217B LEU* 3.5 24.2 - - + -
293B LEU* 3.5 14.6 - - + +
294B PRO 3.0 8.0 + - - +
296B PHE* 1.3 94.5 - - + +
298B ARG* 1.3 61.7 + - - +
299B HIS* 3.2 12.3 + - - -
300B ILE* 3.3 22.1 + - + +
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Residues in contact with ARG 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LYS* 5.0 11.7 - - - +
283A ASP* 4.8 6.7 - - - +
293B LEU* 4.2 17.0 - - + +
294B PRO 3.0 12.7 + - - +
295B ARG* 3.2 66.8 + - - +
297B ALA* 1.3 78.3 - - - +
299B HIS* 1.3 66.8 + - - +
300B ILE 3.1 2.6 + - - -
301B ASN* 3.3 5.3 + - - +
302B ASN* 3.2 45.7 + - - +
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Residues in contact with HIS 299 (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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217B LEU* 3.7 24.1 - - + +
221B GLU* 3.2 37.3 + - + +
225B ARG* 4.7 8.2 + - - +
228B ARG* 5.6 1.0 + - - -
295B ARG 5.0 0.8 + - - -
296B PHE 3.2 27.9 + - - -
297B ALA* 4.0 4.7 - - - -
298B ARG* 1.3 84.6 + - + +
300B ILE* 1.3 68.5 + - + +
301B ASN 3.4 0.2 - - - -
302B ASN* 4.1 19.0 + - - +
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Residues in contact with ILE 300 (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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213B ILE* 4.5 7.6 - - + -
217B LEU* 3.4 31.9 - - + -
220B ILE* 3.6 30.7 - - + -
221B GLU* 4.9 9.2 - - - +
224B SER* 3.9 17.3 + - - +
228B ARG* 3.9 20.5 + - - +
235B VAL 4.5 4.0 - - - +
237B TYR* 3.6 27.1 - - + +
253B LEU* 4.8 1.6 - - + -
293B LEU* 4.1 8.5 - - + -
297B ALA* 3.4 16.8 - - + +
298B ARG 3.1 0.8 - - - -
299B HIS* 1.3 90.3 - - + +
301B ASN* 1.3 59.1 + - - +
302B ASN 5.2 0.3 - - - -
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Residues in contact with ASN 301 (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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235B VAL 5.4 0.2 - - - -
236B GLN* 2.8 45.9 + - - +
237B TYR* 2.6 46.4 + - - +
291B PHE* 3.1 29.0 + - - +
293B LEU* 3.6 14.7 - - + +
298B ARG 3.3 7.1 + - - +
300B ILE* 1.3 79.3 - - - +
302B ASN* 1.3 68.9 + - - +
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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