Contacts of the helix formed by residues 294 - 301 (chain A) in PDB entry 3BWC
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A ILE* 3.8 30.5 - - + -
214A TRP* 5.2 1.3 - - + -
239A LEU* 4.1 11.0 - - + -
293A LEU* 1.3 87.2 - - + +
295A ARG* 1.3 66.5 - - - +
296A PHE* 3.1 24.9 - - + -
297A ALA* 2.8 15.3 + - + -
298A ARG 2.9 10.4 + - - -
241B HIS* 5.2 0.9 - - + +
281B TYR* 3.5 41.5 - - + +
286B MSE 3.6 9.6 - - + -
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Residues in contact with ARG 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A LEU 3.6 1.6 + - - -
294A PRO* 1.3 68.8 - - - +
296A PHE* 1.3 62.0 + - - +
297A ALA 3.2 0.9 + - - -
298A ARG* 3.2 29.2 + - - +
299A HIS* 4.7 2.3 + - - -
276B ALA* 3.5 19.4 + - - -
277B LYS* 3.1 53.7 + - - +
279B LEU 2.7 30.9 + - - +
280B LYS 3.5 6.9 + - - +
281B TYR 3.0 11.3 + - - +
282B TYR 3.8 15.5 - - - +
283B ASP* 3.6 24.2 + - - +
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Residues in contact with PHE 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ILE* 3.4 43.1 - - + -
214A TRP* 3.6 38.8 - + - -
217A LEU* 4.0 15.1 - - + +
294A PRO* 3.1 23.0 + - + -
295A ARG* 1.3 73.2 - - - +
297A ALA* 1.3 65.8 + - + +
299A HIS* 3.3 20.3 + - - -
76B TYR* 6.0 0.9 - - - -
79B PHE* 4.0 11.9 - + + -
280B LYS* 2.9 38.8 + - + +
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ILE* 4.2 18.4 - - + -
217A LEU* 3.7 24.5 - - + -
293A LEU* 3.5 14.0 - - + +
294A PRO* 2.8 8.9 + - + +
296A PHE* 1.3 89.0 - - + +
298A ARG* 1.3 63.7 + - - +
299A HIS* 3.3 9.4 - - - -
300A ILE* 3.3 22.5 + - + +
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Residues in contact with ARG 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A ALA* 6.4 0.4 - - - +
293A LEU* 4.2 18.7 + - + +
294A PRO 2.9 9.4 + - - +
295A ARG* 3.2 28.9 + - - +
297A ALA* 1.3 77.7 - - - +
299A HIS* 1.3 63.8 + - - +
300A ILE 2.9 1.9 + - - -
301A ASN* 3.0 16.0 + - + +
302A ASN* 3.0 30.2 + - - +
283B ASP* 3.1 30.4 + - - -
285B GLU* 4.0 25.5 - - - +
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Residues in contact with HIS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A LEU* 4.3 5.4 - - + -
221A GLU* 2.7 42.0 + - + +
295A ARG 4.7 2.2 + - - -
296A PHE 3.3 26.9 + - - -
297A ALA* 4.1 8.3 - - - -
298A ARG* 1.3 78.2 + - - +
300A ILE* 1.3 65.9 + - + +
301A ASN 3.3 0.2 - - - -
302A ASN* 3.0 31.7 + - - +
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Residues in contact with ILE 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ILE* 4.9 3.6 - - + -
217A LEU* 3.5 29.4 - - + -
220A ILE* 3.4 33.0 - - + -
221A GLU* 3.9 23.6 - - + -
224A SER* 4.3 21.7 + - - +
228A ARG* 4.7 7.4 + - - -
235A VAL 4.7 5.4 - - - +
236A GLN* 4.9 0.3 + - - -
237A TYR* 3.8 19.1 - - + +
253A LEU* 5.3 0.7 - - + -
293A LEU* 4.2 4.0 - - + -
297A ALA* 3.3 16.1 + - + +
298A ARG 2.9 0.8 + - - -
299A HIS* 1.3 84.5 - - - +
301A ASN* 1.3 70.3 + - - +
302A ASN* 4.8 2.9 + - - -
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Residues in contact with ASN 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A GLN* 3.2 39.8 + - - +
237A TYR* 2.8 50.0 + - - +
291A PHE* 3.1 28.5 + - - +
293A LEU* 3.5 13.4 - - + +
298A ARG* 3.0 7.3 + - + +
300A ILE* 1.3 80.7 - - - +
302A ASN* 1.3 73.8 + - - +
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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