Contacts of the helix formed by residues 334 - 339 (chain B) in PDB entry 3CRX
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 ALA 334 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A MET* 5.5 9.0 - - - -
308A GLU* 5.9 3.4 - - - +
311A GLN* 6.2 0.4 - - - +
312A ALA* 5.6 6.5 - - + -
330B SER 5.0 9.6 - - - +
331B GLU* 5.2 5.6 - - - +
332B THR 3.1 11.1 + - - +
333B GLY* 1.3 69.7 - - - +
335B MET* 1.3 66.3 + - + +
336B VAL* 6.0 0.2 - - + -
337B ARG* 3.1 27.3 + - - +
338B LEU* 3.3 10.6 + - - +
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Residues in contact with MET 335 (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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139A ARG* 6.2 0.2 - - - +
168A TYR* 3.5 47.8 - - + +
169A ASN* 3.7 20.4 - - - +
171A LEU* 3.8 15.7 - - + -
211A LYS* 6.3 0.7 - - - +
295A ALA* 3.6 21.5 - - - +
298A ASP* 4.8 0.4 - - + -
299A MET* 3.8 21.7 - - + -
312A ALA* 5.1 3.6 - - + -
334B ALA* 1.3 77.8 - - + +
336B VAL* 1.3 56.6 + - + +
338B LEU* 2.9 30.9 + - + +
339B LEU* 2.7 39.0 + - + +
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Residues in contact with VAL 336 (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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169A ASN* 4.1 8.3 - - - +
192A ARG* 3.9 17.0 - - - +
212A ALA* 3.1 32.5 - - + +
213A LEU 4.5 0.7 - - - +
214A SER* 3.6 20.9 - - - +
331B GLU* 5.0 8.5 - - + +
332B THR* 5.7 0.4 - - - -
333B GLY* 2.8 23.8 + - - +
334B ALA* 6.0 0.4 - - + -
335B MET* 1.3 72.5 - - + +
337B ARG* 1.3 58.6 + - - +
339B LEU* 2.8 19.1 + - - +
340B GLU* 2.9 34.2 + - - +
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Residues in contact with ARG 337 (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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302A ALA* 4.6 20.6 + - - +
303A GLY 5.0 1.4 + - - -
304A VAL* 4.7 14.5 - - - +
333B GLY* 3.1 17.8 + - - -
334B ALA* 3.1 25.7 + - - +
336B VAL* 1.3 81.5 - - - +
338B LEU* 1.3 72.6 + - - +
340B GLU* 4.1 6.5 - - - +
341B ASP 3.5 21.7 + - - +
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Residues in contact with LEU 338 (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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139A ARG* 2.8 39.5 + - - +
168A TYR* 5.3 2.2 - - - +
298A ASP* 3.7 26.2 - - + +
299A MET* 4.0 13.7 - - + -
302A ALA* 4.1 20.2 - - + -
304A VAL* 5.4 3.6 - - + -
334B ALA 3.3 9.8 + - - +
335B MET* 2.9 33.0 + - + +
337B ARG* 1.3 91.9 - - + +
339B LEU* 1.3 59.8 - - - +
341B ASP 3.0 12.0 - - - +
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Residues in contact with LEU 339 (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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139A ARG* 3.1 26.5 + - - +
142A PHE* 3.8 31.0 - - + -
168A TYR* 4.0 20.0 - - + -
169A ASN* 3.3 46.9 - - + +
214A SER* 3.4 15.0 - - - +
216A GLY* 4.5 4.9 - - - +
217A VAL* 4.2 7.9 - - + -
335B MET* 2.7 18.3 + - + +
336B VAL 2.8 7.3 + - - +
338B LEU* 1.3 72.0 - - - +
340B GLU* 1.3 69.3 + - - +
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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