Contacts of the helix formed by residues 337 - 343 (chain B) in PDB entry 2Y01
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 337 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B VAL* 6.0 2.0 - - + -
54B LEU* 4.3 27.8 - - + +
55B ILE* 3.6 25.4 - - + +
58B GLY* 6.0 0.2 - - - -
334B ALA* 3.3 13.5 - - - +
335B ASN 3.0 0.6 - - - -
336B SER* 1.3 78.4 - - - +
338B MET* 1.3 64.0 + - + +
339B ASN 3.7 1.1 - - - -
340B PRO* 3.7 12.6 - - - +
341B ILE* 3.6 17.6 - - + +
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Residues in contact with MET 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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298B VAL* 3.6 27.6 - - + -
302B CYS* 3.7 22.4 - - - -
331B LEU* 4.9 5.6 - - + -
334B ALA* 3.7 31.4 - - + +
335B ASN* 3.1 11.3 + - - +
337B ALA* 1.3 81.1 - - + +
339B ASN* 1.3 67.5 + - - +
341B ILE* 3.1 13.9 + - + +
342B ILE* 3.0 36.2 + - + +
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Residues in contact with ASN 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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59B ASN* 5.2 2.2 - - - +
83B LEU* 3.7 23.0 - - - +
87B ASP* 4.0 18.8 + - - +
295B ILE* 3.2 38.2 - - + +
298B VAL* 5.8 0.7 - - - +
335B ASN* 4.1 19.2 + - - +
336B SER 5.1 0.2 - - - -
338B MET* 1.3 77.9 - - - +
340B PRO* 1.4 68.9 - - + +
342B ILE* 3.3 5.1 + - - +
343B TYR* 3.0 51.8 + - + +
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Residues in contact with PRO 340 (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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54B LEU 5.6 0.7 - - - +
58B GLY* 3.3 46.0 - - - +
59B ASN* 3.7 21.5 - - - +
62B VAL* 3.9 15.9 - - + -
336B SER 4.5 0.7 - - - +
337B ALA 3.7 14.8 - - - +
338B MET 3.6 3.1 - - - -
339B ASN* 1.4 95.0 - - + +
341B ILE* 1.3 63.5 + - + +
343B TYR* 3.4 10.9 + - + +
344B CYS* 3.6 13.2 - - - -
353B PHE* 3.8 8.7 - - + -
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Residues in contact with ILE 341 (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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54B LEU* 5.1 18.6 - - + -
337B ALA* 3.6 20.4 - - + +
338B MET* 3.1 13.0 + - + +
340B PRO* 1.3 76.5 - - + +
342B ILE* 1.3 63.1 + - + +
344B CYS* 2.8 35.9 + - + +
345B ARG 4.5 0.2 + - - -
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Residues in contact with ILE 342 (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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291B THR* 4.0 12.4 - - + +
294B ILE* 4.0 31.9 - - + -
295B ILE* 3.5 33.7 - - + -
298B VAL* 4.1 21.1 - - + -
338B MET* 3.0 25.0 + - + +
339B ASN* 3.3 8.5 + - - +
341B ILE* 1.3 80.6 - - + +
343B TYR* 1.3 58.9 + - - +
344B CYS 3.1 1.6 + - - -
345B ARG* 3.3 29.0 + - - +
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Residues in contact with TYR 343 (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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59B ASN* 6.1 0.2 - - - -
62B VAL* 3.7 30.7 - - + -
80B ILE* 3.4 47.1 + - + +
83B LEU* 4.4 5.2 - - - +
84B ALA* 6.3 0.4 - - + -
291B THR* 4.3 16.2 - - + -
292B LEU* 5.6 2.0 - - + -
295B ILE* 3.7 23.6 - - + +
339B ASN* 3.0 47.0 + - + +
340B PRO 3.7 6.1 - - - +
341B ILE 3.2 0.6 + - - -
342B ILE* 1.3 73.4 - - - +
344B CYS* 1.3 55.4 + - - +
345B ARG 3.0 6.3 - - - -
346B SER* 3.0 18.4 + - - -
349B PHE* 3.4 46.4 - + + +
353B PHE* 4.8 2.0 - - + -
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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