Contacts of the helix formed by residues 331 - 336 (chain B) in PDB entry 4Y72
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 LEU 331 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B GLY 4.9 0.7 - - - +
201B ARG* 3.4 10.0 + - - +
202B ALA* 3.4 29.1 - - + +
205B ILE* 4.0 20.6 - - + -
206B ASP* 3.7 24.0 - - + +
209B VAL* 5.0 2.7 - - + -
327B GLU 4.0 16.4 - - - +
328B LEU* 3.4 11.8 + - + +
329B THR 3.1 0.8 - - - -
330B MET* 1.3 86.1 - - + +
332B ASP* 1.3 58.1 + - - +
333B TYR 3.6 1.9 + - - -
385B ASN* 5.9 1.6 - - - +
396B HIS* 3.7 35.2 - - + +
399B VAL* 4.0 22.0 - - + -
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Residues in contact with ASP 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ARG* 4.1 1.7 + - - -
328B LEU 4.5 0.4 - - - +
329B THR 3.1 16.3 + - - +
331B LEU* 1.3 74.5 - - - +
333B TYR* 1.3 59.7 + - - +
334B ASP* 3.0 17.7 + - - +
335B MET* 3.0 39.2 + - + +
336B VAL* 3.7 6.8 + - - +
384B LYS* 2.7 32.5 + - - -
385B ASN* 2.9 34.9 + - - +
388B MET* 5.5 1.3 - - - -
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Residues in contact with TYR 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LYS* 3.0 32.0 + - + +
190B TYR* 4.3 14.6 - + - -
191B LEU* 3.0 52.4 + - + +
192B LEU* 3.8 0.7 + - - -
198B GLY* 3.7 37.7 - - - +
201B ARG* 4.2 17.5 - - - +
331B LEU 3.6 4.4 + - - -
332B ASP* 1.3 73.8 + - - +
334B ASP* 1.3 71.6 + - - +
335B MET 3.1 4.7 + - - -
336B VAL* 3.4 27.4 - - + +
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Residues in contact with ASP 334 (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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189B LYS* 4.7 12.4 + - - +
332B ASP* 3.0 12.7 + - - +
333B TYR* 1.3 92.3 - - - +
335B MET* 1.3 59.9 + - - +
336B VAL 3.7 0.4 - - - -
337B HIS* 3.5 20.9 + - - -
338B PHE* 4.2 2.4 - - - -
381B HIS* 4.4 14.5 + - + -
384B LYS* 4.3 14.2 + - - +
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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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329B THR* 3.4 42.8 - - + +
332B ASP* 3.0 33.1 + - + +
334B ASP* 1.3 79.2 - - - +
336B VAL* 1.3 64.9 + - - +
337B HIS 3.0 4.9 + - - -
338B PHE* 3.2 30.8 + - + +
343B ILE* 3.6 21.2 - - + +
378B VAL* 4.0 18.2 - - + +
381B HIS* 3.5 35.4 - - + -
382B LEU* 4.3 2.2 - - + -
385B ASN* 3.8 9.2 - - - -
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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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186B VAL* 3.6 32.3 + - + +
187B ARG 3.9 18.8 - - - +
188B PRO* 4.7 5.8 - - + -
189B LYS 4.8 0.4 - - - +
190B TYR* 4.2 10.1 - - + -
201B ARG* 3.4 39.5 - - - +
230B ASP* 3.9 5.6 - - - +
329B THR 5.9 0.7 - - - +
332B ASP 4.0 6.1 - - - +
333B TYR* 3.4 27.4 - - + +
334B ASP 3.7 0.4 - - - -
335B MET* 1.3 77.8 - - - +
337B HIS* 1.3 62.5 + - - +
338B PHE 3.5 4.7 + - - +
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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