Contacts of the helix formed by residues 330 - 339 (chain B) in PDB entry 2PY5
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 ASN 330 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282B PRO 4.5 4.7 + - - -
283B LEU* 3.4 20.4 - - - +
284B HIS* 2.8 65.0 + - + +
328B LEU 3.8 0.2 + - - -
329B SER* 1.3 70.6 - - - +
331B VAL* 1.3 72.8 + - - +
333B LEU* 3.8 6.2 - - - +
334B GLU* 3.0 34.6 + - + +
432B PHE* 3.2 14.9 - - - -
436B TRP* 5.5 1.8 - - - -
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Residues in contact with VAL 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B SER* 3.1 7.1 - - - +
330B ASN* 1.3 87.5 - - - +
332B ASP* 1.3 62.7 + - - +
334B GLU* 3.6 3.8 + - - +
335B LEU* 3.2 24.8 + - + +
432B PHE* 4.4 12.6 - - + -
435B ALA* 3.7 28.7 - - + +
436B TRP* 3.7 41.7 - - + +
439B TYR* 3.7 29.0 - - + -
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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
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225B ALA 4.7 5.2 - - - +
227B ARG* 6.3 0.4 - - - -
301B THR* 5.1 1.4 + - - +
302B ILE* 5.0 3.7 - - + +
328B LEU* 4.3 17.7 - - + -
329B SER* 2.7 32.6 + - - +
331B VAL* 1.3 74.4 - - - +
333B LEU* 1.3 60.5 + - - +
335B LEU* 3.4 15.5 + - - +
336B MET* 2.9 29.6 + - - +
435B ALA* 3.3 9.2 - - - +
438B ARG* 3.0 41.0 + - - -
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B HIS* 4.2 15.5 - - + +
286B GLN* 4.0 29.8 - - + +
288B ILE* 3.7 31.6 - - + -
328B LEU* 3.9 15.1 - - + +
329B SER 2.8 20.7 + - - +
330B ASN* 3.8 4.9 - - - +
331B VAL 3.4 0.2 - - - -
332B ASP* 1.3 73.0 - - - +
334B GLU* 1.3 62.3 + - - +
336B MET* 3.2 7.2 + - - +
337B LYS* 2.9 60.7 + - + +
342B LEU* 5.5 1.6 - - + -
347B TYR* 4.6 7.2 - - + -
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Residues in contact with GLU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B HIS* 6.0 1.2 - - - -
330B ASN* 3.0 26.1 + - + +
331B VAL* 4.0 4.7 - - - +
333B LEU* 1.3 77.8 - - - +
335B LEU* 1.3 65.9 + - - +
337B LYS* 3.8 28.5 + - - +
338B GLU* 3.0 26.5 + - - +
439B TYR* 6.5 0.9 - - + -
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Residues in contact with LEU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B THR* 4.3 11.4 - - + +
331B VAL* 3.2 18.5 + - + +
332B ASP* 3.5 20.6 - - - +
334B GLU* 1.3 75.8 - - - +
336B MET* 1.3 63.0 + - - +
338B GLU* 3.2 9.4 + - - +
339B HIS* 2.9 53.4 + - + +
435B ALA 5.3 0.2 - - - +
438B ARG* 5.3 0.4 - - + -
439B TYR* 4.0 35.4 - - + +
442B ILE* 4.1 31.2 - - + -
443B THR* 4.2 19.3 - - + -
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Residues in contact with MET 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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288B ILE* 4.3 9.6 - - - -
290B CYS* 4.9 3.1 - - - -
292B PHE* 5.1 2.0 - - + -
301B THR* 4.1 3.8 + - - -
302B ILE* 2.7 52.5 - - + -
326B LEU* 3.5 16.6 - - + -
328B LEU* 2.6 40.8 - - + -
332B ASP 2.9 10.4 + - - +
333B LEU* 3.4 10.3 - - + +
335B LEU* 1.3 77.2 - - - +
337B LYS* 1.3 57.2 + - - +
340B TYR* 2.9 49.4 + - + +
342B LEU* 4.2 24.0 - - + +
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Residues in contact with LYS 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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274B LYS* 4.1 15.0 - - - +
295B LYS* 3.2 18.0 + - - -
333B LEU* 2.9 42.5 + - + +
334B GLU* 3.8 28.1 + - - +
335B LEU 3.3 0.2 - - - -
336B MET* 1.3 76.0 - - - +
338B GLU* 1.3 56.8 + - - +
340B TYR 3.3 9.9 - - - +
342B LEU* 4.0 22.4 - - + -
347B TYR* 2.8 31.7 + - - -
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Residues in contact with GLU 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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295B LYS* 3.0 22.6 + - - +
298B TYR* 3.6 29.6 + - + +
334B GLU 3.0 18.0 + - - +
335B LEU* 3.6 13.1 - - - +
336B MET 3.2 0.4 - - - -
337B LYS* 1.3 78.1 - - - +
339B HIS* 1.3 73.0 + - + +
340B TYR 3.6 0.2 - - - -
439B TYR* 6.1 0.9 - - - -
443B THR* 5.7 3.8 - - - +
446B GLN* 4.7 5.9 - - - +
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Residues in contact with HIS 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B LEU* 3.5 7.8 - - - +
295B LYS* 2.9 28.1 + - - +
298B TYR* 3.7 15.2 - + + +
299B ILE* 2.6 35.1 + - + +
301B THR* 3.5 4.8 - - + +
335B LEU* 2.9 43.6 + - + +
338B GLU* 1.3 97.3 + - + +
340B TYR* 1.3 72.2 + - + +
442B ILE* 3.7 24.5 - - + +
443B THR* 6.0 0.8 - - - +
446B GLN* 3.3 28.9 - - + +
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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