Contacts of the helix formed by residues 340 - 350 (chain B) in PDB entry 2P2B
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 340 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338B THR* 3.0 9.2 + - - +
339B PRO* 1.3 77.0 - - - +
341B ARG* 1.3 65.0 + - - +
342B MET 3.4 1.3 - - - -
343B CYS* 3.2 5.6 + - - +
344B GLN* 2.9 37.4 + - - +
370B LYS 3.4 15.7 + - - +
371B ALA 3.4 12.3 - - - +
373B GLU* 3.8 20.2 - - + +
375B THR* 4.3 3.8 - - + -
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Residues in contact with ARG 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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98B GLU* 2.7 26.9 + - - -
99B GLY 3.0 18.4 + - - -
100B ASP* 2.7 25.1 + - - -
102B THR* 3.6 20.1 - - - +
330B PHE* 3.6 21.5 - - + -
333B VAL 4.0 8.7 - - - +
334B PRO 3.3 11.9 - - - +
336B TRP 3.1 34.8 + - - +
337B PRO* 3.7 15.1 - - + +
338B THR 3.0 14.7 + - - +
339B PRO 3.2 1.6 - - - -
340B ALA* 1.3 74.7 - - - +
342B MET* 1.3 64.7 + - - +
344B GLN* 2.9 23.6 + - - +
345B VAL* 2.9 33.2 + - + +
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Residues in contact with MET 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B TRP* 3.4 33.3 - - + -
304B THR* 4.9 3.4 - - + -
330B PHE* 6.1 0.2 - - - -
334B PRO* 3.0 35.6 + - + +
339B PRO 5.4 0.4 - - - +
340B ALA 3.3 0.8 + - - -
341B ARG* 1.3 73.2 - - - +
343B CYS* 1.3 61.1 + - - +
345B VAL* 3.3 1.1 + - - -
346B VAL* 3.1 23.7 + - + +
354B LEU* 3.8 33.2 - - + -
356B THR* 4.7 17.3 - - + -
360B ALA* 5.6 1.8 - - - -
361B ILE* 5.8 2.0 - - + -
364B LEU* 3.5 32.3 - - + -
398B TYR* 5.0 5.4 - - + -
402B ILE* 4.0 26.5 - - + -
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Residues in contact with CYS 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ALA 3.2 3.4 + - - -
342B MET* 1.3 81.5 - - - +
344B GLN* 1.3 59.7 + - - +
346B VAL* 3.3 10.1 + - - +
347B ASP* 3.0 32.1 + - - +
364B LEU* 6.1 0.4 - - - -
371B ALA 3.7 21.2 + - - +
372B ILE* 4.1 0.4 - - - -
375B THR* 3.5 24.7 - - + +
377B ARG* 3.6 27.8 - - + -
402B ILE* 3.7 31.0 - - - -
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Residues in contact with GLN 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B PRO* 5.4 3.0 - - - +
338B THR* 4.4 8.2 + - - -
340B ALA* 2.9 25.5 + - - +
341B ARG* 2.9 35.0 + - - +
343B CYS* 1.3 75.8 - - - +
345B VAL* 1.3 52.4 + - - +
347B ASP* 3.3 6.3 + - - +
348B LYS* 2.8 36.2 + - - +
373B GLU 5.1 2.3 - - - +
374B GLY 6.0 0.2 - - - +
375B THR* 3.8 16.6 - - + +
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Residues in contact with VAL 345 (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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98B GLU* 4.1 19.7 - - + +
302B TRP* 3.6 30.1 - - + -
328B LEU* 4.0 27.6 - - + -
330B PHE* 4.4 6.1 - - + -
341B ARG* 2.9 39.8 + - + +
342B MET 3.6 6.5 - - - +
344B GLN* 1.3 73.0 - - - +
346B VAL* 1.3 64.5 + - - +
348B LYS* 4.4 6.3 - - - -
349B HIS* 3.0 34.1 + - + +
351B VAL* 4.1 0.7 - - - +
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Residues in contact with VAL 346 (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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302B TRP* 4.1 14.4 - - + -
342B MET* 3.1 18.9 + - + +
343B CYS* 3.5 15.3 - - - +
345B VAL* 1.3 74.9 - - - +
347B ASP* 1.3 55.1 + - - +
350B GLN* 2.8 30.8 + - - -
351B VAL* 3.0 26.1 + - + +
354B LEU* 4.5 13.5 - - + -
377B ARG* 4.4 14.1 - - + -
379B SER* 3.6 11.7 + - - +
380B LEU* 3.8 38.4 - - + -
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Residues in contact with ASP 347 (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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343B CYS 3.0 14.8 + - - +
344B GLN* 3.5 10.0 - - - +
346B VAL* 1.3 75.1 - - - +
348B LYS* 1.3 64.9 + - - +
349B HIS 3.2 0.9 + - - -
350B GLN* 2.8 28.5 + - - +
374B GLY 4.6 0.7 - - - +
375B THR* 3.3 12.1 - - - +
376B ASP* 2.6 33.5 + - - +
377B ARG* 2.8 28.8 + - - -
378B SER 4.7 0.5 + - - -
379B SER* 5.1 1.4 + - - -
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Residues in contact with LYS 348 (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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98B GLU* 2.8 26.9 + - - +
102B THR* 2.9 40.7 + - - +
105B SER* 3.9 14.6 + - - -
344B GLN 2.8 20.3 + - - +
345B VAL* 3.3 6.5 + - - +
347B ASP* 1.3 73.6 - - - +
349B HIS* 1.3 82.3 + - + +
350B GLN* 3.5 2.6 + - - +
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Residues in contact with HIS 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ILE* 3.5 35.3 - - + +
98B GLU* 2.9 28.5 + - + +
105B SER* 4.6 6.0 - - - -
107B HIS* 4.0 23.9 + + - -
300B ILE* 3.7 16.7 - - + +
328B LEU* 3.8 28.7 - - + -
345B VAL* 3.0 21.9 + - + +
348B LYS* 1.3 103.3 + - + +
350B GLN* 1.3 73.4 + - - +
351B VAL* 3.3 2.9 + - + -
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Residues in contact with GLN 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ILE* 3.6 14.4 - - + +
346B VAL 2.8 11.1 + - - -
347B ASP* 2.8 26.2 + - - +
348B LYS 4.9 2.2 - - - +
349B HIS* 1.3 81.7 - - - +
351B VAL* 1.3 65.8 + - - +
352B ASN* 3.3 11.8 + - - +
379B SER* 3.3 24.0 + - - +
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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