Contacts of the helix formed by residues 340 - 354 (chain B) in PDB entry 2A72
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 ASP 340 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326B ARG* 2.9 41.9 + - - +
329B ARG* 5.0 3.6 + - - -
330B TRP* 3.0 30.5 + - + +
336B GLU 3.4 12.4 + - - +
337B ALA 3.2 2.1 - - - +
338B LEU 3.3 1.1 - - - -
339B LYS* 1.3 81.9 - - + +
341B PRO* 1.4 62.0 - - - +
342B VAL* 3.0 15.2 + - - +
343B GLY 3.3 3.1 + - - +
344B ARG* 2.8 28.9 + - - +
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Residues in contact with PRO 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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326B ARG* 4.5 6.7 - - - +
338B LEU 5.3 0.7 - - - +
339B LYS 3.6 7.6 - - - +
340B ASP* 1.4 90.7 - - - +
342B VAL* 1.3 57.3 + - + +
344B ARG* 3.5 9.3 + - + +
345B GLU* 3.1 35.6 + - - +
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Residues in contact with VAL 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B MET* 5.2 16.4 - - + -
322B PRO* 4.2 15.5 - - + -
326B ARG* 3.3 23.1 - - - +
330B TRP* 3.7 21.3 - - + -
340B ASP* 3.0 7.6 + - - +
341B PRO* 1.3 76.7 - - + +
343B GLY* 1.3 61.0 + - - +
345B GLU* 3.2 17.4 + - - +
346B GLN* 2.9 45.3 + - + +
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Residues in contact with GLY 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A PHE* 4.6 3.3 - - - -
330B TRP* 3.4 34.6 - - - -
337B ALA* 3.3 12.1 - - - +
340B ASP* 3.2 11.7 + - - -
342B VAL* 1.3 77.7 - - - +
344B ARG* 1.3 57.1 + - - +
346B GLN* 3.3 2.4 + - - +
347B PHE* 2.9 30.3 + - - +
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Residues in contact with ARG 344 (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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337B ALA 3.1 6.6 + - - +
338B LEU* 2.9 48.3 + - + +
339B LYS* 5.0 2.0 - - - +
340B ASP 2.8 15.9 + - - +
341B PRO* 3.8 8.5 - - + +
343B GLY* 1.3 76.2 - - - +
345B GLU* 1.3 63.1 + - + +
347B PHE* 3.4 6.0 + - - +
348B LEU* 3.1 25.4 + - + +
360B LEU* 4.9 2.7 - - + +
363B TRP* 4.2 17.9 - - - -
364B LEU* 3.6 37.4 - - + +
367B GLU* 6.0 2.8 - - - +
371B LYS* 6.0 1.6 - - - +
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Residues in contact with GLU 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B MET* 5.7 4.5 - - - +
341B PRO* 3.1 22.4 + - - +
342B VAL* 3.5 22.6 - - - +
344B ARG* 1.3 77.5 - - + +
346B GLN* 1.3 66.0 + - - +
348B LEU* 3.9 6.6 - - - +
349B LYS* 2.9 31.3 + - - +
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Residues in contact with GLN 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A PHE* 3.6 17.8 - - + -
443A ALA* 6.2 0.5 - - - +
447A LEU* 4.5 14.3 - - + +
330B TRP* 4.1 22.4 - - + -
342B VAL* 2.9 29.1 + - + +
343B GLY 3.8 3.6 - - - +
345B GLU* 1.3 84.3 + - - +
347B PHE* 1.3 64.0 + - - +
349B LYS* 3.8 24.8 + - - +
350B PHE* 3.0 24.8 + - - +
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Residues in contact with PHE 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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430A MET* 5.0 2.2 - - - -
434A SER* 3.6 26.0 - - - -
435A TYR* 3.7 24.7 - + + -
438A PHE* 3.6 37.1 - + + -
334B MET* 4.0 26.7 - - + -
337B ALA* 4.8 9.4 - - + -
338B LEU* 3.9 19.7 - - + -
343B GLY 2.9 17.3 + - - +
344B ARG* 3.7 5.6 - - - +
345B GLU 3.4 0.2 - - - -
346B GLN* 1.3 77.2 - - - +
348B LEU* 1.3 62.3 + - - +
350B PHE* 3.4 2.4 + - - +
351B LEU* 3.2 37.9 + - + +
360B LEU* 3.9 20.2 - - + -
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Residues in contact with LEU 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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344B ARG* 3.1 18.4 + - + +
345B GLU* 3.9 6.1 - - - +
347B PHE* 1.3 76.0 - - - +
349B LYS* 1.3 65.6 + - - +
351B LEU* 3.1 3.5 + - - +
352B GLU* 2.9 46.3 + - + +
357B SER* 4.1 10.8 - - - -
360B LEU* 3.9 25.3 - - + +
361B ARG* 3.8 27.6 - - + -
364B LEU* 4.6 14.6 - - + -
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Residues in contact with LYS 349 (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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345B GLU 2.9 19.2 + - - +
346B GLN* 3.8 27.5 + - - +
347B PHE 3.4 0.2 - - - -
348B LEU* 1.3 76.4 - - - +
350B PHE* 1.3 64.4 + - - +
352B GLU* 3.4 8.8 + - + +
353B SER* 3.1 22.2 + - - -
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Residues in contact with PHE 350 (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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437A ARG* 3.5 33.2 - - + -
438A PHE* 3.6 45.3 - + + -
441A SER* 3.3 24.9 - - - -
443A ALA* 4.4 14.4 - - + -
346B GLN 3.0 18.0 + - - +
347B PHE 3.5 2.7 - - - +
349B LYS* 1.3 76.5 - - - +
351B LEU* 1.3 80.7 + - + +
353B SER* 2.5 30.1 + - - -
354B GLU* 3.4 37.4 + - + +
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Residues in contact with LEU 351 (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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434A SER* 3.9 31.9 - - - +
437A ARG* 5.5 3.4 - - - +
347B PHE* 3.2 30.2 + - + +
348B LEU* 3.1 5.0 + - - +
350B PHE* 1.3 101.0 - - + +
352B GLU* 1.3 61.3 + - - +
354B GLU* 3.2 4.5 + - - +
355B PHE 3.2 3.6 + - - -
356B SER* 2.9 44.8 + - - +
357B SER* 3.7 18.6 - - - -
360B LEU* 3.7 34.8 - - + -
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Residues in contact with GLU 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 2.9 49.3 + - + +
349B LYS* 3.6 8.1 - - - +
351B LEU* 1.3 76.1 - - - +
353B SER* 1.3 61.7 + - - +
355B PHE* 3.0 23.9 + - - +
356B SER 5.0 0.2 - - - +
357B SER* 3.2 24.8 + - - +
361B ARG* 4.2 13.2 + - - -
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Residues in contact with SER 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B LYS* 3.1 14.3 + - - -
350B PHE* 2.5 28.7 + - - -
352B GLU* 1.3 76.4 - - - +
354B GLU* 1.3 65.7 + - - +
355B PHE* 3.6 13.1 - - - -
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Residues in contact with GLU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A ARG* 2.5 41.0 + - - +
350B PHE* 3.4 35.2 + - + +
351B LEU* 3.2 4.8 + - - +
352B GLU 3.1 0.6 - - - -
353B SER* 1.3 85.8 + - - +
355B PHE* 1.3 70.0 + - - +
356B SER* 2.7 26.1 + - - +
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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