Contacts of the helix formed by residues 376 - 389 (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 GLU 376 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B ARG* 4.1 5.0 + - - -
373B PRO* 2.9 44.6 + - + +
375B LYS* 1.3 78.8 - - - +
377B VAL* 1.3 62.4 + - - +
378B PRO 3.5 0.9 - - - -
379B SER* 3.4 10.1 + - - +
380B ARG* 2.7 67.2 + - + +
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Residues in contact with VAL 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A PRO 3.7 11.0 - - - +
415A GLY* 3.5 34.3 - - - -
416A ARG* 3.7 33.4 - - + +
369B LEU* 4.5 14.4 - - + +
372B ARG* 4.5 2.0 - - + +
373B PRO 3.8 2.7 - - - +
374B ILE* 3.0 28.5 + - + +
376B GLU* 1.3 77.4 - - - +
378B PRO* 1.4 59.3 - - + +
380B ARG* 3.2 0.8 + - - +
381B VAL* 2.7 41.5 + - + +
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Residues in contact with PRO 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A PRO 5.7 0.9 - - - +
374B ILE 3.6 9.0 - - - +
375B LYS* 3.6 10.1 - - - +
376B GLU 3.6 3.6 - - - -
377B VAL* 1.4 96.5 - - + +
379B SER* 1.3 61.1 + - - +
381B VAL* 3.8 5.7 - - + +
382B GLN* 3.3 29.2 + - - +
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Residues in contact with SER 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B LYS 5.3 1.1 + - - -
376B GLU* 3.4 13.8 + - - +
377B VAL 3.3 0.4 - - - -
378B PRO* 1.3 77.3 - - - +
380B ARG* 1.3 66.7 + - - +
382B GLN* 3.2 8.9 + - - +
383B GLU* 2.9 41.6 + - - +
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Residues in contact with ARG 380 (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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368B ASP* 3.9 14.1 + - - -
369B LEU* 3.9 15.3 - - + +
372B ARG* 3.3 59.0 - - - +
376B GLU* 2.7 44.1 + - - +
377B VAL 3.9 2.2 - - - +
379B SER* 1.3 82.4 + - - +
381B VAL* 1.3 65.7 + - - +
383B GLU* 3.2 27.3 + - - +
384B ILE* 3.1 29.9 + - + +
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Residues in contact with VAL 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A GLY* 3.5 25.8 - - - +
418A THR* 3.8 26.7 - - + +
419A PHE* 3.5 15.9 - - + -
369B LEU* 3.9 15.5 - - + -
377B VAL* 2.7 32.7 + - + +
378B PRO* 3.8 5.8 - - + +
380B ARG* 1.3 73.6 - - - +
382B GLN* 1.3 67.4 + - - +
384B ILE 3.4 0.7 + - - -
385B TRP* 3.1 24.1 + - - +
410B ASN 5.6 0.4 - - - +
411B VAL* 4.2 12.1 - - + -
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Residues in contact with GLN 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B PRO 3.3 14.8 + - - +
379B SER* 3.2 10.9 + - - +
381B VAL* 1.3 81.8 - - - +
383B GLU* 1.3 59.4 + - + +
385B TRP* 3.3 10.7 + - - +
386B GLN* 2.9 39.5 + - + +
411B VAL* 3.1 45.2 + - - +
412B LYS* 4.4 6.6 + - - -
414B PRO* 5.7 2.4 - - - +
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Residues in contact with GLU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B SER* 2.9 29.7 + - - +
380B ARG* 3.2 33.0 + - - +
382B GLN* 1.3 75.7 - - - +
384B ILE* 1.3 58.1 + - + +
386B GLN* 3.3 8.4 + - - +
387B GLU* 2.9 30.7 + - - +
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Residues in contact with ILE 384 (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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419A PHE* 3.7 27.1 - - + -
362B PHE* 3.9 24.0 - - + -
365B ALA* 3.5 37.7 - - + +
366B VAL* 4.4 4.5 - - + +
369B LEU* 3.9 21.3 - - + -
380B ARG* 3.1 17.3 + - + +
381B VAL 3.8 6.3 - - - +
382B GLN 3.3 0.2 - - - -
383B GLU* 1.3 76.4 - - + +
385B TRP* 1.3 63.2 + - - +
387B GLU* 4.7 0.9 - - - -
388B PHE* 3.0 39.2 + - + +
389B LEU* 5.0 0.3 - - - +
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Residues in contact with TRP 385 (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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419A PHE* 4.1 3.8 - - + -
381B VAL 3.1 13.9 + - - +
382B GLN* 3.6 11.4 - - - +
384B ILE* 1.3 77.9 - - - +
386B GLN* 1.3 74.5 + - - +
389B LEU* 2.9 48.8 + - + +
390B ALA* 2.7 51.9 + - + +
391B PRO* 4.6 7.9 - - + +
404B TYR* 4.3 7.4 - + - -
407B THR* 4.5 6.3 - - + -
408B THR* 3.7 40.2 - - + -
411B VAL* 3.6 40.4 - - + -
412B LYS* 3.7 27.6 - - - +
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Residues in contact with GLN 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B GLN* 2.9 27.7 + - + +
383B GLU* 3.6 7.2 - - - +
385B TRP* 1.3 96.4 - - - +
387B GLU* 1.3 60.3 + - - +
390B ALA* 3.7 15.3 - - - +
393B ALA* 3.4 19.4 - - - +
394B PRO* 3.6 5.2 - - - +
412B LYS* 5.7 0.8 - - - +
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Residues in contact with GLU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B ARG* 4.2 3.4 + - - +
383B GLU 2.9 17.0 + - - +
384B ILE* 4.7 0.2 - - - -
386B GLN* 1.3 77.7 - - - +
388B PHE* 1.3 88.7 + - + +
393B ALA* 3.3 5.2 - - - +
394B PRO* 3.6 23.5 - - - +
395B SER* 2.5 52.6 + - - +
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Residues in contact with PHE 388 (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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358B GLU 3.7 7.6 - - - -
361B ARG* 3.7 31.0 - - + -
362B PHE* 3.5 42.2 - + + -
365B ALA* 3.8 20.6 - - + -
384B ILE* 3.0 30.9 + - + +
387B GLU* 1.3 96.4 - - + +
389B LEU* 1.3 65.7 + - + +
393B ALA* 3.7 6.5 - - - -
395B SER* 3.3 32.5 - - - +
396B ALA* 3.4 2.9 - - - +
397B ILE* 3.1 31.5 + - + +
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Residues in contact with LEU 389 (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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419A PHE* 3.9 20.2 - - + -
362B PHE* 3.8 29.4 - - + -
385B TRP* 2.9 28.7 + - + +
388B PHE* 1.3 82.1 - - + +
390B ALA* 1.3 69.4 + - - +
391B PRO* 4.6 0.3 - - - +
393B ALA* 3.7 1.0 - - - +
396B ALA* 5.5 0.7 - - - +
397B ILE* 3.7 18.4 - - + +
399B LEU* 3.5 22.4 - - + -
404B TYR* 2.7 51.0 + - + +
407B THR* 4.1 13.0 - - + -
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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