Contacts of the helix formed by residues 371 - 383 (chain B) in PDB entry 2HA6
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 SER 371 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364B ARG* 3.6 2.2 - - - +
369B GLN 3.7 3.4 + - - -
370B ALA* 1.3 78.0 - - - +
372B ASP* 1.3 66.1 + - - +
373B LEU 3.6 2.8 + - - -
374B ALA* 3.2 18.2 + - - +
375B ALA* 3.0 19.8 + - - +
540B LEU* 3.2 27.5 - - - +
543B THR* 4.1 15.6 - - - +
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Residues in contact with ASP 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B ARG* 3.3 30.2 + - - +
371B SER* 1.3 73.6 - - - +
373B LEU* 1.3 57.2 + - - +
375B ALA* 3.4 3.3 + - - +
376B GLU* 3.1 37.9 + - - +
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Residues in contact with LEU 373 (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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535A PHE* 4.2 17.3 - - + -
538A LYS* 4.1 24.7 - - + +
539A LEU* 3.9 30.5 - - + +
542A ALA* 5.3 11.4 - - + -
371B SER* 3.2 7.1 + - - +
372B ASP* 1.3 77.9 - - - +
374B ALA* 1.3 60.5 + - - +
376B GLU* 3.3 20.1 + - + +
377B ALA* 3.0 25.3 + - - +
539B LEU* 4.2 18.2 - - + -
543B THR* 4.6 16.4 - - + +
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Residues in contact with ALA 374 (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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370B ALA* 4.0 8.7 - - + -
371B SER* 3.2 27.6 + - - +
373B LEU* 1.3 73.7 - - - +
375B ALA* 1.3 61.9 + - - +
377B ALA* 3.2 4.3 + - - +
378B VAL* 2.9 32.9 + - - +
536B LEU* 4.5 11.8 - - + +
539B LEU* 3.8 16.3 - - + +
540B LEU* 3.9 21.8 - - + -
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Residues in contact with ALA 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B VAL* 4.0 14.6 - - + +
364B ARG* 3.5 34.5 - - - +
370B ALA* 4.0 9.7 - - + +
371B SER 3.0 17.0 + - - +
372B ASP 3.6 5.6 - - - +
374B ALA* 1.3 76.0 - - - +
376B GLU* 1.3 56.8 + - - +
378B VAL* 3.2 4.8 + - - +
379B VAL* 2.9 34.0 + - + +
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Residues in contact with GLU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A PHE* 5.6 0.9 - - + -
538A LYS* 3.1 46.2 + - + +
372B ASP* 3.1 21.5 + - - +
373B LEU* 3.5 26.3 - - + +
374B ALA 3.2 0.4 - - - -
375B ALA* 1.3 74.3 - - + +
377B ALA* 1.3 60.0 + - - +
379B VAL* 3.3 7.3 + - - +
380B LEU* 2.8 39.9 + - + +
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Residues in contact with ALA 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A PHE* 3.6 32.2 - - + -
961A P6G 3.7 9.9 - - - +
373B LEU 3.0 10.6 + - - +
374B ALA* 3.2 12.5 + - - +
376B GLU* 1.3 75.5 - - - +
378B VAL* 1.3 62.2 + - - +
380B LEU* 3.4 0.4 + - - -
381B HIS* 3.0 25.6 + - - +
531B PHE* 3.8 20.5 - - + -
535B PHE* 4.7 0.9 - - + -
536B LEU* 4.5 0.4 - - + -
539B LEU* 4.5 7.2 - - + -
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Residues in contact with VAL 378 (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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363B VAL* 3.9 19.5 - - + -
367B VAL* 4.7 6.7 - - + -
374B ALA 2.9 21.8 + - - +
375B ALA* 3.4 8.7 - - - +
377B ALA* 1.3 74.3 - - - +
379B VAL* 1.3 66.1 + - - +
381B HIS 3.3 1.0 + - - -
382B TYR* 3.1 29.8 + - + +
401B VAL* 3.8 34.1 - - + -
531B PHE* 3.9 16.6 - - + -
532B TRP* 3.8 25.6 - - + -
536B LEU* 4.4 4.9 - - + -
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Residues in contact with VAL 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B ARG* 3.5 19.3 - - - +
359B PHE* 4.1 11.9 - - + -
360B LEU* 3.5 41.3 - - + +
363B VAL* 4.0 25.1 - - + -
375B ALA* 2.9 21.8 + - + +
376B GLU* 3.3 7.8 + - - +
378B VAL* 1.3 76.7 - - - +
380B LEU* 1.3 62.9 + - + +
383B THR* 2.7 36.9 + - - +
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Residues in contact with LEU 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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530A ALA 4.8 0.9 - - - +
534A ARG* 4.0 16.8 - - + +
535A PHE* 3.9 39.9 - - + +
538A LYS* 4.7 16.2 - - + +
961A P6G 3.4 26.9 - - - +
356B ARG* 4.7 1.3 - - - +
376B GLU* 2.8 26.2 + - + +
377B ALA 4.1 0.4 - - - +
379B VAL* 1.3 82.0 - - + +
381B HIS* 1.3 62.4 + - - +
383B THR 3.8 1.9 + - - +
385B TRP* 3.0 55.7 + - + -
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Residues in contact with HIS 381 (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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527A GLN* 3.7 4.3 + - - -
961A P6G 2.9 85.5 + - - +
377B ALA 3.0 17.6 + - - +
378B VAL 3.8 3.6 - - - +
379B VAL 3.3 0.2 - - - -
380B LEU* 1.3 77.1 - - - +
382B TYR* 1.3 86.5 + + + +
527B GLN* 5.6 0.9 - - + -
528B THR* 3.0 39.2 + - + +
531B PHE* 4.2 25.9 - + + +
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Residues in contact with TYR 382 (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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359B PHE* 4.1 16.8 - - + -
378B VAL* 3.1 28.1 + - + +
381B HIS* 1.3 92.8 - + + +
383B THR* 1.3 65.2 + - - +
384B ASP* 3.5 2.6 + - - +
397B ALA* 3.8 28.0 - - + +
400B ALA* 3.7 17.7 - - + -
401B VAL* 3.7 22.4 - - + -
404B ASP* 2.5 33.7 + - - +
528B THR* 3.2 10.5 - - + +
531B PHE* 4.8 2.7 - + - -
532B TRP* 2.9 40.9 + + - -
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Residues in contact with THR 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A GLN* 2.9 26.0 + - - +
356B ARG* 3.1 35.9 + - - +
359B PHE* 4.0 6.6 - - - -
379B VAL* 2.7 24.1 + - - +
380B LEU 3.9 0.2 - - - +
381B HIS 3.5 0.4 - - - -
382B TYR* 1.3 77.0 - - - +
384B ASP* 1.3 68.5 + - - +
385B TRP* 3.4 44.9 + - + -
388B PRO* 4.0 7.9 - - + +
394B LEU* 5.6 4.0 - - + -
397B ALA* 5.8 0.2 - - - -
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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