Contacts of the helix formed by residues 334 - 351 (chain A) in PDB entry 2HBH
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 THR 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A GLY 4.9 3.4 - - - +
333A HIS* 1.3 79.0 - - - +
335A LEU* 1.3 63.9 + - - +
336A GLU* 3.3 14.3 - - - +
337A LEU* 2.9 20.3 + - - +
338A LEU* 3.0 15.8 + - - +
426A GLN* 2.8 31.8 + - + +
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Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A ILE* 3.8 33.4 - - + -
329A THR* 4.5 15.3 - - + +
334A THR* 1.3 73.6 - - - +
336A GLU* 1.3 61.9 + - - +
338A LEU* 4.0 5.4 - - + -
339A GLU* 2.6 42.5 + - + +
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Residues in contact with GLU 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A THR* 3.3 16.9 + - - +
335A LEU* 1.3 78.3 - - - +
337A LEU* 1.3 56.4 + - - +
339A GLU* 5.2 0.4 - - - -
340A PRO* 3.3 19.3 - - - +
422A GLU* 3.4 31.6 - - - +
425A LYS* 5.9 0.4 - - - +
426A GLN* 3.8 2.2 - - - +
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Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A MET* 4.5 11.7 - - + -
328A VAL* 5.8 0.4 - - + -
333A HIS* 3.5 34.1 - - + +
334A THR 2.9 5.3 + - - +
336A GLU* 1.3 78.3 - - - +
338A LEU* 1.3 72.4 + - + +
339A GLU 3.2 1.6 - - - -
340A PRO* 3.1 12.6 - - - +
341A LEU* 3.1 15.8 + - + +
419A LEU* 3.5 38.4 - - + +
422A GLU* 3.7 9.0 - - + -
423A HIS* 3.9 29.6 - - + +
426A GLN* 3.2 17.5 - - - +
500A XE4 5.9 3.6 - - + -
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Residues in contact with LEU 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A TRP* 6.1 0.7 - - + -
325A ILE* 3.5 50.4 - - + +
328A VAL* 3.3 38.1 - - + -
329A THR* 3.5 15.9 - - - +
333A HIS* 3.8 16.4 - - + +
334A THR 3.0 14.5 + - - +
335A LEU* 4.0 4.9 - - - +
337A LEU* 1.3 81.9 - - + +
339A GLU* 1.3 62.5 + - - +
341A LEU* 3.6 18.5 - - + +
342A VAL* 3.3 26.7 + - - +
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Residues in contact with GLU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A ILE* 4.9 6.3 - - - -
335A LEU* 2.6 34.1 + - + +
336A GLU 5.0 0.2 - - - -
338A LEU* 1.3 75.9 - - - +
340A PRO* 1.3 81.5 - - + +
342A VAL* 3.3 3.1 + - - +
343A LYS* 3.0 45.6 + - - +
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Residues in contact with PRO 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A GLU* 3.3 19.3 - - - +
337A LEU 3.1 14.1 - - - +
339A GLU* 1.3 107.7 - - + +
341A LEU* 1.3 55.2 + - - +
343A LYS* 3.5 5.3 - - + +
344A PHE* 2.6 37.8 + - - +
419A LEU* 3.4 19.9 - - + +
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Residues in contact with LEU 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A MET* 3.4 32.1 - - + -
314A TRP* 3.6 25.6 - - + -
337A LEU* 3.1 19.8 + - + +
338A LEU* 3.6 23.3 - - + +
339A GLU 3.1 0.2 - - - -
340A PRO* 1.3 77.4 - - - +
342A VAL* 1.3 53.5 + - + +
344A PHE* 3.2 2.1 + - - +
345A GLN* 2.7 64.5 + - + +
419A LEU* 3.5 11.2 - - + +
500A XE4 4.1 25.4 - - + -
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Residues in contact with VAL 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A PHE* 4.0 15.3 - - + -
312A MET* 3.7 35.9 - - + +
314A TRP* 4.4 17.7 - - + -
325A ILE* 3.5 30.3 - - + -
338A LEU 3.4 13.7 - - - +
339A GLU* 3.3 6.8 + - - +
341A LEU* 1.3 72.5 - - - +
343A LYS* 1.3 67.1 + - - +
345A GLN* 3.1 8.4 + - - +
346A VAL* 2.8 23.6 + - - +
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Residues in contact with LYS 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A GLU* 3.0 33.6 + - - +
340A PRO* 3.5 10.3 - - + +
342A VAL* 1.3 77.7 - - - +
344A PHE* 1.3 57.7 + - - +
346A VAL* 3.4 7.6 + - + +
347A GLY* 3.0 24.9 + - - -
412A LYS* 5.4 0.2 + - - -
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Residues in contact with PHE 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A MET 4.3 7.0 - - - -
301A LEU* 3.9 19.5 - - + -
340A PRO 2.6 21.5 + - - +
341A LEU* 3.3 4.7 - - + +
343A LYS* 1.3 70.5 - - - +
345A GLN* 1.3 87.7 + - - +
347A GLY 3.3 1.1 + - - +
348A LEU* 2.9 42.0 + - + +
412A LYS* 3.7 48.4 + - + +
415A ASP* 3.9 20.6 - - + -
416A LEU* 3.6 23.3 - - + -
419A LEU* 3.8 17.9 - - + -
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Residues in contact with GLN 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A MET 3.0 22.0 + - - -
303A SER* 3.4 9.2 + - - -
304A ASN* 2.9 46.8 + - - +
307A PHE* 3.7 22.7 - - + +
314A TRP* 3.5 25.1 + - + -
341A LEU* 2.7 42.9 + - - +
342A VAL* 3.4 7.9 - - - +
344A PHE* 1.3 84.8 - - - +
346A VAL* 1.3 58.3 + - - +
348A LEU* 4.5 0.2 - - - -
349A LYS* 2.8 26.9 + - - +
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Residues in contact with VAL 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A PHE* 3.9 4.5 - - + -
309A LEU* 3.7 21.3 - - + -
312A MET* 3.5 38.6 - - + -
342A VAL* 2.8 20.3 + - + +
343A LYS* 3.5 7.0 - - - +
345A GLN* 1.3 73.5 - - - +
347A GLY* 1.3 68.2 + - - +
349A LYS* 3.1 2.8 + - - +
350A LYS* 3.0 46.0 + - - +
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Residues in contact with GLY 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A LYS 3.0 14.0 + - - -
344A PHE 3.3 2.2 + - - -
346A VAL* 1.3 79.5 - - - +
348A LEU* 1.3 61.0 + - - +
350A LYS* 3.4 18.4 + - - +
351A LEU* 3.5 16.8 + - - +
412A LYS* 3.8 18.6 + - - -
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Residues in contact with LEU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A LEU* 3.9 26.0 - - + +
304A ASN* 3.6 33.4 - - + +
344A PHE* 2.9 36.1 + - + +
345A GLN 3.7 3.4 - - - +
347A GLY* 1.3 73.4 - - - +
349A LYS* 1.3 66.9 + - - +
351A LEU* 3.2 28.6 + - + +
352A LYS 4.1 1.0 + - - -
353A LEU* 4.0 28.4 + - + +
358A HIS* 5.2 5.4 - - + -
361A LEU* 4.6 8.7 - - + -
412A LYS* 4.0 15.1 - - + +
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Residues in contact with LYS 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A ASN* 3.0 43.5 + - - +
305A GLN* 4.3 9.5 + - - +
307A PHE* 3.1 23.2 + - + +
308A SER* 5.1 1.8 - - - +
309A LEU* 3.5 35.0 - - + +
345A GLN 2.8 16.9 + - - +
346A VAL 3.4 5.2 - - - +
348A LEU* 1.3 77.0 - - - +
350A LYS* 1.3 52.4 + - - +
352A LYS* 2.8 33.1 + - - +
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Residues in contact with LYS 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A LEU* 4.6 13.9 - - + -
346A VAL* 3.0 36.0 + - + +
347A GLY* 3.5 14.8 - - - +
348A LEU 3.3 0.4 - - - -
349A LYS* 1.3 74.8 - - - +
351A LEU* 1.3 60.7 + - + +
352A LYS* 3.1 13.0 + - - +
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Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A GLY 3.5 14.5 + - - +
348A LEU* 3.2 18.7 + - + +
349A LYS 2.9 1.6 + - - -
350A LYS* 1.3 79.5 - - + +
352A LYS* 1.3 69.3 + - - +
353A LEU* 2.9 28.8 + - + +
399A HIS* 4.7 3.8 - - - -
405A LEU* 4.1 16.1 - - + +
408A LYS* 3.7 46.0 - - + +
409A MET* 4.4 7.6 - - + -
412A LYS* 4.4 25.6 - - + -
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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