Contacts of the helix formed by residues 354 - 367 (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 HIS 354 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A LYS 4.4 3.1 - - - -
353A LEU* 1.3 78.5 - - - +
355A GLU* 1.3 61.0 + - - +
356A GLU* 3.1 6.3 - - - +
357A GLU* 2.7 24.8 + - + +
358A HIS* 3.0 26.4 + - - +
394A TYR* 2.6 31.0 + + - +
398A GLN* 3.6 22.9 - - + -
399A HIS* 3.2 36.3 + + - -
400A PRO* 5.2 1.3 - - + +
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Residues in contact with GLU 355 (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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168A VAL* 3.9 14.8 - - + +
171A HIS* 4.2 16.9 - - + -
172A HIS* 2.7 42.5 + - - -
305A GLN* 4.6 7.8 - - - +
353A LEU 3.9 0.4 + - - -
354A HIS* 1.3 73.4 - - - +
356A GLU* 1.3 65.4 + - - +
358A HIS* 3.8 7.5 + - + +
359A VAL* 2.9 34.3 + - + +
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Residues in contact with GLU 356 (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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164A ILE* 3.4 30.2 - - + +
168A VAL* 3.9 17.8 - - + +
354A HIS* 3.1 2.5 - - - +
355A GLU* 1.3 93.6 + - - +
357A GLU* 1.3 56.3 + - - +
359A VAL* 3.5 2.1 - - - +
360A LEU* 3.1 35.6 + - + +
394A TYR* 3.6 42.5 + - + +
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Residues in contact with GLU 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LEU* 3.6 7.1 - - + +
354A HIS* 2.7 33.7 + - + +
356A GLU* 1.3 74.6 - - - +
358A HIS* 1.3 60.6 + - - +
360A LEU* 3.7 1.5 - - - +
361A LEU 2.8 22.9 + - - -
391A LEU* 4.0 13.5 - - + -
394A TYR* 3.5 28.0 - - + -
395A ILE* 3.4 16.7 - - - +
399A HIS* 2.6 40.7 + - - +
405A LEU* 4.0 5.2 - - - -
409A MET* 3.0 30.2 - - + +
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Residues in contact with HIS 358 (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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171A HIS* 4.2 10.0 + - - -
301A LEU* 3.4 27.3 + - + +
302A ARG* 4.0 5.6 + - - -
304A ASN* 4.8 10.2 - - - +
305A GLN* 3.5 33.1 + - + +
348A LEU* 5.2 7.2 - - + -
353A LEU* 4.1 24.6 - - + +
354A HIS 3.0 16.3 + - - +
355A GLU* 3.8 8.3 + - - +
357A GLU* 1.3 77.2 - - - +
359A VAL* 1.3 63.6 + - - +
361A LEU* 3.5 4.4 + - + +
362A MET* 3.3 47.4 + - + +
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Residues in contact with VAL 359 (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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164A ILE* 5.1 1.3 - - + +
167A LEU* 3.3 34.2 - - + +
168A VAL* 3.9 16.6 - - + +
171A HIS* 3.3 41.7 - - + -
272A PHE* 3.7 16.6 - - + -
355A GLU* 2.9 17.0 + - + +
356A GLU 3.5 11.0 - - - +
358A HIS* 1.3 77.6 - - - +
360A LEU* 1.3 62.1 + - + +
362A MET* 3.5 7.2 + - + -
363A ALA* 3.2 25.5 + - - +
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Residues in contact with LEU 360 (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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163A ILE* 4.7 2.7 - - + -
164A ILE* 4.4 12.3 - - + -
167A LEU* 3.4 26.5 - - + -
356A GLU 3.1 22.8 + - - +
357A GLU* 3.7 5.8 - - - +
358A HIS 3.2 0.2 - - - -
359A VAL* 1.3 81.1 - - + +
361A LEU* 1.3 59.0 + - - +
362A MET 3.2 0.2 - - - -
363A ALA* 3.3 1.6 + - - +
364A ILE* 2.9 36.3 + - + +
387A LEU* 4.2 26.9 - - + +
390A VAL* 3.9 20.2 - - + +
391A LEU* 3.7 37.5 - - + +
394A TYR* 4.9 4.9 - - + -
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Residues in contact with LEU 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU* 4.1 25.6 - - + -
348A LEU* 4.6 7.9 - - + -
353A LEU* 4.4 12.3 - - + -
357A GLU 2.8 17.9 + - - +
358A HIS* 3.7 7.6 - - + +
360A LEU* 1.3 77.5 - - - +
362A MET* 1.3 58.0 + - - +
364A ILE* 3.7 5.1 - - + +
365A CYS* 3.0 28.2 + - - +
391A LEU* 4.7 6.3 - - + -
409A MET* 3.6 51.8 - - + +
410A ILE* 5.4 1.3 - - + -
412A LYS* 4.6 8.1 - - + -
413A LEU* 4.0 20.9 - - + -
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Residues in contact with MET 362 (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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171A HIS* 3.7 28.5 - - + +
272A PHE* 3.9 30.4 - - + -
298A ILE* 3.4 25.8 - - + +
301A LEU* 3.8 28.5 - - + -
302A ARG* 3.8 33.2 - - - +
358A HIS* 3.3 19.5 + - + +
359A VAL* 3.8 17.0 - - + +
360A LEU 3.2 0.4 - - - -
361A LEU* 1.3 75.6 - - - +
363A ALA* 1.3 63.4 - - - +
366A LEU* 3.1 21.3 + - - +
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Residues in contact with ALA 363 (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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167A LEU* 3.9 24.5 - - + -
272A PHE* 4.1 2.6 - - + -
276A ILE* 3.9 32.0 - - + +
359A VAL 3.2 14.4 + - - +
360A LEU 3.8 3.8 - - - +
362A MET* 1.3 79.3 - - - +
364A ILE* 1.3 63.2 + - - +
366A LEU* 3.5 2.4 + - - +
367A LEU* 3.3 28.1 + - - +
387A LEU* 4.0 9.6 - - + +
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Residues in contact with ILE 364 (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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360A LEU* 2.9 25.6 + - + +
361A LEU* 3.7 6.1 - - + +
363A ALA* 1.3 76.2 - - - +
365A CYS* 1.3 64.7 + - - +
367A LEU 3.1 10.2 + - - -
384A GLN* 3.5 28.8 + - + +
387A LEU* 3.7 23.3 - - + +
388A CYS* 3.8 40.4 - - - +
391A LEU* 3.4 36.6 - - + -
410A ILE* 5.0 2.0 - - + -
413A LEU* 3.9 23.6 - - + -
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Residues in contact with CYS 365 (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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294A SER* 4.6 0.2 - - - -
297A GLU* 3.2 36.1 - - - -
298A ILE* 3.6 18.8 - - + -
301A LEU* 4.1 4.9 - - + -
361A LEU 3.0 17.9 + - - +
362A MET 3.8 4.9 - - - +
363A ALA 3.4 0.2 - - - -
364A ILE* 1.3 76.4 - - - +
366A LEU* 1.3 58.6 + - - +
368A SER* 2.6 23.5 + - - -
371A ARG* 2.8 19.5 + - - -
413A LEU* 3.6 19.5 - - + -
416A LEU* 4.0 11.2 - - - -
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Residues in contact with LEU 366 (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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269A VAL* 4.5 14.6 - - + +
272A PHE* 4.8 4.9 - - + -
273A ALA* 3.4 33.4 - - + +
276A ILE* 3.5 18.4 - - + -
279A PHE* 4.5 6.7 - - + -
290A LEU* 3.6 36.8 - - + +
291A LEU* 4.3 12.1 - - + +
294A SER* 2.9 33.2 + - - +
298A ILE* 4.0 8.1 - - + -
362A MET 3.1 17.3 + - - +
363A ALA 3.9 4.7 - - - +
364A ILE 3.2 0.2 - - - -
365A CYS* 1.3 76.0 - - - +
367A LEU* 1.3 58.2 + - - +
368A SER* 3.2 3.3 + - - -
371A ARG* 5.2 0.3 + - - -
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Residues in contact with LEU 367 (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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276A ILE* 4.1 14.1 - - + -
277A PRO 4.9 2.2 - - - +
279A PHE* 3.9 20.2 - - + -
282A LEU* 4.3 8.5 - - + -
290A LEU* 3.8 22.9 - - + -
363A ALA 3.3 11.5 + - - +
364A ILE 3.1 10.1 + - - +
366A LEU* 1.3 78.1 - - + +
368A SER* 1.3 63.3 + - - +
369A PRO* 3.2 3.5 - - - +
380A ILE* 3.3 12.9 - - + +
383A LEU* 3.7 31.0 - - + -
384A GLN* 3.2 27.4 - - + +
387A LEU* 3.5 28.7 - - + -
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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