Contacts of the helix formed by residues 378 - 392 (chain A) in PDB entry 1HXK
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 378 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A PHE* 5.1 0.7 - - - +
86A VAL* 4.0 7.0 - - - +
125A LYS* 4.1 15.0 - - + -
126A PHE 4.9 0.4 - - - +
127A ILE* 4.1 10.1 - - + -
156A GLY 3.6 23.8 - - - +
157A GLN 4.3 3.1 - - - +
159A GLU* 2.6 41.9 + - + +
377A GLY* 1.3 80.3 - - - +
379A LEU* 1.3 62.8 + - - +
381A GLU* 3.0 28.1 + - - +
382A TYR* 3.2 18.9 + - - +
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Residues in contact with LEU 379 (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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86A VAL* 4.1 4.3 - - - +
127A ILE* 3.8 11.2 - - + +
159A GLU* 3.4 1.4 + - - +
161A VAL* 3.6 33.4 - - + -
199A ALA* 4.1 7.6 - - + -
200A SER 3.6 26.7 - - - +
201A TRP* 3.9 32.1 - - + -
225A LEU* 4.2 10.1 - - + -
335A LEU* 4.3 14.1 - - + -
378A THR* 1.3 74.9 - - - +
380A GLN* 1.3 62.1 + - - +
382A TYR* 3.1 16.7 + - + +
383A PHE* 3.1 43.4 + - + -
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Residues in contact with GLN 380 (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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159A GLU* 2.8 33.4 + - - +
198A THR* 3.1 26.1 + - - +
199A ALA* 3.5 20.4 + - + +
222A LYS* 6.1 2.6 - - - +
223A ASN* 4.6 11.7 + - - +
378A THR* 4.2 0.2 - - - +
379A LEU* 1.3 73.0 - - - +
381A GLU* 1.3 57.5 + - + +
383A PHE* 3.4 4.4 + - - +
384A ASP* 2.7 70.2 + - - +
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Residues in contact with GLU 381 (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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84A PHE* 4.1 20.7 - - + -
125A LYS* 3.5 20.3 + - - -
156A GLY 5.2 2.0 - - - +
159A GLU* 4.9 0.7 - - - +
376A PHE 4.2 0.7 - - - +
377A GLY* 3.1 13.0 - - - -
378A THR* 3.0 39.0 + - - +
379A LEU 3.2 0.6 - - - -
380A GLN* 1.3 77.5 - - + +
382A TYR* 1.3 63.6 + - - +
384A ASP* 3.7 8.6 - - - +
385A ALA* 3.1 23.7 + - - +
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Residues in contact with TYR 382 (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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84A PHE* 4.0 15.2 - + + -
244A GLU* 2.6 33.2 + - - -
262A HIS* 3.6 16.5 + - - -
329A TYR* 4.8 4.0 - - - +
331A THR* 5.1 0.3 + - - -
333A VAL* 3.4 36.9 + - + -
334A LEU 4.0 2.5 - - - -
335A LEU* 3.4 54.7 + - + +
378A THR 3.2 8.0 + - - +
379A LEU* 3.1 9.7 + - + +
381A GLU* 1.3 78.8 - - - +
383A PHE* 1.3 86.0 + + - +
385A ALA* 3.1 4.7 + - - +
386A VAL* 2.9 44.0 + - + +
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Residues in contact with PHE 383 (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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199A ALA* 4.1 10.1 - - + -
223A ASN* 3.4 46.2 - - + +
224A MET 3.8 24.5 - - - -
225A LEU* 4.4 2.5 - - + -
260A PHE* 3.7 28.9 - + - -
262A HIS* 3.9 17.5 - - + -
379A LEU* 3.1 53.0 + - + -
380A GLN* 3.9 8.3 - - - +
382A TYR* 1.3 93.7 - + - +
384A ASP* 1.3 63.3 - - - +
386A VAL* 3.2 3.3 + - + +
387A HIS* 3.0 31.5 + - - -
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Residues in contact with ASP 384 (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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380A GLN* 2.7 56.4 + - - +
381A GLU* 3.7 8.0 - - - +
383A PHE* 1.3 76.1 - - - +
385A ALA* 1.3 62.0 + - - +
387A HIS* 3.4 5.8 + - - +
388A GLN* 3.1 41.7 + - - +
391A ARG* 4.9 0.3 + - - -
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Residues in contact with ALA 385 (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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82A LYS* 3.9 14.4 + - - +
84A PHE* 3.8 12.3 - - + -
333A VAL* 3.6 27.6 - - + +
381A GLU 3.1 14.3 + - - +
382A TYR 3.5 7.9 - - - +
384A ASP* 1.3 76.4 - - - +
386A VAL* 1.3 64.9 + - - +
388A GLN* 3.2 14.3 + - - +
389A ALA* 3.0 21.7 + - - +
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Residues in contact with VAL 386 (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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244A GLU* 4.4 2.0 - - - +
260A PHE* 4.0 17.9 - - + -
331A THR* 4.1 11.6 - - + +
333A VAL* 4.1 13.7 - - + +
382A TYR* 2.9 58.4 + - + +
383A PHE* 3.2 9.6 + - - +
385A ALA* 1.3 76.1 - - - +
387A HIS* 1.3 59.8 + - + +
389A ALA* 3.1 7.7 + - - +
390A GLU* 2.9 23.0 + - - +
397A PHE* 3.7 28.5 - - + -
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Residues in contact with HIS 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LYS* 4.7 1.0 + - + -
223A ASN* 2.7 34.6 + - - -
246A LEU* 6.0 0.7 - - + -
260A PHE* 3.5 38.9 - + + +
383A PHE* 3.0 26.1 + - + +
384A ASP* 4.1 5.4 - - - +
386A VAL* 1.3 75.8 - - + +
388A GLN* 1.3 59.1 + - - +
390A GLU* 2.7 29.5 + - - +
391A ARG* 2.8 42.1 + - + +
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Residues in contact with GLN 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LYS* 4.5 11.1 + - - +
384A ASP* 3.1 39.0 + - - +
385A ALA* 3.2 13.5 + - - +
387A HIS* 1.3 77.1 - - - +
389A ALA* 1.3 57.3 + - - +
391A ARG* 3.1 32.8 + - - +
392A ALA* 3.0 27.6 + - - +
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Residues in contact with ALA 389 (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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331A THR* 4.0 12.3 - - + -
332A ASN* 4.1 5.8 - - - +
333A VAL* 4.7 1.3 - - + -
385A ALA 3.0 12.2 + - - +
386A VAL* 3.3 9.4 - - - +
388A GLN* 1.3 74.9 - - - +
390A GLU* 1.3 64.6 + - - +
392A ALA* 3.1 11.0 + - - +
394A GLN* 3.1 59.9 + - + +
395A ALA* 5.2 0.2 - - - -
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Residues in contact with GLU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 5.5 7.3 - - - +
260A PHE* 5.6 0.2 - - - -
386A VAL 2.9 12.8 + - - +
387A HIS* 2.7 41.0 + - - +
389A ALA* 1.3 76.9 - - - +
391A ARG* 1.3 59.8 + - + +
393A GLY* 2.8 21.1 + - - -
395A ALA* 3.9 25.8 - - - +
396A GLU* 5.6 0.5 - - - -
397A PHE* 3.4 33.8 + - + +
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Residues in contact with ARG 391 (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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384A ASP 4.9 0.4 + - - -
387A HIS* 2.8 25.1 + - + +
388A GLN* 3.1 38.2 - - - +
390A GLU* 1.3 75.7 - - + +
392A ALA* 1.3 57.6 + - - +
393A GLY* 2.9 10.2 + - - -
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Residues in contact with ALA 392 (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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388A GLN 3.0 15.2 + - - +
389A ALA* 3.1 14.5 + - - +
391A ARG* 1.3 75.5 - - - +
393A GLY* 1.3 61.4 + - - +
394A GLN* 3.5 7.9 + - + +
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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