Contacts of the helix formed by residues 351 - 366 (chain A) in PDB entry 7EHI
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 ASP 351 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A THR* 2.6 39.9 + - - +
318A SER* 3.9 9.1 + - - -
349A GLU 4.4 0.4 + - - -
350A ILE* 1.3 76.1 - - - +
352A HIS* 1.4 66.2 + - - +
353A HIS* 3.4 16.1 + - + +
354A PHE* 2.8 35.8 + - - +
355A TRP* 3.2 19.6 + - - -
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Residues in contact with HIS 352 (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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350A ILE 3.8 0.4 + - - -
351A ASP* 1.4 70.4 - - - +
353A HIS* 1.3 67.0 + - - +
355A TRP* 3.2 2.8 + - - +
356A ARG* 2.9 42.9 + - - +
381A SER* 3.5 35.8 + - - -
382A TRP* 3.3 34.7 + + - -
387A GLU* 2.6 36.4 + - - +
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Residues in contact with HIS 353 (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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317A THR 5.4 1.2 + - - -
318A SER* 5.8 5.0 - - - -
323A VAL* 5.2 8.4 - - + +
351A ASP* 3.2 13.1 + - + +
352A HIS* 1.3 79.1 - - - +
354A PHE* 1.3 64.1 + - - +
356A ARG* 3.4 11.4 + - - +
357A LYS* 3.2 66.1 + - + +
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Residues in contact with PHE 354 (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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254A PHE* 4.1 12.8 - + + -
317A THR* 4.4 12.3 - - - +
323A VAL* 4.1 38.8 - - + -
326A LEU* 3.7 37.0 - - + -
327A LEU* 4.3 11.0 - - + -
350A ILE* 3.6 23.8 - - + -
351A ASP* 2.8 27.9 + - - +
352A HIS 3.3 0.2 - - - -
353A HIS* 1.3 79.2 + - - +
355A TRP* 1.3 87.2 + + - +
357A LYS* 3.1 7.3 + - + +
358A PHE* 2.8 38.5 + + + +
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Residues in contact with TRP 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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252A ALA 6.1 0.4 - - - -
254A PHE* 4.7 8.1 - + + -
344A LEU* 3.5 40.6 - - + -
345A ASN 5.4 0.9 - - - -
347A ALA* 2.9 35.0 + - + -
350A ILE* 3.4 45.2 + - + +
351A ASP 3.2 18.4 + - - -
352A HIS 3.2 3.7 + - - +
354A PHE* 1.3 103.5 - + - +
356A ARG* 1.3 57.5 + - - +
358A PHE* 3.6 20.6 - + + +
359A HIS* 2.8 30.1 + - - +
382A TRP* 3.9 11.0 - + - -
386A ASP 4.1 0.2 - - - +
387A GLU* 3.8 26.2 - - + +
388A PHE* 3.5 23.6 - + + -
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Residues in contact with ARG 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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352A HIS* 2.9 33.0 + - - +
353A HIS* 3.7 9.1 - - - +
355A TRP* 1.3 73.1 - - - +
357A LYS* 1.3 60.6 + - + +
359A HIS* 3.4 1.4 + - - +
360A ASP* 2.9 38.9 + - - +
381A SER 5.9 0.2 + - - -
386A ASP* 3.6 31.8 + - + +
387A GLU* 3.1 32.3 + - + +
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Residues in contact with LYS 357 (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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320A PRO* 5.9 4.6 - - - +
323A VAL* 3.8 29.0 - - + +
327A LEU* 4.0 18.2 - - + +
353A HIS* 3.2 48.2 + - + +
354A PHE* 3.1 8.1 + - - +
356A ARG* 1.3 79.5 - - + +
358A PHE* 1.3 61.9 + - - +
360A ASP* 3.4 7.6 + - - +
361A ALA* 3.0 24.6 + - - +
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Residues in contact with PHE 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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254A PHE* 3.8 13.5 - + - -
327A LEU* 3.6 12.9 - - + +
330A ALA* 3.5 28.7 - - + -
342A TRP* 3.6 26.7 - + + -
344A LEU* 3.9 17.7 - - + -
354A PHE* 2.8 37.5 + + + +
355A TRP* 3.6 22.7 - + + +
357A LYS* 1.3 76.3 - - - +
359A HIS* 1.3 64.7 + - - +
361A ALA* 3.2 2.4 + - - +
362A MET* 2.9 41.3 + - + +
371A ILE* 3.9 33.2 - - + -
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Residues in contact with HIS 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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355A TRP 2.8 16.6 + - - +
356A ARG 3.6 1.3 - - - +
358A PHE* 1.3 73.3 - - - +
360A ASP* 1.3 79.9 + - - +
362A MET* 3.2 1.7 + - - +
363A MET* 2.9 62.1 + - + +
371A ILE* 4.0 10.3 - - - -
385A GLY 3.3 27.0 + - - -
386A ASP* 3.2 27.2 - - - +
387A GLU 2.9 22.9 + - - +
388A PHE 5.4 2.2 - - - -
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Residues in contact with ASP 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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356A ARG* 2.9 25.6 + - - +
357A LYS* 3.8 6.9 - - - +
359A HIS* 1.3 90.6 - - - +
361A ALA* 1.3 63.2 + - - +
363A MET* 4.0 3.1 - - - +
364A ALA* 3.1 25.3 + - - +
386A ASP* 5.0 1.4 - - - +
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Residues in contact with ALA 361 (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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327A LEU* 4.3 17.9 - - + -
331A THR* 4.3 9.6 - - + +
357A LYS 3.0 18.3 + - - +
358A PHE 3.6 4.0 - - - +
360A ASP* 1.3 77.5 - - - +
362A MET* 1.3 74.7 + - + +
364A ALA* 3.4 7.3 + - - +
365A LEU* 3.2 25.5 + - - +
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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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327A LEU* 5.7 0.4 - - + -
330A ALA* 3.8 21.3 - - + +
331A THR* 3.4 33.2 - - + -
334A VAL* 4.0 11.7 - - - -
342A TRP* 3.8 26.5 - - - -
358A PHE* 2.9 40.7 + - + +
359A HIS 3.9 2.7 - - - +
361A ALA* 1.3 81.5 - - + +
363A MET* 1.3 58.8 + - - +
365A LEU* 3.0 10.7 + - + +
366A LYS* 2.9 30.6 + - - +
369A PHE* 3.8 24.9 - - + +
371A ILE* 4.2 7.0 - - + -
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Residues in contact with MET 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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359A HIS* 2.9 48.8 + - + +
360A ASP* 4.2 3.4 - - - +
362A MET* 1.3 76.3 - - - +
364A ALA* 1.3 61.4 + - - +
366A LYS 3.6 8.5 - - - +
367A PRO* 3.3 48.2 - - + +
369A PHE* 3.6 27.1 - - + +
371A ILE* 3.7 31.0 - - + -
388A PHE 6.5 0.4 - - - -
389A THR* 4.7 5.6 - - - +
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Residues in contact with ALA 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 ASP 3.1 18.4 + - - +
361A ALA* 3.7 6.5 - - - +
362A MET 3.2 0.2 - - - -
363A MET* 1.3 79.0 - - - +
365A LEU* 1.3 63.5 + - + +
367A PRO* 5.1 2.1 - - - +
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Residues in contact with LEU 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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331A THR* 3.7 42.0 - - + +
334A VAL* 4.0 28.7 - - + -
335A LYS* 3.5 37.0 - - + +
361A ALA 3.2 11.2 + - - +
362A MET* 3.0 12.4 + - + +
364A ALA* 1.3 83.4 - - + +
366A LYS* 1.3 63.4 + - + +
367A PRO* 4.0 4.5 - - - +
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Residues in contact with LYS 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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334A VAL* 3.7 23.6 - - + -
338A ASP* 2.6 37.5 + - - +
339A ILE 2.8 28.8 + - - +
340A ASP* 4.1 10.7 + - - -
362A MET 2.9 13.2 + - - +
363A MET* 3.4 5.1 + - - -
365A LEU* 1.3 79.4 - - + +
367A PRO* 1.3 69.4 - - - +
368A ASP* 3.1 15.3 - - - +
369A PHE* 2.9 35.1 + - + +
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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