Contacts of the helix formed by residues 390 - 407 (chain B) in PDB entry 2H9Y
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 390 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B HIS* 3.2 24.5 + - + +
388B PRO 3.5 0.4 - - - -
389B GLU* 1.3 75.3 - - - +
391B PRO* 1.3 69.4 - - - +
392B THR* 3.7 12.0 + - - -
393B HIS* 2.6 42.8 + - - +
394B LEU* 2.9 28.6 + - - +
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Residues in contact with PRO 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B LEU* 3.7 29.3 - - + -
354B ILE 3.2 28.8 + - - +
355B SER* 5.7 1.1 - - - -
389B GLU 3.2 9.2 - - - +
390B ASP* 1.3 91.5 - - - +
392B THR* 1.3 55.0 + - - +
394B LEU* 4.4 0.4 - - + -
395B ARG* 2.9 32.1 + - - +
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Residues in contact with THR 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B LEU* 3.3 22.3 - - - +
390B ASP* 3.3 12.7 + - - +
391B PRO* 1.3 75.6 - - - +
393B HIS* 1.3 68.3 + - + +
395B ARG* 3.6 15.6 + - - +
396B ASP* 3.1 38.8 + - - +
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Residues in contact with HIS 393 (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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384B ASP* 3.7 31.2 + - + +
387B HIS* 3.6 40.2 + + + +
390B ASP* 2.6 40.4 + - + +
392B THR* 1.3 82.3 - - + +
394B LEU* 1.3 59.2 + - + +
396B ASP* 3.3 5.2 + - - +
397B ALA* 2.8 31.5 + - - +
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Residues in contact with LEU 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B ILE* 3.7 20.0 - - + +
355B SER 3.7 3.1 - - - -
356B ARG* 3.5 37.2 - - - +
359B PHE* 3.7 36.4 - - + -
383B THR* 5.3 4.3 - - - +
387B HIS 5.6 0.4 - - - +
388B PRO 3.5 19.5 - - - +
389B GLU* 3.6 28.9 - - - +
390B ASP 2.9 13.2 + - - +
391B PRO 3.9 3.8 - - - +
393B HIS* 1.3 76.5 - - + +
395B ARG* 1.3 58.2 + - - +
397B ALA* 3.3 6.0 + - + +
398B MET* 2.9 30.5 + - - +
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Residues in contact with ARG 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B PHE* 3.6 17.9 - - + -
351B GLU* 3.0 36.0 + - - +
352B SER 3.1 24.8 + - - +
353B LEU* 3.9 18.2 - - - +
354B ILE* 3.6 12.6 - - + +
391B PRO 2.9 18.8 + - - +
392B THR* 3.9 14.1 + - - +
394B LEU* 1.3 76.1 - - - +
396B ASP* 1.3 96.6 + - - +
398B MET* 3.3 5.2 + - - +
399B SER* 3.2 20.0 + - - -
442B TRP* 3.4 43.2 + - + +
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Residues in contact with ASP 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B THR* 3.1 31.3 + - - +
393B HIS* 3.9 4.4 - - - +
395B ARG* 1.3 105.4 + - - +
397B ALA* 1.3 60.5 + - - +
399B SER* 3.3 9.6 + - - -
400B ALA* 3.0 26.4 + - - +
442B TRP* 4.4 7.1 - - - +
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Residues in contact with ALA 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B PHE* 4.0 16.8 - - + -
382B TYR* 3.7 28.2 - - + +
393B HIS 2.8 19.0 + - - +
394B LEU* 3.6 7.6 - - + +
396B ASP* 1.3 74.5 - - - +
398B MET* 1.3 59.3 + - - +
400B ALA* 3.0 8.4 + - - +
401B VAL* 2.8 32.6 + - - +
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Residues in contact with MET 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU* 3.8 13.0 - - + -
343B VAL* 4.5 2.9 - - + -
346B PHE* 3.6 27.1 - - + -
354B ILE* 4.4 0.9 - - + -
358B GLN 4.9 0.4 - - - +
359B PHE* 3.7 22.8 - - + +
362B GLY* 3.4 45.5 - - - +
363B VAL* 3.8 11.0 - - + +
366B GLY* 4.7 0.7 - - - -
394B LEU 2.9 13.6 + - - +
395B ARG 3.3 10.5 + - - +
397B ALA* 1.3 78.0 - - - +
399B SER* 1.3 61.9 + - - +
401B VAL* 3.3 11.7 + - + +
402B VAL* 3.3 39.2 + - + +
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Residues in contact with SER 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ASP* 4.8 10.9 + - - +
335B GLY* 3.5 12.1 + - - -
336B SER* 3.2 25.5 + - - -
339B LEU* 3.5 22.5 - - - +
395B ARG 3.2 7.8 + - - -
396B ASP* 3.5 12.6 - - - -
397B ALA 3.2 0.2 - - - -
398B MET* 1.3 77.1 - - - +
400B ALA* 1.3 64.2 + - - +
402B VAL 3.2 1.9 + - - -
403B GLY* 3.0 20.4 + - - -
442B TRP* 5.3 2.7 - - - -
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Residues in contact with ALA 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B TYR* 3.7 19.1 - - + -
396B ASP 3.0 14.6 + - - +
397B ALA* 3.0 10.3 + - - +
399B SER* 1.3 77.6 + - - +
401B VAL* 1.3 56.8 + - - +
403B GLY* 5.1 0.9 - - - -
404B ASP* 2.8 44.6 + - - +
525B ARG* 5.1 9.0 - - - +
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Residues in contact with VAL 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B PHE* 4.4 10.5 - - + -
363B VAL* 4.7 3.1 - - + -
367B VAL* 3.6 29.8 - - + -
378B VAL* 3.7 17.0 - - + -
382B TYR* 3.4 39.7 - - + -
397B ALA 2.8 21.8 + - - +
398B MET* 3.7 20.6 - - + +
399B SER 3.3 0.2 - - - -
400B ALA* 1.3 71.3 - - - +
402B VAL* 1.3 61.0 + - + +
405B HIS* 3.0 34.0 + - - +
532B TRP* 3.9 3.1 - - + -
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Residues in contact with VAL 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ILE* 3.8 24.7 - - + -
295B PHE* 4.0 14.8 - - + -
335B GLY* 4.2 15.5 - - - +
338B PHE* 4.4 2.0 - - + -
339B LEU* 3.8 13.7 - - + -
366B GLY* 4.2 12.3 - - - +
398B MET* 3.3 33.4 + - + +
399B SER 3.2 4.1 + - - +
400B ALA 3.2 0.6 - - - -
401B VAL* 1.3 78.3 - - + +
403B GLY* 1.3 62.2 + - - +
405B HIS* 4.7 0.7 - - - -
406B ASN* 2.8 48.5 + - - +
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Residues in contact with GLY 403 (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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295B PHE* 5.8 0.9 - - - -
334B GLU* 3.7 10.1 - - - -
335B GLY* 3.6 23.4 - - - -
399B SER 3.0 12.1 + - - -
400B ALA* 3.8 1.1 - - - -
402B VAL* 1.3 77.4 - - - +
404B ASP* 1.3 58.8 + - - +
407B VAL* 2.9 28.7 + - - +
408B VAL* 3.0 14.4 + - - +
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Residues in contact with ASP 404 (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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382B TYR* 2.5 37.7 + - - +
400B ALA* 2.8 26.8 + - - +
403B GLY* 1.3 71.1 - - - +
405B HIS* 1.3 65.7 + - - +
406B ASN 3.3 0.2 + - - -
408B VAL* 3.6 14.3 - - - +
409B CYS* 3.1 34.7 + - - +
410B PRO* 3.3 4.3 - - - +
525B ARG* 3.2 38.1 + - - -
528B THR* 3.6 9.6 - - - +
532B TRP* 3.8 5.6 - - - +
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Residues in contact with HIS 405 (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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235B PRO* 3.6 25.9 - - + +
296B ARG* 3.0 22.5 + - - -
366B GLY 3.7 22.7 - - - -
367B VAL* 3.9 16.4 - - + +
369B GLN* 6.0 1.0 + - + +
401B VAL 3.0 20.1 + - - +
402B VAL* 4.1 2.0 - - - +
404B ASP* 1.3 76.9 - - - +
406B ASN* 1.3 73.4 + - - +
410B PRO* 3.4 17.5 - - - +
532B TRP* 3.2 44.5 - + + -
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Residues in contact with ASN 406 (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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230B GLY* 5.9 0.5 - - - -
231B THR* 4.9 0.7 + - - -
235B PRO* 3.4 10.8 - - - +
236B TRP* 2.8 29.3 + - - +
295B PHE* 3.4 48.1 - - + +
296B ARG* 2.9 26.3 + - - +
366B GLY 4.3 4.2 + - - -
402B VAL* 2.8 33.5 + - - +
405B HIS* 1.3 89.2 - - - +
407B VAL* 1.3 60.6 + - - +
410B PRO* 3.6 12.0 - - - +
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Residues in contact with VAL 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B SER* 3.7 33.7 - - - +
230B GLY* 4.2 1.8 - - - +
231B THR* 6.0 0.4 - - - -
236B TRP* 5.1 2.0 - - + +
295B PHE* 3.7 27.6 - - + -
330B VAL* 4.0 9.0 - - + -
334B GLU* 3.6 39.7 - - + +
403B GLY 2.9 12.0 + - - +
405B HIS 3.7 0.2 - - - -
406B ASN* 1.3 84.5 - - - +
408B VAL* 1.3 59.9 + - - +
409B CYS 3.3 2.4 + - - -
410B PRO* 3.4 3.5 - - - +
411B VAL* 2.8 35.8 + - + +
447B HIS* 4.6 1.1 - - - +
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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
------------------------------------------------------------
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