Contacts of the helix formed by residues 363 - 384 (chain B) in PDB entry 5HP1
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 ASN 363 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A TRP* 4.6 0.2 - - - -
410A TRP* 3.2 30.8 - - + +
359B GLY* 2.9 11.5 + - - +
362B THR* 1.3 87.8 - - + +
364B ASP* 1.3 62.3 + - - +
365B VAL* 2.8 19.2 + - - +
366B LYS* 2.7 38.6 + - + +
367B GLN* 3.2 24.0 + - - +
405B TYR* 2.7 36.8 + - - -
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Residues in contact with ASP 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A TRP* 3.3 30.9 - - - +
408A ALA* 3.7 10.3 - - + -
409A THR 3.3 34.0 + - - +
410A TRP* 4.3 1.2 - - - -
331B LYS* 2.6 39.0 + - - -
337B TRP* 3.7 16.6 - - + -
362B THR 4.2 0.8 - - - -
363B ASN* 1.3 71.4 - - - +
365B VAL* 1.3 58.2 + - - +
367B GLN* 3.3 11.7 + - - +
368B LEU* 2.8 29.5 + - - +
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Residues in contact with VAL 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ALA* 5.0 1.6 - - - -
409A THR* 4.6 2.7 - - - -
410A TRP* 3.8 22.7 - - + +
363B ASN* 2.8 10.3 + - - +
364B ASP* 1.3 71.1 - - + +
366B LYS* 1.3 61.3 + - - +
368B LEU* 3.3 5.9 + - - +
369B THR* 2.9 35.4 + - - +
393B ILE* 4.1 17.7 - - + -
397B THR* 4.2 7.4 - - + +
398B TRP* 4.3 20.0 - - + -
401B TRP* 3.7 38.1 - - + -
402B TRP 4.5 3.8 - - - +
405B TYR* 4.2 10.5 - - + -
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Residues in contact with LYS 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ARG* 3.7 56.2 - - + +
359B GLY* 3.7 8.9 - - - +
363B ASN* 2.7 31.5 + - - +
365B VAL* 1.3 74.3 - - - +
367B GLN* 1.3 62.6 + - - +
369B THR* 3.1 3.5 + - - -
370B GLU* 2.9 22.9 + - - +
405B TYR* 3.7 38.7 - - + -
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Residues in contact with GLN 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A TRP* 5.1 1.6 - - - -
335B GLY* 3.3 21.3 - - - +
337B TRP* 2.9 35.0 + - + +
357B MET* 3.7 16.7 + - + +
358B ARG 3.4 20.8 + - - +
359B GLY 2.9 21.0 + - - -
360B ALA* 3.3 15.3 - - - +
361B HIS* 3.6 7.1 - - - +
362B THR 4.6 0.2 - - - +
363B ASN 3.2 16.6 + - - +
364B ASP* 3.5 17.6 + - - +
366B LYS* 1.3 77.7 - - - +
368B LEU* 1.3 56.6 + - - +
370B GLU* 3.3 5.4 + - - +
371B ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ALA* 4.3 8.7 - - + -
329B ILE* 3.7 40.4 - - + -
337B TRP* 4.2 15.2 - - + -
364B ASP 2.8 19.6 + - - +
365B VAL* 3.9 5.4 - - - +
367B GLN* 1.3 72.2 - - - +
369B THR* 1.3 57.2 + - - +
371B ALA* 3.1 4.9 + - + +
372B VAL* 2.8 40.4 + - + +
391B LEU* 4.4 5.2 - - + -
392B PRO* 4.1 16.2 - - + -
393B ILE* 3.9 29.6 - - + -
398B TRP* 3.7 21.8 - - + -
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Residues in contact with THR 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ARG* 4.0 0.9 - - - +
365B VAL 2.9 23.4 + - - -
366B LYS 3.4 4.5 - - - -
368B LEU* 1.3 76.6 - - - +
370B GLU* 1.3 62.4 + - - +
372B VAL* 3.3 3.3 + - - +
373B GLN* 3.0 26.2 + - - +
398B TRP* 3.4 22.9 - - - -
402B TRP* 4.2 10.7 - - - +
405B TYR* 3.6 37.7 - - + +
406B TRP* 3.6 27.1 - - + +
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Residues in contact with GLU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LYS* 2.9 29.6 + - - -
357B MET* 3.9 23.8 - - + -
358B ARG* 2.6 44.4 + - + +
366B LYS 2.9 13.1 + - - +
367B GLN* 3.6 9.0 - - - +
369B THR* 1.3 77.4 - - - +
371B ALA* 1.3 50.5 + - - +
373B GLN* 3.1 11.1 + - - +
374B LYS* 2.7 60.7 + - - +
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Residues in contact with ALA 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ILE* 4.2 19.5 - - + -
337B TRP* 4.9 4.0 - - + -
354B TYR* 4.1 25.4 - - + -
357B MET* 4.0 9.1 - - + -
367B GLN 2.9 14.5 + - - +
368B LEU* 3.4 13.9 - - + +
370B GLU* 1.3 76.4 - - - +
372B VAL* 1.3 56.9 + - - +
374B LYS* 3.1 1.9 + - - +
375B ILE* 2.8 37.6 + - + +
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Residues in contact with VAL 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ILE* 3.9 10.8 - - + -
368B LEU* 2.8 26.5 + - + +
369B THR* 3.7 5.6 - - - +
371B ALA* 1.3 70.6 - - - +
373B GLN* 1.3 58.4 + - - +
375B ILE 3.5 0.2 + - - -
376B THR* 2.9 34.5 + - - -
389B PHE* 3.5 20.1 - - + -
391B LEU* 3.6 29.8 - - + -
398B TRP* 4.4 7.0 - - + -
406B TRP* 3.9 13.9 - - + -
412B PRO* 3.7 28.9 - - + -
414B TRP* 5.2 5.2 - - + -
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Residues in contact with GLN 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LYS* 4.4 4.2 - - - +
358B ARG* 3.2 12.0 - - - +
369B THR* 3.0 16.5 + - - +
370B GLU* 3.1 29.8 + - - +
372B VAL* 1.3 76.7 - - - +
374B LYS* 1.3 62.4 + - + +
377B THR* 3.0 27.6 + - - -
405B TYR 3.5 2.3 - - - +
406B TRP* 3.4 32.8 - - + -
407B GLN* 2.7 40.3 + - - +
408B ALA* 3.9 7.6 + - + -
410B TRP* 3.6 14.8 - - + -
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Residues in contact with LYS 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B TYR* 3.5 42.0 - - + +
357B MET* 4.3 16.8 - - - -
370B GLU* 2.7 48.5 + - - +
371B ALA 3.6 3.6 - - - +
373B GLN* 1.3 73.9 - - - +
375B ILE* 1.3 63.0 + - - +
377B THR* 3.2 6.8 + - - -
378B GLU* 3.0 27.5 + - - +
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Residues in contact with ILE 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ALA* 4.1 6.3 - - + -
329B ILE* 3.6 25.4 - - + -
339B TYR* 3.5 35.4 - - + -
341B ILE* 3.8 29.4 - - + -
354B TYR* 3.6 20.9 - - + +
371B ALA* 2.8 25.7 + - + +
374B LYS* 1.3 72.1 - - - +
376B THR* 1.3 64.4 + - - +
378B GLU* 3.2 6.4 + - - +
379B SER* 2.9 28.8 + - - +
387B PRO* 4.3 0.4 - - + -
389B PHE* 3.7 22.9 - - + -
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Residues in contact with THR 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B VAL 2.9 19.4 + - - -
375B ILE* 1.3 75.3 - - - +
377B THR* 1.3 62.7 + - - +
379B SER* 3.2 2.4 + - - -
380B ILE* 3.0 26.1 + - + +
386B THR* 3.6 33.7 - - + -
387B PRO* 4.1 8.7 - - - -
389B PHE* 3.2 20.3 - - - -
410B TRP* 3.4 32.9 - - + -
412B PRO* 3.8 9.5 - - + +
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Residues in contact with THR 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B VAL* 5.8 0.9 - - + -
188B TYR* 5.0 8.6 + - + -
234B LEU* 3.8 39.3 - - + -
239B TRP* 4.8 5.2 - - + -
373B GLN 3.0 19.5 + - - -
374B LYS* 3.5 7.2 - - - +
375B ILE 3.2 0.2 - - - -
376B THR* 1.3 77.2 - - - +
378B GLU* 1.3 64.3 + - + +
380B ILE* 3.3 11.3 + - - +
381B VAL* 3.1 23.5 + - + +
410B TRP* 3.6 14.7 - - - -
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Residues in contact with GLU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TRP* 3.7 44.2 + - + +
339B TYR* 2.7 27.3 + - - -
341B ILE* 5.0 3.0 - - + +
350B LYS* 3.2 17.6 - - + +
354B TYR* 2.7 31.0 + - - -
374B LYS* 3.0 14.8 + - - +
375B ILE* 3.6 6.7 - - - +
377B THR* 1.3 77.1 - - + +
379B SER* 1.3 57.3 + - - +
381B VAL* 3.4 0.9 + - - +
382B ILE* 2.9 41.6 + - + +
383B TRP* 5.0 0.2 - - - -
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Residues in contact with SER 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LEU* 4.3 3.1 - - - -
341B ILE* 3.5 15.6 - - - +
375B ILE 2.9 16.1 + - - -
376B THR 3.6 1.3 - - - -
378B GLU* 1.3 76.3 - - - +
380B ILE* 1.3 57.2 + - - +
383B TRP* 2.8 45.1 + - - +
384B GLY 3.1 5.0 + - - -
385B LYS 3.1 20.1 + - - +
387B PRO* 3.4 29.4 - - - +
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Residues in contact with ILE 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B HIS* 3.3 5.0 - - - -
181B TYR* 4.0 10.3 - - + -
183B TYR* 3.8 41.1 - - + -
188B TYR* 3.8 26.2 - - + +
376B THR* 3.0 21.8 + - + +
377B THR* 3.7 4.5 - - - +
378B GLU 3.3 0.2 - - - -
379B SER* 1.3 77.1 - - - +
381B VAL* 1.3 60.1 + - - +
384B GLY* 2.7 28.1 + - - +
385B LYS 3.7 5.4 - - - +
386B THR* 3.8 21.8 - - + -
410B TRP* 3.6 36.1 - - + +
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Residues in contact with VAL 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B HIS* 3.0 21.1 + - - -
100B LEU* 4.2 19.1 - - + +
101B LYS* 3.7 36.2 + - + +
106B VAL* 4.9 3.4 - - + -
188B TYR* 4.1 19.1 - - + -
234B LEU* 4.0 25.6 - - + -
236B PRO* 4.1 7.2 - - + -
239B TRP* 3.8 21.1 - - + -
377B THR 3.1 16.9 + - - +
380B ILE* 1.3 77.3 - - - +
382B ILE* 1.3 58.8 + - - +
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Residues in contact with ILE 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B HIS* 3.0 13.1 + - - -
101B LYS* 4.1 40.6 + - + -
239B TRP* 4.0 25.1 - - + -
350B LYS* 4.1 25.6 - - + -
378B GLU* 2.9 25.5 + - + +
381B VAL* 1.3 78.2 - - - +
383B TRP* 1.3 98.8 + - + +
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Residues in contact with TRP 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B HIS* 3.6 18.4 - - - +
319B TYR* 3.3 69.8 + + + +
325B LEU* 3.8 18.4 - - + -
341B ILE* 3.9 28.7 - - + -
349B LEU* 3.7 29.0 - - + +
350B LYS* 4.1 22.0 - - + -
379B SER* 2.8 42.0 + - - +
382B ILE* 1.3 108.1 - - + +
384B GLY* 1.3 60.4 + - - +
385B LYS* 3.5 1.8 + - + +
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Residues in contact with GLY 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B HIS* 3.3 9.0 - - - -
181B TYR* 3.4 23.5 + - - -
183B TYR* 3.5 19.6 - - - -
379B SER 3.1 0.4 + - - -
380B ILE* 2.7 29.4 + - - -
383B TRP* 1.3 73.5 - - - +
385B LYS* 1.3 62.3 + - - +
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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
------------------------------------------------------------
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