Contacts of the helix formed by residues 358 - 381 (chain B) in PDB entry 5A86
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 GLN 358 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B LEU* 4.6 9.4 - - + -
268B PRO* 3.9 24.7 - - + -
271B ASP* 2.9 19.1 + - - +
356B VAL* 4.0 4.7 - - - -
357B LEU* 1.3 81.2 + - + +
359B HIS* 1.3 62.3 + - - +
360B ARG* 3.0 5.9 + - - -
361B VAL* 3.1 27.9 + - + +
362B VAL* 3.0 21.4 + - + +
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Residues in contact with HIS 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B PRO* 3.1 38.6 + - + +
352B ASP* 4.7 5.9 + - - +
356B VAL* 3.8 18.9 - - - +
357B LEU 3.0 10.1 + - - +
358B GLN* 1.3 75.0 - - - +
360B ARG* 1.4 62.4 + - - +
362B VAL* 4.1 1.8 - - - -
363B ASP* 3.1 33.3 + - + +
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Residues in contact with ARG 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B GLN* 3.0 2.1 + - - -
359B HIS* 1.4 85.0 + - - +
361B VAL* 1.3 70.0 + - + +
363B ASP* 3.0 33.2 + - - +
364B GLN* 3.1 39.3 + - - +
367B GLU* 6.3 0.8 - - - -
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Residues in contact with VAL 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 4.3 11.4 - - + -
358B GLN* 3.1 31.0 + - + +
360B ARG* 1.3 79.7 - - + +
362B VAL* 1.3 56.7 + - - +
364B GLN* 3.2 18.0 + - + +
365B LEU* 2.9 51.6 + - + +
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Residues in contact with VAL 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 4.2 28.0 - - + -
271B ASP* 5.0 1.1 - - - +
275B LEU* 4.3 8.5 - - + -
349B PHE* 3.5 23.3 - - + +
350B SER 3.6 3.8 - - - +
351B PRO* 3.4 30.7 - - + -
356B VAL* 4.0 16.4 - - + -
358B GLN* 3.0 17.5 + - + +
359B HIS* 4.1 4.0 - - - +
361B VAL* 1.3 74.8 - - - +
363B ASP* 1.3 56.8 + - - +
365B LEU* 3.1 9.6 + - - +
366B GLN* 2.8 28.2 + - - +
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Residues in contact with ASP 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B PRO* 3.5 27.9 - - + +
359B HIS* 3.1 27.4 + - - +
360B ARG* 3.0 37.6 + - - +
362B VAL* 1.3 74.7 - - - +
364B GLN* 1.3 62.0 + - - +
366B GLN* 3.5 6.6 + - - +
367B GLU* 3.1 24.1 + - - +
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Residues in contact with GLN 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B ARG* 3.1 33.9 + - - +
361B VAL* 3.5 18.8 - - + +
363B ASP* 1.3 73.8 - - - +
365B LEU* 1.3 72.6 + - + +
367B GLU* 3.5 8.6 + - - +
368B GLN* 3.2 35.6 + - + +
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Residues in contact with LEU 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B MET* 6.2 1.6 - - + -
263B TYR* 3.8 41.7 - - + +
267B LEU* 4.6 4.7 - - + -
349B PHE* 3.6 36.3 - - + -
361B VAL* 2.9 39.0 + - + +
362B VAL* 3.5 8.1 - - - +
364B GLN* 1.3 79.3 - - + +
366B GLN* 1.3 66.1 + - - +
368B GLN* 3.1 10.6 + - + +
369B PHE* 3.1 31.7 + - + -
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Residues in contact with GLN 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ILE* 2.9 45.2 + - + +
347B SER* 5.2 0.2 - - - +
349B PHE* 3.1 25.3 + - - +
350B SER* 3.6 14.6 + - - +
351B PRO* 3.4 17.5 - - + +
352B ASP* 5.4 0.8 + - - -
362B VAL 2.8 11.5 + - - +
363B ASP* 3.8 8.7 - - - +
365B LEU* 1.3 75.4 - - - +
367B GLU* 1.3 57.4 + - - +
369B PHE* 3.2 12.1 + - - +
370B ALA* 2.9 29.6 + - + +
394B MET* 6.1 1.8 - - + -
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Residues in contact with GLU 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B ARG* 6.3 0.9 - - - -
363B ASP* 3.1 18.5 + - - +
364B GLN* 3.7 8.3 - - - +
366B GLN* 1.3 74.7 - - - +
368B GLN* 1.3 70.4 + - - +
370B ALA* 3.2 7.0 + - - +
371B ILE* 2.8 52.0 + - + +
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Residues in contact with GLN 368 (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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150B MET* 4.0 18.2 - - + -
364B GLN* 3.2 21.7 + - + +
365B LEU* 3.1 12.2 + - + +
367B GLU* 1.3 96.9 + - - +
369B PHE* 1.3 58.5 + - - +
371B ILE* 3.5 20.6 + - - +
372B THR* 2.8 32.9 + - - -
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Residues in contact with PHE 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B MET* 3.4 39.9 - - + -
154B LEU* 3.9 25.4 - - + -
263B TYR* 4.1 24.7 - + - -
342B LEU* 4.0 7.3 - - + +
345B ALA* 3.8 20.4 - - + -
346B ILE* 3.9 17.4 - - + +
349B PHE* 3.4 38.8 - + - -
365B LEU* 3.1 34.4 + - + -
366B GLN* 3.5 8.1 - - - +
368B GLN* 1.3 74.6 - - - +
370B ALA* 1.3 57.7 + - - +
372B THR* 3.3 3.7 + - - -
373B LEU* 2.9 28.8 + - - +
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Residues in contact with ALA 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ILE* 3.9 13.6 - - + +
366B GLN* 2.9 14.1 + - + +
367B GLU* 3.2 11.6 + - + +
369B PHE* 1.3 74.5 - - - +
371B ILE* 1.3 59.2 + - + +
373B LEU 3.2 1.2 + - - -
374B LYS* 2.9 25.6 + - - +
390B PHE* 3.3 19.2 - - + -
394B MET* 4.2 24.5 - - + -
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Residues in contact with ILE 371 (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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147B GLN* 3.9 16.6 - - - +
367B GLU* 2.8 46.8 + - + +
368B GLN* 3.8 25.4 - - - +
370B ALA* 1.3 71.7 - - + +
372B THR* 1.3 57.0 + - - +
374B LYS* 3.4 10.5 + - + +
375B SER* 2.9 35.8 + - - +
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Residues in contact with THR 372 (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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143B LEU* 5.1 1.1 - - + +
147B GLN* 3.8 33.5 + - + +
150B MET* 3.2 21.9 - - - +
151B ILE* 3.6 33.9 - - + -
342B LEU* 4.0 10.1 - - + -
368B GLN 2.8 21.7 + - - -
369B PHE* 3.5 5.4 - - - -
371B ILE* 1.3 77.0 - - - +
373B LEU* 1.3 55.7 + - - +
375B SER* 3.3 1.7 + - - -
376B TYR* 2.8 28.8 + - - +
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Residues in contact with LEU 373 (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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339B GLU* 4.1 24.5 - - + +
342B LEU* 3.7 32.5 - - + +
343B MET* 4.8 3.6 - - + -
346B ILE* 3.8 22.0 - - + -
369B PHE 2.9 13.6 + - - +
370B ALA* 3.2 8.0 + - - +
372B THR* 1.3 77.0 - - - +
374B LYS* 1.3 61.9 + - - +
376B TYR* 3.3 2.1 + - + +
377B ILE* 3.0 43.0 + - + +
390B PHE* 3.9 17.3 - - + -
393B ILE* 3.8 27.8 - - + -
394B MET* 4.7 0.4 - - - -
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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
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370B ALA 2.9 15.7 + - - +
371B ILE* 3.6 9.9 - - + +
373B LEU* 1.3 75.9 - - - +
375B SER* 1.3 56.9 + - - +
377B ILE* 3.4 3.5 + - - +
378B GLU* 3.0 55.5 + - + +
390B PHE* 3.7 43.9 - - + +
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Residues in contact with SER 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 4.8 6.3 - - - -
147B GLN* 3.3 29.0 + - - -
371B ILE* 2.9 26.5 + - - +
372B THR 3.6 3.8 - - - -
374B LYS* 1.3 73.4 - - - +
376B TYR* 1.3 65.6 + - - +
378B GLU* 3.2 12.6 + - - +
379B CYS* 2.9 32.0 + - - -
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Residues in contact with TYR 376 (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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143B LEU* 4.3 13.1 - - + +
151B ILE* 3.8 26.9 - - + -
336B HIS* 2.8 29.5 + + - -
338B GLU* 3.4 37.3 + - + -
339B GLU* 3.6 36.3 - - + -
342B LEU* 4.5 4.3 - - + -
372B THR 2.8 20.5 + - - +
373B LEU* 3.3 8.3 + - + +
375B SER* 1.3 71.7 - - - +
377B ILE* 1.3 65.3 + - + +
379B CYS* 3.3 1.7 + - - +
380B ASN* 3.0 58.8 + - + +
381B ARG* 5.2 0.2 - - - -
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Residues in contact with ILE 377 (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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339B GLU* 3.5 18.6 - - - +
373B LEU* 3.0 34.7 + - + +
374B LYS* 3.6 7.9 - - - +
375B SER 3.2 0.2 - - - -
376B TYR* 1.3 76.8 - - + +
378B GLU* 1.3 57.8 + - + +
381B ARG* 2.8 53.8 + - + +
386B HIS 5.0 2.9 - - - +
389B LEU* 4.0 18.6 - - + +
390B PHE* 3.7 37.5 - - + +
393B ILE* 4.0 13.5 - - + -
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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
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141B GLN 5.4 2.0 + - - -
374B LYS* 3.0 56.7 + - + +
375B SER* 3.5 12.0 + - - +
377B ILE* 1.3 78.6 - - + +
379B CYS* 1.3 64.1 + - - +
380B ASN 3.6 0.3 + - - -
381B ARG 4.3 5.5 + - - -
382B PRO* 5.2 2.8 - - - +
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Residues in contact with CYS 379 (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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141B GLN* 3.4 38.2 + - - +
142B GLY 3.1 39.3 - - - +
143B LEU* 3.5 28.7 - - + -
375B SER* 2.9 22.2 + - - +
376B TYR 3.9 2.7 - - - +
378B GLU* 1.3 79.0 - - - +
380B ASN* 1.3 62.1 + - - +
381B ARG 3.9 0.2 - - - -
382B PRO* 5.3 2.1 - - - +
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Residues in contact with ASN 380 (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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141B GLN* 3.9 10.6 + - - -
143B LEU* 4.8 4.6 - - - +
336B HIS* 4.8 7.3 - - + -
376B TYR* 3.0 61.1 + - + +
379B CYS* 1.3 89.6 - - - +
381B ARG* 1.3 72.3 + - + +
382B PRO* 3.3 12.9 - - - +
383B GLN* 3.9 4.9 + - - -
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Residues in contact with ARG 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LEU 4.3 3.2 + - - -
334B GLN 3.2 23.6 + - - -
335B LEU* 3.9 2.0 - - - +
336B HIS* 3.0 32.8 + - - -
339B GLU* 2.9 34.7 + - - +
377B ILE* 2.8 47.5 + - + +
378B GLU* 4.3 2.6 + - - -
379B CYS 3.9 0.4 - - - -
380B ASN* 1.3 86.3 - - + +
382B PRO* 1.4 63.0 - - - +
383B GLN* 3.3 7.8 + - - +
386B HIS* 3.6 50.8 + - + +
389B LEU* 3.9 15.2 - - + +
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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