Contacts of the helix formed by residues 358 - 381 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A LEU* 4.6 8.3 - - + -
268A PRO* 3.8 24.0 - - + +
271A ASP* 3.0 20.9 + - - +
356A VAL* 4.1 5.4 - - - -
357A LEU* 1.3 81.0 - - + +
359A HIS* 1.4 61.7 + - - +
360A ARG* 3.2 4.3 - - - -
361A VAL* 3.2 29.7 + - + +
362A VAL* 3.0 22.0 + - + +
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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
----------------------------------------------------------
351A PRO* 3.4 40.2 + - + +
352A ASP* 4.9 5.1 - - + -
356A VAL* 4.0 15.1 - - + +
357A LEU 3.0 10.7 + - - +
358A GLN* 1.4 74.1 - - - +
360A ARG* 1.3 61.0 + - + +
362A VAL* 4.7 0.2 - - - -
363A ASP* 2.9 36.8 + - + +
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Residues in contact with ARG 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A GLN 3.2 0.9 - - - -
359A HIS* 1.3 84.9 - - + +
361A VAL* 1.3 68.2 + - + +
363A ASP* 3.7 3.6 - - - +
364A GLN* 3.1 63.5 + - - +
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Residues in contact with VAL 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 4.2 11.7 - - + -
358A GLN* 3.2 35.6 + - + +
360A ARG* 1.3 81.5 - - + +
362A VAL* 1.3 58.6 + - - +
364A GLN* 3.3 12.4 + - + +
365A LEU* 2.9 51.1 + - + +
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Residues in contact with VAL 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 4.2 29.2 - - + -
271A ASP* 5.0 1.6 - - - +
275A LEU* 4.3 8.3 - - + -
349A PHE* 3.5 24.2 - - + +
350A SER 3.6 3.6 - - - +
351A PRO* 3.4 30.7 - - + -
356A VAL* 4.0 16.4 - - + -
358A GLN* 3.0 18.1 + - + +
359A HIS 4.0 2.9 - - - +
361A VAL* 1.3 72.7 - - - +
363A ASP* 1.3 58.9 + - - +
365A LEU* 3.0 9.3 + - - +
366A GLN* 2.8 28.1 + - - +
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Residues in contact with ASP 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A PRO* 3.6 26.9 - - + +
359A HIS* 2.9 31.7 + - + +
360A ARG* 3.7 4.2 - - - +
362A VAL* 1.3 74.2 - - - +
364A GLN* 1.3 62.1 + - - +
366A GLN* 3.4 6.8 + - - +
367A GLU* 3.0 29.2 + - - +
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Residues in contact with GLN 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A ARG* 3.1 69.5 + - - +
361A VAL* 3.5 10.0 - - - +
362A VAL 3.2 0.2 - - - -
363A ASP* 1.3 77.2 - - - +
365A LEU* 1.3 66.6 + - + +
367A GLU* 3.5 11.2 + - - +
368A GLN* 3.2 31.1 + - + +
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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
----------------------------------------------------------
150A MET* 6.2 1.3 - - + -
263A TYR* 3.8 41.3 - - + +
267A LEU* 4.5 5.2 - - + -
349A PHE* 3.7 36.6 - - + -
361A VAL* 2.9 37.6 + - + +
362A VAL* 3.0 7.4 + - - +
364A GLN* 1.3 73.4 - - + +
366A GLN* 1.3 66.6 + - - +
368A GLN* 3.1 10.6 + - + +
369A PHE* 3.0 31.4 + - + -
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Residues in contact with GLN 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ILE* 2.9 45.5 + - + +
349A PHE* 3.1 24.8 + - - +
350A SER* 3.6 14.6 + - - +
351A PRO* 3.4 16.9 - - + +
352A ASP* 5.4 0.6 + - - -
362A VAL 2.8 15.1 + - - +
363A ASP* 3.7 9.0 - - - +
365A LEU* 1.3 71.6 - - - +
367A GLU* 1.4 56.1 + - - +
369A PHE* 3.1 12.5 + - - +
370A ALA* 2.8 28.6 + - + +
394A MET* 5.9 2.7 - - + -
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Residues in contact with GLU 367 (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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363A ASP* 3.0 19.4 + - - +
364A GLN* 3.8 10.3 - - - +
365A LEU 3.3 0.2 - - - -
366A GLN* 1.4 74.9 - - - +
368A GLN* 1.3 64.7 + - - +
370A ALA* 3.2 7.0 + - + +
371A ILE* 2.8 56.1 + - + +
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Residues in contact with GLN 368 (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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146A GLU* 5.5 2.6 - - - +
150A MET* 3.9 18.8 - - + -
364A GLN* 3.2 15.1 + - + +
365A LEU* 3.1 13.3 + - + +
367A GLU* 1.3 96.8 + - - +
369A PHE* 1.3 53.0 + - - +
371A ILE* 3.9 20.2 - - - +
372A THR* 2.8 37.2 + - - -
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Residues in contact with PHE 369 (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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150A MET* 3.4 39.7 - - + -
154A LEU* 3.9 24.2 - - + -
261A ILE* 5.0 0.2 - - + -
263A TYR* 4.0 26.2 - + + -
342A LEU* 4.0 7.3 - - + +
345A ALA* 3.8 21.8 - - + -
346A ILE* 3.9 17.3 - - + -
349A PHE* 3.5 37.9 - + - -
365A LEU* 3.0 34.0 + - + -
366A GLN* 3.5 8.1 - - - +
368A GLN* 1.3 74.2 - - - +
370A ALA* 1.3 57.8 + - - +
372A THR* 3.2 3.8 + - - -
373A LEU* 2.9 28.6 + - - +
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Residues in contact with ALA 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ILE* 3.9 19.4 - - + +
366A GLN* 2.8 17.7 + - + +
367A GLU* 3.5 9.2 - - + +
369A PHE* 1.3 73.7 - - - +
371A ILE* 1.3 58.0 + - + +
373A LEU 3.2 1.2 + - - -
374A LYS* 2.9 26.2 + - - +
390A PHE* 3.4 26.1 - - + -
394A MET* 4.4 10.1 - - + -
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Residues in contact with ILE 371 (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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147A GLN* 3.9 16.4 - - - +
367A GLU* 2.8 45.1 + - + +
368A GLN* 3.9 26.0 - - - +
370A ALA* 1.3 72.5 - - + +
372A THR* 1.3 58.3 + - - +
374A LYS* 3.4 10.3 + - + +
375A SER* 2.8 38.0 + - - +
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Residues in contact with THR 372 (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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147A GLN* 3.8 34.6 + - + +
150A MET* 3.1 20.2 - - - +
151A ILE* 3.7 34.1 - - + -
342A LEU* 3.9 9.6 - - + -
368A GLN 2.8 21.7 + - - -
369A PHE 3.2 5.8 + - - -
371A ILE* 1.3 76.2 - - - +
373A LEU* 1.3 57.5 + - - +
375A SER* 3.3 2.4 + - - -
376A TYR* 2.8 28.9 + - - +
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Residues in contact with LEU 373 (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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339A GLU* 4.1 23.8 - - + -
342A LEU* 3.8 32.5 - - + +
343A MET* 4.9 3.1 - - + -
346A ILE* 3.7 23.1 - - + -
369A PHE 2.9 14.6 + - - +
370A ALA 3.2 8.3 + - - +
372A THR* 1.3 76.8 - - - +
374A LYS* 1.3 62.9 + - - +
376A TYR* 3.3 2.6 + - + +
377A ILE* 3.0 42.7 + - + +
390A PHE* 3.9 17.3 - - + -
393A ILE* 3.9 28.5 - - + -
394A MET* 4.9 0.4 - - - -
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Residues in contact with LYS 374 (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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370A ALA 2.9 16.2 + - - +
371A ILE* 3.6 10.3 - - + +
373A LEU* 1.3 75.9 - - - +
375A SER* 1.3 57.2 + - - +
377A ILE* 3.4 3.6 + - - +
378A GLU* 3.0 48.5 + - + +
390A PHE* 3.8 48.1 - - + -
391A LEU* 5.5 6.1 - - - +
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Residues in contact with SER 375 (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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143A LEU 4.4 7.2 - - - -
147A GLN* 3.3 29.1 + - - -
371A ILE* 2.8 27.0 + - - +
372A THR 3.6 3.6 - - - -
374A LYS* 1.3 73.0 - - - +
376A TYR* 1.3 65.6 + - - +
378A GLU* 3.1 15.5 + - - +
379A CYS* 2.9 31.1 + - - -
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Residues in contact with TYR 376 (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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143A LEU 5.5 1.8 - - - +
151A ILE* 3.8 25.8 - - + -
336A HIS* 2.8 27.7 + + - -
338A GLU* 3.5 39.3 + - + -
339A GLU* 3.6 36.8 - - + -
342A LEU* 4.6 3.4 - - + -
372A THR 2.8 21.0 + - - +
373A LEU* 3.3 7.8 + - + +
375A SER* 1.3 72.8 - - - +
377A ILE* 1.3 59.4 + - + +
379A CYS* 3.4 2.4 + - - -
380A ASN* 2.9 66.6 + - + +
381A ARG* 5.0 0.2 - - - -
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Residues in contact with ILE 377 (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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339A GLU* 3.5 19.1 - - - +
373A LEU* 3.0 34.7 + - + +
374A LYS* 3.6 7.6 - - - +
376A TYR* 1.3 77.3 - - + +
378A GLU* 1.3 59.0 + - + +
381A ARG* 2.9 48.3 + - + +
386A HIS* 4.0 20.2 - - + +
389A LEU* 4.0 17.7 - - + -
390A PHE* 3.7 36.6 - - + +
393A ILE* 4.0 6.5 - - + -
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Residues in contact with GLU 378 (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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374A LYS* 3.0 43.8 + - + +
375A SER* 3.1 14.8 + - - +
377A ILE* 1.3 79.5 - - + +
379A CYS* 1.3 63.7 + - - +
381A ARG 4.1 9.6 - - - +
382A PRO 4.9 2.6 - - - +
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Residues in contact with CYS 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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143A LEU* 3.5 48.0 - - + -
375A SER* 2.9 23.4 + - - +
376A TYR* 3.9 3.8 - - - +
378A GLU* 1.3 81.7 - - - +
380A ASN* 1.3 68.1 + - - +
381A ARG 3.5 0.6 - - - -
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Residues in contact with ASN 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A HIS* 4.9 8.3 - - + -
376A TYR* 2.9 75.3 + - + +
379A CYS* 1.3 80.5 - - - +
381A ARG* 1.3 66.9 + - + +
382A PRO* 3.5 10.7 - - - +
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Residues in contact with ARG 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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333A LEU 4.3 3.8 + - - -
334A GLN 3.4 22.8 + - - -
335A LEU* 4.0 1.8 - - - +
336A HIS* 3.6 23.7 + - + -
339A GLU* 2.7 41.7 + - - -
377A ILE* 2.9 28.7 + - - +
378A GLU* 4.1 6.6 - - - +
379A CYS 3.5 1.2 - - - -
380A ASN* 1.3 86.7 - - + +
382A PRO* 1.4 73.3 - - + +
383A GLN* 3.1 6.1 + - - +
386A HIS* 3.2 48.0 + - + +
389A LEU* 3.5 23.4 - - - +
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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