Contacts of the helix formed by residues 368 - 383 (chain A) in PDB entry 1N54
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 ILE 368 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A TRP* 5.0 6.5 - - + -
367A HIS* 1.3 78.0 - - + +
369A ASP* 1.3 71.0 + - + +
370A VAL* 3.3 23.6 - - + +
371A MET* 2.7 25.3 + - + +
372A TYR* 3.9 2.9 + - - -
1558A GOL 3.2 30.7 - - - +
62B LYS 3.5 11.7 - - - +
63B SER* 3.8 4.3 - - - -
96B ASN* 3.7 23.8 - - - +
100B TYR* 3.6 31.4 - - + +
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Residues in contact with ASP 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A LEU* 4.4 10.8 - - + +
365A PRO* 3.8 21.7 - - - +
367A HIS 3.9 2.1 + - - +
368A ILE* 1.3 74.4 - - + +
370A VAL* 1.3 62.7 + - - +
371A MET 3.0 1.6 + - - -
372A TYR* 3.0 26.3 + - - +
373A THR* 3.5 10.7 + - - -
412A ARG* 3.2 32.1 - - + +
415A ASN* 5.6 5.4 - - + +
62B LYS 5.8 1.1 - - - +
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Residues in contact with VAL 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ILE* 3.3 35.8 - - + +
369A ASP* 1.3 75.0 - - - +
371A MET* 1.3 66.8 + - - +
373A THR* 3.1 17.1 + - - -
374A THR* 3.1 17.4 + - + -
419A HIS* 4.2 22.4 - - + -
62B LYS* 3.5 25.4 + - + +
63B SER* 4.5 3.6 - - - -
100B TYR* 3.9 24.7 - - + -
101B ILE* 4.6 13.2 - - + -
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Residues in contact with MET 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ILE* 3.7 15.0 - - + -
326A TRP* 4.0 12.6 - - + +
329A ARG* 5.6 3.5 - - + +
332A CYS* 5.9 0.2 - - - -
367A HIS* 3.4 40.4 - - + -
368A ILE* 2.7 34.3 + - + +
370A VAL* 1.3 76.4 - - - +
372A TYR* 1.3 80.5 + - + +
374A THR* 2.7 20.5 + - - -
375A LEU* 3.0 35.9 + - - +
100B TYR* 3.4 36.6 - - + +
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Residues in contact with TYR 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ILE* 5.3 3.8 - - + -
355A ILE* 3.9 31.2 - - + -
358A GLU* 2.5 44.0 + - + -
359A LEU* 3.7 39.3 - - + -
365A PRO* 4.0 10.8 - - + -
366A PRO* 3.4 4.9 - - - +
367A HIS* 3.3 22.9 + - + -
368A ILE 4.1 10.3 - - - -
369A ASP* 3.0 18.2 + - - +
371A MET* 1.3 96.2 - - + +
373A THR* 1.3 68.1 + - - +
375A LEU* 3.1 9.8 + - + +
376A LEU* 3.0 28.9 + - + +
416A TRP* 5.1 1.8 - - + -
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Residues in contact with THR 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ASP 3.5 10.8 + - - -
370A VAL* 3.1 10.9 + - - -
372A TYR* 1.3 81.6 - - - +
374A THR* 1.3 62.4 + - + +
376A LEU* 3.5 4.2 + - - +
377A ILE* 3.3 29.2 + - + +
415A ASN 5.4 0.2 + - - -
416A TRP* 3.5 38.6 + - + +
419A HIS* 3.9 38.9 + - + +
420A HIS* 3.9 13.6 + - + +
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Residues in contact with THR 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ARG* 3.8 15.5 - - - +
370A VAL* 3.1 13.0 + - + +
371A MET* 2.7 21.5 + - - -
373A THR* 1.3 77.4 - - + +
375A LEU* 1.3 57.8 + - - +
377A ILE* 3.1 15.4 + - + +
378A GLU* 2.9 31.5 + - - +
419A HIS* 5.7 4.0 - - + +
100B TYR* 2.7 45.1 - - + +
104B THR* 3.8 14.6 - - + -
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Residues in contact with LEU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ILE* 4.1 10.3 - - + -
329A ARG* 4.3 21.5 - - + +
332A CYS* 3.9 31.4 - - - -
333A ALA* 4.4 7.4 - - + +
336A LEU* 4.9 6.1 - - + -
355A ILE* 4.6 13.7 - - + -
371A MET* 3.0 39.3 + - + +
372A TYR* 3.5 8.7 - - + +
374A THR* 1.3 73.2 + - - +
376A LEU* 1.3 69.1 + - + +
378A GLU* 2.8 10.9 + - + +
379A LEU* 2.8 40.0 + - + +
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Residues in contact with LEU 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A VAL* 4.8 9.0 - - + -
355A ILE* 3.2 44.0 - - + -
356A PHE* 4.5 8.3 - - + -
359A LEU* 6.5 0.4 - - + -
372A TYR* 3.0 13.8 + - + +
373A THR 3.6 7.4 - - - +
375A LEU* 1.3 78.4 - - - +
377A ILE* 1.3 64.9 + - + +
379A LEU* 3.0 12.9 + - + +
380A CYS* 2.9 27.4 + - - -
387A LEU* 4.4 7.7 - - + +
391A LEU* 4.5 26.5 - - + -
416A TRP* 3.8 36.3 - - + +
420A HIS* 5.5 2.5 - - + -
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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
----------------------------------------------------------
373A THR* 3.3 25.4 - - + +
374A THR* 3.1 21.4 + - + +
376A LEU* 1.3 74.9 - - - +
378A GLU* 1.3 65.4 + - - +
380A CYS* 3.3 10.6 + - - +
381A LYS* 3.1 33.2 + - + +
420A HIS* 4.1 9.4 - - - +
423A ASN* 3.9 37.2 - - + +
424A PHE* 3.8 28.2 - - + -
104B THR* 5.7 2.5 - - + -
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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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329A ARG* 3.9 39.2 + - + +
330A LYS* 3.0 37.7 - - - +
333A ALA* 4.4 15.7 - - + +
374A THR 2.9 16.0 + - - +
375A LEU* 2.8 10.8 + - - +
377A ILE* 1.3 78.5 - - - +
379A LEU* 1.3 63.2 + - - +
381A LYS* 2.8 45.6 + - - +
382A LEU* 2.9 14.9 + - - +
14B TYR* 4.6 2.0 + - - -
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Residues in contact with LEU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ALA* 4.2 17.5 - - + +
336A LEU* 4.7 3.4 - - + -
337A VAL* 3.6 30.7 - - + -
351A ILE* 3.6 33.0 - - + -
355A ILE* 3.9 18.4 - - + -
375A LEU* 2.8 28.2 + - + +
376A LEU* 3.0 12.8 + - + +
378A GLU* 1.3 76.9 - - - +
380A CYS* 1.3 63.4 + - - +
382A LEU* 3.0 5.6 + - + +
383A GLN* 2.9 26.4 + - + +
387A LEU* 3.8 22.3 - - + +
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Residues in contact with CYS 380 (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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376A LEU 2.9 18.0 + - - -
377A ILE* 3.5 11.2 - - - +
379A LEU* 1.3 76.8 - - - +
381A LYS* 1.3 63.3 + - + +
383A GLN 4.5 0.2 - - - -
384A PRO* 3.4 25.6 - - - +
387A LEU* 3.8 25.5 - - - +
388A PRO* 4.6 11.3 - - + +
391A LEU* 4.1 15.7 - - - -
420A HIS* 4.9 1.6 - - - -
424A PHE* 4.7 11.2 - - + -
1560A GOL 3.8 25.4 - - - +
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Residues in contact with LYS 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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330A LYS* 6.1 0.6 - - - +
377A ILE* 3.1 23.9 + - + +
378A GLU* 2.8 37.4 + - - +
380A CYS* 1.3 79.3 - - + +
382A LEU* 1.3 63.6 + - - +
384A PRO* 3.3 17.3 - - - +
424A PHE* 6.1 1.8 - - + -
103B GLY 5.9 1.0 + - - -
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Residues in contact with LEU 382 (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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330A LYS* 5.7 6.3 - - - +
333A ALA* 3.7 15.3 - - + -
334A ALA* 3.7 37.0 - - + +
337A VAL* 3.9 22.4 - - + -
378A GLU 2.9 11.5 + - - +
379A LEU* 3.0 8.7 + - - +
381A LYS* 1.3 78.2 - - - +
383A GLN* 1.3 64.5 + - + +
384A PRO* 3.2 7.8 - - - +
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Residues in contact with GLN 383 (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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337A VAL* 4.2 35.6 - - + +
348A ASN* 4.8 8.5 + - - +
379A LEU* 2.9 10.9 + - + +
380A CYS 3.5 3.5 - - - +
382A LEU* 1.3 83.0 - - + +
384A PRO* 1.3 65.6 - - - +
385A GLY* 3.2 4.6 + - - -
386A SER* 3.7 24.3 + - - +
387A LEU* 3.3 12.1 + - + +
388A PRO* 3.2 16.8 - - - +
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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