Contacts of the helix formed by residues 365 - 385 (chain A) in PDB entry 1NM8
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 THR 365 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A THR* 5.3 0.7 - - - +
248A ASP* 6.6 0.2 - - + -
363A ASN* 3.8 6.6 + - + +
364A ILE* 1.3 79.7 - - - +
366A PRO* 1.3 77.9 - - + +
367A GLU* 3.6 11.4 + - - +
368A ILE* 3.1 31.7 + - + +
369A LYS* 2.9 22.4 + - - +
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Residues in contact with PRO 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A THR* 1.3 88.7 - - + +
367A GLU* 1.3 61.4 + - + +
369A LYS* 3.3 8.2 + - + +
370A SER* 2.9 33.1 + - - -
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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
----------------------------------------------------------
244A THR* 3.9 24.2 - - + +
247A LYS* 5.4 7.1 + - - +
365A THR* 3.2 9.6 + - - +
366A PRO* 1.3 83.8 - - + +
368A ILE* 1.3 62.5 + - - +
370A SER* 3.2 9.6 + - - -
371A ASP* 3.1 27.2 + - - +
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Residues in contact with ILE 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A VAL* 5.5 0.4 - - + -
230A LEU* 4.7 6.1 - - + -
241A ALA 5.9 0.4 - - - +
244A THR* 4.1 19.7 - - + +
245A LEU* 4.1 27.8 - - + -
248A ASP* 6.1 0.2 - - + -
251A ASN* 3.7 14.8 - - - +
363A ASN 3.5 24.9 - - - +
364A ILE* 4.1 13.2 - - + -
365A THR* 3.1 26.5 + - + +
367A GLU* 1.3 73.4 - - - +
369A LYS* 1.3 67.0 + - - +
371A ASP* 3.1 10.5 + - + +
372A ILE* 2.9 38.8 + - + +
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Residues in contact with LYS 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLU* 2.7 41.1 + - + +
364A ILE* 4.0 11.1 - - + +
365A THR 2.9 16.5 + - - +
366A PRO* 3.6 9.6 - - + +
368A ILE* 1.3 76.3 - - - +
370A SER* 1.3 58.9 + - - +
372A ILE* 3.1 8.3 + - + +
373A GLU* 2.9 61.8 + - + +
376A LYS* 4.5 3.4 - - - +
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Residues in contact with SER 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A PRO* 2.9 17.6 + - - +
367A GLU* 3.4 11.8 - - - -
368A ILE 3.2 0.2 - - - -
369A LYS* 1.3 78.1 - - - +
371A ASP* 1.3 62.4 + - - +
373A GLU* 3.4 7.9 + - - +
374A LYS* 3.1 42.1 + - - +
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Residues in contact with ASP 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LEU* 3.4 22.2 - - + +
233A ASN* 5.0 1.4 + - - -
240A LYS* 3.0 25.1 + - - -
241A ALA* 3.5 28.9 - - + +
244A THR* 4.4 11.8 + - - +
367A GLU* 3.1 20.1 + - - +
368A ILE* 3.1 10.7 + - - +
370A SER* 1.3 74.8 - - - +
372A ILE* 1.3 60.5 + - - +
374A LYS* 3.3 15.6 + - - +
375A ALA* 2.9 24.4 + - - +
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Residues in contact with ILE 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLU* 3.8 40.6 - - + +
226A PRO* 4.1 23.3 - - + +
227A VAL* 4.2 19.1 - - + -
229A ILE* 4.2 1.7 - - + +
230A LEU* 3.7 24.7 - - + -
364A ILE* 4.4 2.9 - - + -
368A ILE* 2.9 31.4 + - + +
369A LYS* 3.1 10.3 + - - +
371A ASP* 1.3 77.4 - - - +
373A GLU* 1.3 65.2 + - - +
375A ALA* 3.2 4.0 + - - +
376A LYS* 3.0 30.5 + - - +
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Residues in contact with GLU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A LYS* 2.9 55.9 + - + +
370A SER* 3.8 8.1 - - - +
371A ASP 3.3 0.2 - - - -
372A ILE* 1.3 77.1 - - - +
374A LYS* 1.3 63.7 + - + +
376A LYS* 2.9 33.7 + - - +
377A GLN* 3.1 40.7 + - - +
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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
----------------------------------------------------------
233A ASN* 4.1 8.2 + - - +
240A LYS* 5.4 6.3 - - - +
370A SER* 3.1 30.1 + - - +
371A ASP* 3.7 16.9 + - - +
373A GLU* 1.3 77.6 - - + +
375A ALA* 1.3 62.5 + - - +
377A GLN* 3.4 16.0 + - - +
378A ASN* 3.0 24.8 + - - +
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Residues in contact with ALA 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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229A ILE* 3.7 30.1 - - + +
230A LEU* 4.0 12.6 - - + -
232A SER* 4.3 2.6 + - - +
233A ASN* 3.6 23.2 - - + +
371A ASP 2.9 17.0 + - - +
372A ILE 3.2 5.4 + - - +
374A LYS* 1.3 78.7 - - - +
376A LYS* 1.3 60.9 + - - +
378A ASN* 3.4 1.6 + - - +
379A LEU* 3.0 26.5 + - - +
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Residues in contact with LYS 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLU* 4.9 1.8 + - - -
226A PRO* 4.3 17.9 - - + +
229A ILE* 3.9 20.0 - - + -
293A SER* 3.7 34.6 - - - +
369A LYS* 4.5 4.8 - - - +
372A ILE* 3.0 22.4 + - + +
373A GLU* 2.9 44.8 + - - +
375A ALA* 1.3 76.5 - - - +
377A GLN* 1.3 63.2 + - + +
379A LEU* 3.5 1.6 + - - +
380A SER* 2.9 30.0 + - - -
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Residues in contact with GLN 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLU* 3.1 31.2 + - - +
374A LYS* 3.7 15.1 - - - +
375A ALA 3.3 0.2 - - - -
376A LYS* 1.3 75.3 - - + +
378A ASN* 1.3 64.9 + - - +
380A SER* 3.4 6.0 + - - -
381A ILE* 3.2 32.1 + - + +
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Residues in contact with ASN 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PRO* 4.6 3.7 - - - +
232A SER 3.9 8.1 - - - +
233A ASN* 3.3 29.0 + - - +
234A HIS* 4.4 5.9 + - - +
374A LYS 3.0 16.9 + - - +
375A ALA 3.8 4.1 - - - +
377A GLN* 1.3 76.8 - - - +
379A LEU* 1.3 62.1 + - - +
381A ILE* 3.3 12.1 + - - +
382A MET* 3.1 49.1 + - - +
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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
----------------------------------------------------------
94A VAL* 4.1 15.9 - - + -
229A ILE* 3.9 11.7 - - + -
232A SER* 3.7 25.4 - - - +
289A HIS* 4.3 3.1 - - + +
293A SER 5.1 2.7 - - - +
297A SER* 3.4 36.1 - - - +
302A PHE* 5.5 0.7 - - + -
375A ALA 3.0 18.1 + - - +
376A LYS 4.0 2.9 - - - +
378A ASN* 1.3 74.6 + - - +
380A SER* 1.3 62.4 + - - +
382A MET* 3.1 29.9 + - + +
383A ILE* 2.8 46.9 + - + +
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Residues in contact with SER 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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292A GLY* 6.1 0.7 - - - -
293A SER* 3.9 20.3 + - - +
376A LYS 2.9 22.8 + - - -
377A GLN* 3.7 7.4 - - - -
378A ASN 3.3 0.2 - - - -
379A LEU* 1.3 76.6 - - - +
381A ILE* 1.3 64.8 + - - +
383A ILE* 3.3 6.3 + - - +
384A GLN* 2.9 48.7 + - - +
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Residues in contact with ILE 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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377A GLN* 3.2 18.1 + - + +
378A ASN* 3.5 11.2 - - - +
379A LEU 3.2 0.2 - - - -
380A SER* 1.3 77.4 - - - +
382A MET* 1.3 66.0 + - + +
384A GLN* 3.5 11.4 + - - +
385A ASP* 3.2 24.6 + - + +
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Residues in contact with MET 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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92A PRO* 3.7 17.9 - - + -
94A VAL* 3.2 34.3 - - + +
95A ILE* 4.0 12.1 - - + +
96A TYR* 3.5 34.0 + - + +
232A SER 4.1 2.7 - - - +
378A ASN* 3.1 41.1 + - - +
379A LEU* 3.1 27.5 + - + +
381A ILE* 1.3 79.4 - - + +
383A ILE* 1.3 62.1 + - - +
385A ASP* 3.2 14.1 + - - +
386A LEU* 3.3 13.7 + - - +
571A TYR* 5.8 1.6 - - - -
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Residues in contact with ILE 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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95A ILE* 4.5 5.2 - - + -
289A HIS* 3.4 45.6 - - + +
291A GLY 4.2 9.6 - - - +
292A GLY* 3.4 34.8 - - - +
297A SER* 3.8 2.9 - - - +
379A LEU* 2.8 42.1 + - + +
380A SER* 3.9 4.9 - - - +
382A MET* 1.3 69.9 - - - +
384A GLN* 1.3 70.0 + - + +
386A LEU* 3.1 22.0 + - - +
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Residues in contact with GLN 384 (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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380A SER* 2.9 46.8 + - - +
381A ILE* 3.9 10.6 + - - +
383A ILE* 1.3 80.5 - - + +
385A ASP* 1.3 57.4 + - - +
386A LEU 3.4 0.6 - - - +
572A ASN* 3.0 19.6 + - - +
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Residues in contact with ASP 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 5.7 1.4 + - - +
381A ILE* 3.2 18.6 + - + +
382A MET* 3.8 6.1 - - - +
383A ILE 3.1 1.0 - - - -
384A GLN* 1.3 77.7 - - - +
386A LEU* 1.3 56.5 + - - +
571A TYR* 3.2 24.5 - - + +
572A ASN* 2.8 32.0 + - - +
573A SER* 2.7 50.3 + - - -
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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
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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