Contacts of the helix formed by residues 346 - 360 (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 PRO 346 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297A ASP* 3.8 23.1 - - + +
301A PRO* 3.8 30.1 - - + +
302A VAL 4.4 0.2 - - - -
303A MET* 4.0 31.6 - - + +
345A ILE* 1.3 82.6 - - + +
347A LEU* 1.3 64.1 + - - +
348A ASN* 3.2 4.3 - - - +
349A TYR* 3.0 19.8 + - + -
350A HIS* 3.2 32.0 + - - +
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Residues in contact with LEU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LEU* 4.2 14.8 - - + -
336A LEU 3.6 9.6 - - - +
337A VAL* 3.1 30.7 - - + +
339A TYR* 4.0 32.1 - - + +
345A ILE* 3.2 18.2 + - + +
346A PRO* 1.3 70.3 - - - +
348A ASN* 1.3 60.6 + - - +
350A HIS* 3.5 8.2 - - + +
351A ILE* 2.6 60.7 + - + +
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Residues in contact with ASN 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A VAL* 5.8 2.1 - - - +
346A PRO* 3.1 2.2 + - - +
347A LEU* 1.3 83.2 - - - +
349A TYR* 1.3 61.5 + - + +
351A ILE* 3.2 8.6 + - - +
352A VAL* 3.0 32.4 + - - +
383A GLN* 4.8 11.5 + - - +
386A SER* 3.0 37.5 + - - -
387A LEU* 3.7 19.6 - - + +
390A VAL* 4.1 20.6 - - + +
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Residues in contact with TYR 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A PHE* 3.2 29.9 - + + -
296A ASP* 4.6 2.9 - - + -
297A ASP* 3.8 45.9 + - + +
303A MET* 4.0 21.3 - - + -
346A PRO* 3.0 14.2 + - + +
348A ASN* 1.3 75.4 - - + +
350A HIS* 1.3 60.7 + - - +
352A VAL* 4.7 0.4 - - - -
353A GLU* 2.9 31.5 + - - +
389A GLN* 5.5 0.7 - - - +
390A VAL* 3.6 39.9 - - + +
393A GLN* 3.3 38.3 + - - -
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Residues in contact with HIS 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A MET* 3.5 30.9 - - + +
304A PRO* 3.8 12.0 - - + +
311A ARG* 4.1 13.8 + - - -
314A ILE* 4.0 20.2 - - + +
315A GLU* 5.4 2.6 + - + +
318A LEU* 4.0 14.4 - - + -
345A ILE* 3.5 20.0 - - + +
346A PRO* 3.2 49.4 + - - +
347A LEU* 3.1 10.7 + - - +
349A TYR* 1.3 73.4 - - - +
351A ILE* 1.3 70.2 + - - +
353A GLU* 3.4 8.0 + - - +
354A VAL* 3.0 27.9 + - + +
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Residues in contact with ILE 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LEU* 4.0 13.5 - - + -
336A LEU* 3.9 37.9 - - + +
337A VAL* 4.2 15.3 - - + +
347A LEU* 2.6 53.2 + - + +
348A ASN* 3.5 10.5 - - - +
350A HIS* 1.3 74.2 - - - +
352A VAL* 1.3 67.4 + - + +
354A VAL* 3.0 10.3 + - - +
355A ILE* 3.0 20.2 + - + +
379A LEU* 3.6 31.4 - - + -
387A LEU* 5.3 3.4 - - + -
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Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A PHE* 4.6 6.1 - - + -
348A ASN 3.0 16.9 + - - +
349A TYR* 4.2 3.6 - - - +
351A ILE* 1.3 76.5 - - + +
353A GLU* 1.3 64.1 + - - +
355A ILE* 2.9 20.6 + - - +
356A PHE* 3.0 45.2 + - + -
376A LEU* 4.8 7.9 - - + -
387A LEU* 3.9 27.8 - - + -
390A VAL* 4.4 11.9 - - + -
391A LEU* 4.4 9.4 - - + +
394A ALA* 4.3 15.0 - - + -
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Residues in contact with GLU 353 (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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289A PHE* 3.5 14.2 - - + +
290A ARG* 2.8 25.1 + - - -
291A MET* 3.8 16.2 + - + -
292A PHE* 2.9 37.3 + - + +
303A MET* 4.9 0.6 - - - +
311A ARG* 2.8 18.4 + - - -
315A GLU* 2.6 24.8 - - - +
349A TYR 2.9 21.8 + - - +
350A HIS* 3.8 9.1 + - - +
352A VAL* 1.3 77.4 - - - +
354A VAL* 1.3 56.0 + - - +
357A ALA* 3.0 29.0 + - - +
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Residues in contact with VAL 354 (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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315A GLU* 4.0 29.4 - - + +
318A LEU* 3.8 25.1 - - + -
319A HIS* 2.8 55.0 - - + +
322A ILE* 4.3 9.2 - - + -
350A HIS* 3.0 27.3 + - + +
351A ILE 3.5 4.7 - - - +
353A GLU* 1.3 73.9 - - - +
355A ILE* 1.3 64.1 + - - +
357A ALA* 3.7 5.6 - - - -
358A GLU* 3.2 19.1 + - - +
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Residues in contact with ILE 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ILE* 4.9 15.0 - - + -
336A LEU* 5.3 0.7 - - + -
351A ILE* 3.0 24.2 + - + +
352A VAL* 2.9 8.6 + - - +
354A VAL* 1.3 72.5 - - - +
356A PHE* 1.3 59.7 + - + +
357A ALA 3.0 0.9 - - - -
358A GLU* 2.8 9.3 + - - +
359A LEU* 2.7 34.5 + - + +
372A TYR* 3.9 34.1 - - + -
375A LEU* 4.6 12.1 - - + -
376A LEU* 3.2 44.2 - - + -
379A LEU* 3.9 19.5 - - + -
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Residues in contact with PHE 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A PHE* 3.9 14.4 - - + -
291A MET* 4.5 8.1 - - - -
352A VAL* 3.0 48.0 + - + +
355A ILE* 1.3 80.3 - - + +
357A ALA* 1.3 54.5 + - - +
359A LEU* 4.0 14.4 - - + -
360A PHE* 2.7 71.4 + + + +
376A LEU* 4.5 10.1 - - + -
391A LEU* 3.8 22.9 - - + -
394A ALA* 4.3 7.4 - - + -
395A THR 5.7 0.2 - - - -
398A LEU* 3.7 22.7 - - + -
416A TRP* 4.0 29.6 - + - -
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Residues in contact with ALA 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A PHE* 3.4 36.2 - - + +
315A GLU* 6.2 2.5 - - - +
319A HIS* 4.0 12.8 - - + +
353A GLU* 3.0 20.9 + - + +
354A VAL* 3.3 13.0 - - - +
356A PHE* 1.3 78.4 - - - +
358A GLU* 1.3 57.1 + - - +
360A PHE* 4.1 0.5 - - - +
361A GLN* 3.2 27.2 + - - +
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Residues in contact with GLU 358 (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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319A HIS* 3.4 47.1 + - + +
322A ILE* 4.0 17.3 - - - +
354A VAL 3.2 6.1 + - - +
355A ILE* 2.8 8.6 + - - +
357A ALA* 1.3 76.5 - - - +
359A LEU* 1.3 67.1 + - - +
360A PHE 3.2 1.1 - - - -
361A GLN* 3.1 12.3 + - - +
365A PRO* 3.0 23.7 - - - +
366A PRO* 2.9 35.4 - - + +
367A HIS* 3.3 8.8 + - - -
372A TYR* 2.5 35.5 + - + +
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Residues in contact with LEU 359 (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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355A ILE* 2.7 19.5 + - + +
356A PHE* 3.7 28.7 - - + +
358A GLU* 1.3 73.9 - - - +
360A PHE* 1.3 70.3 + - + +
365A PRO* 3.2 4.7 - - - +
369A ASP* 4.4 16.8 - - + +
372A TYR* 3.7 37.6 - - + -
376A LEU* 6.5 0.7 - - + -
412A ARG* 2.9 55.9 + - + +
416A TRP* 4.4 25.6 - - + -
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Residues in contact with PHE 360 (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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216A VAL* 4.0 18.7 - - + +
289A PHE* 3.9 13.7 - + + -
356A PHE* 2.7 70.0 + + + +
357A ALA 4.1 0.7 - - - -
359A LEU* 1.3 85.8 - - + +
361A GLN* 1.3 59.1 + - - +
362A LEU* 2.8 23.7 + - - +
398A LEU* 4.4 13.7 - - + -
405A MET* 3.6 18.4 - - + -
409A CYS* 3.4 50.2 - - + -
412A ARG* 3.6 7.0 + - + +
413A PHE* 4.2 20.0 - + + -
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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