Contacts of the helix formed by residues 372 - 384 (chain A) in PDB entry 1AX4
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 372 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359A CYS* 4.0 17.3 - - - +
360A LYS* 4.8 5.2 - - + -
363A VAL* 3.9 8.2 - - + +
366A ILE* 3.2 30.0 - - + +
367A PRO 3.1 22.4 - - - +
368A GLY* 3.6 8.5 - - - +
371A PHE* 1.3 81.6 - - - +
373A ALA* 1.3 61.5 + - - +
375A ALA* 3.3 9.1 + - + +
376A VAL* 3.2 19.4 + - - +
411A GLU* 3.3 37.9 - - + +
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Residues in contact with ALA 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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359A CYS* 3.4 18.7 - - - +
371A PHE 3.5 0.4 - - - -
372A PRO* 1.3 79.5 - - - +
374A GLN* 1.3 57.2 + - - +
376A VAL* 2.8 20.8 + - - +
377A ILE* 2.8 17.7 + - - +
390A GLU* 3.6 24.4 + - + +
411A GLU* 3.8 25.9 + - - +
412A PHE 3.9 11.2 - - - +
413A MET* 4.5 1.6 - - - +
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Residues in contact with GLN 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR 4.7 4.0 - - - +
35A ASN* 5.1 0.6 + - - -
36A PRO* 3.1 26.0 - - - +
371A PHE* 3.3 22.3 + - + +
373A ALA* 1.3 77.4 - - - +
375A ALA* 1.3 56.2 + - - +
377A ILE* 3.7 11.4 - - - +
378A ASN* 2.6 63.4 + - - +
388A ALA 5.8 0.2 + - - -
390A GLU* 3.2 35.5 - - + +
394A PHE* 3.8 28.0 - - + -
447A LEU* 4.0 13.0 - - + -
463A LEU* 4.7 2.0 - - + -
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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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366A ILE* 5.0 2.9 - - + -
371A PHE 3.0 15.6 + - - +
372A PRO* 3.9 5.6 - - + +
373A ALA 3.1 0.4 - - - -
374A GLN* 1.3 73.9 - - - +
376A VAL* 1.3 68.5 + - - +
378A ASN* 4.1 4.8 - - - +
379A ALA* 3.1 15.4 + - - +
444A LEU* 3.3 29.9 - - + +
445A LYS 5.7 0.2 - - - +
446A GLY* 4.7 18.4 - - - +
447A LEU* 4.3 12.5 - - + +
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Residues in contact with VAL 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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359A CYS* 3.4 32.8 - - + -
362A LEU* 4.4 4.0 - - + -
363A VAL* 3.9 15.0 - - + -
372A PRO 3.2 16.6 - - - +
373A ALA 2.8 6.0 + - - +
375A ALA* 1.3 76.7 - - - +
377A ILE* 1.3 55.5 + - - +
379A ALA* 2.7 5.6 + - - +
380A LEU* 2.5 36.2 + - - +
413A MET* 4.3 7.0 - - + -
434A LEU* 3.9 20.2 - - + -
437A LEU* 4.5 1.1 - - + -
441A PHE* 3.7 30.3 - - + -
444A LEU* 4.4 6.1 - - + -
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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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36A PRO* 3.9 12.6 - - + -
373A ALA 2.8 13.1 + - - +
374A GLN* 3.6 22.7 - - - +
376A VAL* 1.3 76.4 - - - +
378A ASN* 1.3 52.4 + - - +
380A LEU* 3.0 9.1 + - - +
381A TYR* 2.5 38.0 + - + +
386A VAL 4.5 0.5 - - - +
388A ALA* 3.6 26.9 - - + +
389A VAL* 3.5 7.6 - - - +
390A GLU* 3.1 47.6 - - + +
413A MET* 3.7 26.0 - - + -
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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
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29A LEU* 3.6 25.5 - - + +
34A TYR* 3.1 33.2 + - - +
36A PRO* 4.0 6.2 - - - +
374A GLN* 2.6 59.9 + - - +
375A ALA* 4.1 5.8 - - - +
377A ILE* 1.3 73.6 - - - +
379A ALA* 1.4 53.8 + - - +
381A TYR* 3.3 8.3 + - - +
382A LEU* 2.6 36.6 + - + +
447A LEU* 4.6 9.1 - - + +
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Residues in contact with ALA 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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375A ALA 3.1 16.4 + - - +
376A VAL 2.7 7.3 + - - +
378A ASN* 1.4 71.1 - - - +
380A LEU* 1.3 60.1 + - - +
382A LEU* 3.5 7.6 - - + +
383A GLU* 2.7 47.7 + - - +
437A LEU* 4.2 17.7 - - + -
440A LYS* 6.4 1.3 - - + -
444A LEU* 4.3 20.4 - - + -
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Residues in contact with LEU 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 VAL 2.5 18.7 + - - +
377A ILE* 3.2 9.4 - - - +
379A ALA* 1.3 72.4 - - - +
381A TYR* 1.3 61.6 + - - +
383A GLU* 3.7 1.6 - - + +
384A SER* 2.5 44.8 + - - +
386A VAL* 4.3 20.4 - - + +
388A ALA* 4.7 4.9 - - + -
413A MET* 3.7 29.2 - - + -
415A LEU* 4.2 16.4 - - + -
430A ILE* 4.6 5.4 - - + +
433A ALA* 3.7 23.8 - - + +
434A LEU* 3.9 24.2 - - + +
437A LEU* 4.0 9.9 - - + +
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Residues in contact with TYR 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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20A PRO* 4.1 2.4 - - - +
25A ARG* 3.3 46.5 - - + -
28A ALA* 4.1 2.9 - - - +
29A LEU* 3.9 28.3 - - + -
36A PRO* 5.5 4.7 - - + -
39A LEU* 3.9 23.6 - - + -
43A ALA* 2.5 41.5 + - - +
44A VAL* 4.4 2.7 - - + -
377A ILE* 2.5 28.1 + - + +
378A ASN* 3.5 7.0 - - - +
380A LEU* 1.3 72.2 - - - +
382A LEU* 1.3 63.0 + - - +
385A GLY* 2.8 41.4 + - - +
386A VAL 3.3 23.8 + - - +
387A ARG* 4.7 5.8 - - + -
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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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22A ARG* 3.1 38.8 + - + +
25A ARG* 2.8 26.0 + - - +
26A GLU* 3.1 50.9 - - + +
29A LEU* 3.4 29.2 - - + -
34A TYR* 5.5 4.7 - - + -
378A ASN* 2.6 18.9 + - + +
379A ALA* 3.1 8.5 + - + +
381A TYR* 1.3 77.1 - - + +
383A GLU* 1.3 57.2 + - - +
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Residues in contact with GLU 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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22A ARG* 2.6 42.1 + - - +
25A ARG* 3.5 13.0 + - - -
379A ALA* 2.7 32.4 + - - +
380A LEU* 3.9 2.2 - - - +
382A LEU* 1.3 75.2 - - - +
384A SER* 1.4 61.5 + - - +
429A TYR* 4.8 0.7 + - - -
433A ALA* 5.3 7.3 - - + +
436A GLY 6.5 0.2 - - - -
437A LEU* 3.8 27.0 - - + +
440A LYS* 4.4 23.3 + - - +
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Residues in contact with SER 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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19A VAL* 3.9 5.4 - - - +
25A ARG* 4.3 6.3 - - - -
45A TYR* 3.8 5.5 - - - -
380A LEU* 2.5 33.7 + - - +
383A GLU* 1.4 77.1 - - - +
385A GLY* 1.3 60.8 + - - +
386A VAL* 3.4 15.5 + - - +
429A TYR* 2.6 41.5 + - - -
433A ALA* 3.5 27.1 - - - -
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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
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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