Contacts of the helix formed by residues 439 - 453 (chain A) in PDB entry 3AR2
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 GLU 439 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A VAL 4.9 8.7 - - - +
423A SER* 3.3 5.9 + - - -
436A LYS* 4.2 1.3 - - - -
438A GLY* 1.3 79.0 - - - +
440A ALA* 1.3 61.0 + - - +
441A THR* 4.5 4.7 - - - +
442A GLU* 3.0 26.6 + - + +
443A THR* 2.8 26.7 + - - -
489A ARG* 5.9 1.4 + - - -
724A THR* 5.4 9.5 - - - +
1002A ACP 5.4 7.2 - - - +
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Residues in contact with ALA 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ASN* 3.3 33.3 + - - +
361A MET* 3.3 13.6 - - + +
389A TYR* 3.2 25.0 - - - +
436A LYS* 3.7 19.5 - - - +
439A GLU* 1.3 68.6 + - - +
441A THR* 1.3 67.7 + - - +
442A GLU 3.0 0.3 + - - -
443A THR* 3.1 1.4 + - - +
444A ALA* 2.8 26.7 + - - +
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Residues in contact with THR 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A THR* 5.3 0.9 - - - +
359A ASN* 5.0 2.6 + - - +
361A MET* 3.4 13.9 - - - +
439A GLU* 3.4 4.6 - - - +
440A ALA* 1.3 78.8 - - - +
442A GLU* 1.3 63.5 + - + +
444A ALA* 3.4 12.5 - - - +
445A LEU* 3.6 13.5 + - - +
515A LYS* 5.7 0.2 - - - -
560A ARG* 2.8 40.9 + - + +
562A LEU* 4.3 22.4 - - + -
599A MET* 3.8 18.0 - - + +
1002A ACP 4.6 14.4 - - + +
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Residues in contact with GLU 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ASN* 3.2 20.8 - - - +
422A ASP* 3.0 23.3 + - - +
423A SER* 2.7 33.2 + - - +
439A GLU* 3.0 16.2 + - + +
441A THR* 1.3 75.6 - - - +
443A THR* 1.3 63.9 + - - +
444A ALA 3.2 1.3 - - - -
445A LEU* 3.0 20.6 + - - +
446A THR 3.0 8.5 + - - -
494A MET* 3.5 10.7 - - - +
515A LYS* 2.8 30.8 + - - +
1002A ACP 3.0 25.4 + - + +
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Residues in contact with THR 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A TYR* 3.7 13.0 - - + -
423A SER* 3.9 2.0 - - - -
424A SER 3.1 18.7 + - - +
425A LEU* 3.5 31.9 - - + -
436A LYS* 3.1 27.8 - - + +
437A VAL 3.6 7.6 + - - -
439A GLU 2.8 18.6 + - - -
440A ALA* 4.0 2.2 - - - -
442A GLU* 1.3 68.9 - - - +
444A ALA* 1.3 59.8 + - - +
446A THR* 2.6 32.9 + - - -
447A THR* 2.8 14.8 + - + +
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Residues in contact with ALA 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A MET* 3.6 34.3 - - + -
362A SER* 4.1 2.7 - - - +
363A VAL* 3.6 16.8 - - + +
389A TYR* 4.2 3.6 - - - -
440A ALA 2.8 17.3 + - - +
441A THR 3.4 8.3 - - - +
443A THR* 1.3 76.1 - - - +
445A LEU* 1.3 62.7 + - - +
447A THR* 3.1 10.5 + - - -
448A LEU 3.0 17.8 + - - -
599A MET* 3.9 11.4 - - - -
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Residues in contact with LEU 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A VAL* 4.1 7.0 - - + -
417A CYS* 3.8 37.1 - - + +
421A ASN* 4.9 1.3 - - + -
441A THR 3.8 7.9 - - - +
442A GLU* 3.0 14.0 + - - +
444A ALA* 1.3 80.7 - - - +
446A THR* 1.3 60.6 + - - +
448A LEU* 3.1 7.5 + - + +
449A VAL* 3.0 28.1 + - - +
515A LYS* 3.5 39.5 - - + -
562A LEU* 3.9 8.5 - - + -
564A LEU* 5.5 0.7 - - + -
597A VAL* 4.0 15.5 - - + -
599A MET* 3.3 30.7 - - + -
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Residues in contact with THR 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ASN* 2.8 25.3 + - - -
423A SER 3.6 11.3 + - - -
424A SER* 4.4 1.6 - - - -
425A LEU* 3.9 28.9 - - + +
442A GLU 3.0 6.5 + - - -
443A THR* 2.6 25.5 + - - -
445A LEU* 1.3 70.4 - - - +
447A THR* 1.3 62.0 + - - +
449A VAL* 3.2 12.2 + - - -
450A GLU* 3.2 9.5 + - - +
468A ALA 4.4 2.2 - - - +
469A ASN* 4.1 8.1 - - - +
472A ASN* 3.0 38.3 + - - +
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Residues in contact with THR 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A MET 5.7 0.2 + - - -
362A SER* 5.4 3.5 - - - -
363A VAL 5.4 3.3 + - - -
388A THR 4.6 1.4 + - - -
389A TYR* 3.0 54.7 - - + +
390A ALA 4.4 9.2 - - - -
391A PRO* 4.9 0.4 - - - +
425A LEU* 3.6 12.6 - - + -
443A THR* 2.8 21.8 + - + +
444A ALA* 3.1 9.5 + - - -
446A THR* 1.3 70.8 - - - +
448A LEU* 1.3 67.6 + - - +
450A GLU* 2.9 11.0 + - - +
451A LYS* 2.9 35.7 + - - +
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Residues in contact with LEU 448 (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 VAL* 3.8 33.4 - - + -
366A MET* 4.0 18.4 - - + -
384A ILE* 4.0 29.8 - - + -
413A LEU* 4.6 0.4 - - + -
417A CYS* 4.6 13.0 - - - -
444A ALA 3.0 9.8 + - - +
445A LEU* 3.1 9.4 + - + +
447A THR* 1.3 82.1 + - - +
449A VAL* 1.3 54.2 + - + +
451A LYS* 3.1 7.5 + - + -
452A MET* 2.7 55.7 + - + +
597A VAL* 4.1 16.2 - - + -
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Residues in contact with VAL 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ALA* 4.2 15.2 - - + +
417A CYS* 3.7 24.9 - - + -
418A ALA* 4.1 9.9 - - + +
445A LEU 3.0 18.8 + - - +
446A THR 3.2 1.5 + - - +
448A LEU* 1.3 76.0 - - + +
450A GLU* 1.3 64.8 + - - +
452A MET* 3.7 10.1 - - - +
453A ASN* 3.1 18.0 + - - -
454A VAL* 4.9 0.9 + - - +
471A CYS* 3.8 9.2 - - - +
472A ASN* 3.1 52.3 - - - +
475A ILE* 4.8 3.4 - - + -
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Residues in contact with GLU 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A PRO* 3.7 13.0 - - + -
425A LEU* 5.2 0.2 - - + -
446A THR 3.2 14.7 + - - +
447A THR* 2.9 12.4 + - - +
449A VAL* 1.3 76.0 - - - +
451A LYS* 1.3 64.2 + - - +
453A ASN* 3.5 12.6 + - - +
467A ARG* 2.7 45.1 + - - +
468A ALA 3.4 19.1 - - - +
469A ASN* 2.9 27.4 - - - -
470A ALA* 3.6 6.4 + - - +
471A CYS* 3.0 36.0 + - - -
472A ASN* 3.0 11.8 + - - +
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Residues in contact with LYS 451 (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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362A SER* 5.4 2.2 - - - -
363A VAL 5.4 2.4 + - - -
384A ILE* 3.8 23.5 - - + +
385A THR 2.9 24.9 + - - +
386A GLY* 3.3 24.0 + - - -
388A THR 4.1 7.7 + - - -
390A ALA 3.2 18.4 + - - -
391A PRO 4.1 15.0 - - - +
392A GLU 3.2 19.0 + - - -
393A GLY* 4.0 21.3 - - - +
394A GLU* 5.7 0.2 - - - -
395A VAL* 4.3 11.1 - - + +
447A THR* 2.9 23.9 + - - +
448A LEU* 3.5 8.7 - - + +
450A GLU* 1.3 78.4 - - - +
452A MET* 1.3 62.0 + - - +
453A ASN* 3.3 3.5 + - - +
467A ARG* 4.8 1.1 - - - +
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Residues in contact with MET 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A MET* 3.4 33.7 - - + +
395A VAL* 4.3 2.9 - - + -
404A SER* 3.2 32.8 + - - +
410A LEU* 3.4 47.6 - - + +
413A LEU* 4.2 7.0 - - + -
414A ALA* 3.9 12.6 - - + +
448A LEU* 2.7 42.1 + - + +
449A VAL* 3.7 7.6 - - - +
450A GLU 3.3 0.4 - - - -
451A LYS* 1.3 73.8 - - - +
453A ASN* 1.3 68.4 + - - +
454A VAL* 3.0 16.8 + - + -
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Residues in contact with ASN 453 (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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404A SER 5.7 0.2 + - - -
405A GLY 5.1 0.3 + - - -
449A VAL 3.1 14.7 + - - -
450A GLU 3.5 6.7 + - - +
451A LYS 3.2 4.0 - - - +
452A MET* 1.3 75.0 - - - +
454A VAL* 1.3 58.7 + - - +
455A PHE* 3.8 1.7 + - - +
456A ASN* 3.2 17.2 + - - +
457A THR* 2.8 52.0 + - - +
459A VAL* 4.1 11.7 - - - +
467A ARG* 5.2 0.4 - - - +
471A CYS* 3.6 26.9 - - - +
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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