Contacts of the helix formed by residues 437 - 455 (chain A) in PDB entry 6X70
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 437 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A VAL* 3.9 10.9 + - - +
371A ALA* 4.0 19.5 - - - +
374A CYS* 4.7 11.0 - - + +
375A ARG* 5.8 0.9 - - - -
435A PRO* 3.6 14.1 - - + +
436A TYR* 1.3 79.1 - - - +
438A PHE* 1.3 58.4 + - - +
439A GLU* 3.4 3.4 - - - -
440A GLN* 3.2 24.7 + - - +
441A PHE* 2.8 47.3 + - - -
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Residues in contact with PHE 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ALA 3.6 24.7 - - - -
322A HIS* 3.7 19.5 - - - -
324A ARG* 3.8 17.9 - - + -
327A HIS* 3.6 26.2 - + + -
331A TRP* 3.4 34.4 - + + -
367A PHE* 5.0 0.9 - + - -
393A HIS* 4.7 1.8 - + - -
436A TYR* 3.5 45.7 - + + -
437A THR* 1.3 74.0 - - - +
439A GLU* 1.3 78.0 + - - +
441A PHE* 3.2 17.2 + + - +
442A GLN* 3.2 16.6 + - - +
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Residues in contact with GLU 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A HIS* 5.3 4.3 - - - -
331A TRP* 5.6 0.2 - - - -
437A THR* 3.4 0.9 - - - -
438A PHE* 1.3 90.9 + - - +
440A GLN* 1.3 61.6 - - + +
442A GLN* 3.2 9.3 + - - +
443A LEU* 3.0 33.1 + - + +
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Residues in contact with GLN 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A VAL* 4.0 2.9 - - + -
374A CYS* 3.2 47.9 + - - +
437A THR* 3.2 23.3 + - - +
439A GLU* 1.3 76.3 - - + +
441A PHE* 1.3 67.0 + - - +
443A LEU* 3.2 17.7 + - + +
444A LYS* 2.9 30.5 + - + +
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Residues in contact with PHE 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A TRP* 4.0 9.0 - + + -
366A PHE* 3.4 17.9 - + + -
367A PHE* 3.4 65.3 - + + -
370A VAL* 3.5 22.2 - - + -
371A ALA* 3.9 4.7 - - + -
391A VAL* 4.8 0.9 - - + -
436A TYR* 4.0 20.9 - + - -
437A THR* 2.8 48.4 + - - -
438A PHE* 3.2 23.6 - + - +
440A GLN* 1.3 77.3 - - - +
442A GLN* 1.3 60.7 + - - +
444A LYS* 3.5 0.7 + - - +
445A SER 3.2 14.6 + - - -
466A ILE* 3.7 11.1 - - + +
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Residues in contact with GLN 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A TRP* 3.6 33.0 - - + +
438A PHE 3.2 8.1 + - - +
439A GLU* 3.4 10.7 + - - +
440A GLN 3.1 0.6 - - - -
441A PHE* 1.3 78.5 - - - +
443A LEU* 1.3 66.4 + - - +
445A SER* 3.0 10.7 + - - -
446A GLU* 2.9 58.6 + - - +
466A ILE* 4.2 4.3 - - + -
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Residues in contact with LEU 443 (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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439A GLU* 3.0 22.0 + - + +
440A GLN* 3.2 21.7 + - + +
442A GLN* 1.3 79.7 - - - +
444A LYS* 1.3 65.6 + - + +
446A GLU* 3.1 27.9 + - - +
447A ALA* 3.0 21.7 + - - +
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Residues in contact with LYS 444 (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 PHE* 4.0 4.5 - - + -
366A PHE* 4.3 6.1 - - + -
370A VAL* 3.7 28.5 - - + -
373A LEU* 5.1 6.9 - - - +
374A CYS* 4.4 20.4 - - - -
440A GLN* 2.9 21.9 + - - +
441A PHE 3.8 4.3 - - - +
443A LEU* 1.3 77.0 - - - +
445A SER* 1.3 56.4 + - - +
447A ALA* 3.4 6.4 + - + +
448A PHE* 3.0 26.3 + - - +
501A THR* 3.0 41.9 + - + +
502A ASN* 3.8 13.7 + - - +
504A CYS* 4.0 12.6 - - - -
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Residues in contact with SER 445 (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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335A LEU* 4.8 5.2 - - - +
363A PHE* 5.1 1.3 - - - -
366A PHE* 4.8 2.2 - - - -
441A PHE 3.2 6.2 + - - -
442A GLN* 3.0 15.9 + - - -
444A LYS* 1.3 74.5 - - - +
446A GLU* 1.3 65.1 + - - +
448A PHE* 3.2 4.8 - - - +
449A TYR* 3.0 36.1 + - - -
466A ILE* 2.6 52.8 + - - +
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Residues in contact with GLU 446 (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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442A GLN* 2.9 45.1 + - - +
443A LEU* 3.1 25.7 + - + +
445A SER* 1.3 77.0 - - - +
447A ALA* 1.3 57.8 + - - +
449A TYR* 3.3 3.5 + - - +
450A SER* 2.9 32.9 + - - -
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Residues in contact with ALA 447 (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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443A LEU 3.0 12.4 + - - +
444A LYS* 3.7 9.6 - - + +
446A GLU* 1.3 75.0 - - - +
448A PHE* 1.3 64.0 + - - +
450A SER* 3.7 5.2 - - - -
451A THR* 2.8 30.1 + - - -
500A GLY* 3.4 26.2 - - - +
501A THR* 4.0 10.8 - - + -
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Residues in contact with PHE 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ILE* 3.7 24.0 - - + -
363A PHE* 3.4 31.9 - + + -
444A LYS 3.0 13.8 + - - +
445A SER* 3.2 8.5 - - - +
447A ALA* 1.3 78.9 - - - +
449A TYR* 1.3 92.5 + + - +
451A THR* 3.1 5.0 + - - -
452A LEU* 3.0 45.0 + - + +
466A ILE 4.2 4.7 - - - -
467A ASP 4.0 2.2 - - - -
468A GLU 3.9 19.7 - - - -
469A ALA* 4.0 13.2 - - + -
497A ILE* 3.6 31.6 - - + -
501A THR* 4.2 6.0 - - - +
506A VAL* 4.5 1.3 - - + -
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Residues in contact with TYR 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LEU* 3.8 19.1 - - + -
338A LYS* 5.8 6.7 - - - +
445A SER* 3.0 37.0 + - - +
446A GLU* 4.2 3.4 - - - +
448A PHE* 1.3 97.8 - + - +
450A SER* 1.3 62.7 + - - +
452A LEU* 3.3 13.7 + - + +
453A LYS* 3.2 24.1 + - - +
461A ILE* 4.4 16.2 - - + +
463A PRO* 3.3 29.1 - - + +
465A SER 2.7 28.2 + - - -
466A ILE 3.8 0.4 - - - -
468A GLU 3.1 13.7 + - - -
469A ALA* 3.9 17.3 - - + -
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Residues in contact with SER 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A GLU 2.9 18.6 + - - -
447A ALA* 3.7 6.7 - - - -
449A TYR* 1.3 76.9 - - - +
451A THR* 1.3 62.5 + - - +
453A LYS* 3.4 12.0 + - - +
454A ARG* 3.1 30.8 + - - +
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Residues in contact with THR 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ALA* 2.8 24.7 + - - +
448A PHE 3.1 4.7 + - - -
450A SER* 1.3 78.4 - - - +
452A LEU* 1.3 62.6 + - - +
454A ARG* 3.3 23.9 + - - +
455A LEU* 3.2 27.3 + - + +
496A GLU* 3.8 38.7 + - + +
497A ILE* 3.8 21.8 - - + -
500A GLY* 4.3 11.3 - - - -
501A THR* 5.8 0.2 - - - +
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Residues in contact with LEU 452 (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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361A ILE* 3.7 28.0 - - + -
448A PHE* 3.0 49.5 + - + +
449A TYR* 3.3 17.2 + - + +
451A THR* 1.3 77.5 - - - +
453A LYS* 1.3 62.0 + - - +
455A LEU* 3.6 18.7 + - + +
456A ASN 4.1 2.8 + - - -
457A ILE 5.1 0.2 + - - -
458A PHE* 4.0 21.4 - - + +
461A ILE* 3.9 20.5 - - + +
469A ALA* 4.1 15.0 - - + -
471A CYS* 4.2 5.6 - - - -
493A ILE* 4.5 3.6 - - + -
497A ILE* 4.0 18.6 - - + -
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Residues in contact with LYS 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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338A LYS* 5.1 5.9 - - - +
342A GLU* 4.5 17.3 + - - -
449A TYR 3.2 16.4 + - - +
450A SER* 3.9 9.0 - - - +
452A LEU* 1.3 76.7 - - - +
454A ARG* 1.3 65.5 + - - +
456A ASN* 3.2 16.3 + - - +
461A ILE* 3.9 15.0 - - + +
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Residues in contact with ARG 454 (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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450A SER* 3.1 24.9 + - - +
451A THR* 3.3 32.8 + - - +
453A LYS* 1.3 78.6 - - - +
455A LEU* 1.3 67.8 + - - +
456A ASN* 3.2 6.2 + - - +
496A GLU* 3.1 29.7 + - - +
499A GLN* 5.8 1.8 + - - -
500A GLY* 6.2 2.0 - - - -
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Residues in contact with LEU 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A THR* 3.2 23.6 + - + +
452A LEU* 3.7 14.1 - - + +
453A LYS 3.2 0.4 - - - -
454A ARG* 1.3 83.8 - - - +
456A ASN* 1.3 68.4 + - - +
457A ILE* 3.2 40.2 + - + +
458A PHE* 5.0 1.8 - - + -
492A GLU* 3.5 20.9 - - - +
493A ILE* 3.8 31.2 - - + +
496A GLU* 3.8 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
------------------------------------------------------------
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