Contacts of the helix formed by residues 431 - 454 (chain A) in PDB entry 1XR2
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 SER 431 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430A ILE* 1.3 77.0 - - - +
432A LYS* 1.3 54.7 + - - +
433A GLU* 2.7 9.9 + - - -
434A GLU* 2.7 41.3 + - - +
435A TYR* 2.9 13.3 + - - +
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Residues in contact with LYS 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ILE 3.7 3.6 + - - -
431A SER* 1.3 69.4 - - - +
433A GLU* 1.3 55.9 + - - +
435A TYR* 4.2 8.4 - - - +
436A GLU* 3.4 23.0 + - - +
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Residues in contact with GLU 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A SER* 2.7 10.3 + - - -
432A LYS* 1.3 75.1 - - - +
434A GLU* 1.3 58.4 + - - +
435A TYR 3.2 1.6 - - - -
436A GLU* 3.9 5.0 - - - +
437A ALA* 2.9 30.5 + - - +
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Residues in contact with GLU 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ILE 4.9 5.4 - - - +
431A SER* 2.7 32.5 + - - +
433A GLU* 1.3 75.3 - - - +
435A TYR* 1.3 56.4 + - - +
437A ALA* 3.6 5.8 - - - +
438A PHE* 2.9 26.5 + - - +
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Residues in contact with TYR 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A VAL 5.5 0.7 - - - -
421A MET* 4.1 24.0 - - + +
422A ARG* 4.2 24.0 - - - +
430A ILE* 5.8 2.4 - - - +
431A SER 2.9 13.6 + - - +
432A LYS* 4.5 6.7 - - - +
434A GLU* 1.3 74.8 - - - +
436A GLU* 1.3 59.4 + - - +
437A ALA 2.9 3.8 - - - -
438A PHE* 2.7 41.4 + + + +
439A ILE* 2.8 19.6 + - + +
463A PHE 4.2 5.3 + - - -
464A GLU* 3.9 30.7 + - + -
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Residues in contact with GLU 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A LYS 3.4 19.4 + - - +
433A GLU* 4.1 5.4 - - - +
435A TYR* 1.3 81.7 - - - +
437A ALA* 1.3 57.7 - - - +
439A ILE* 3.8 7.3 + - - +
440A LYS* 3.3 31.0 + - - +
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Residues in contact with ALA 437 (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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433A GLU 2.9 20.4 + - - +
434A GLU* 3.6 7.2 - - - +
435A TYR 2.9 0.4 - - - -
436A GLU* 1.3 77.5 - - - +
438A PHE* 1.3 64.1 + - - +
440A LYS* 3.6 11.9 + - - +
441A GLU* 3.2 21.8 + - - +
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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
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417A GLU* 3.8 24.5 - - + -
418A VAL* 3.8 21.3 - - + -
421A MET* 3.5 26.2 - - + -
434A GLU 2.9 14.9 + - - +
435A TYR* 2.7 27.5 + + + +
437A ALA* 1.3 70.6 - - - +
439A ILE* 1.3 67.0 + - - +
441A GLU* 3.4 8.3 + - + +
442A GLN* 3.1 61.5 + - + +
463A PHE* 6.2 0.4 - - + -
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Residues in contact with ILE 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A TYR* 2.8 21.9 + - + +
436A GLU* 3.9 8.7 - - - +
438A PHE* 1.3 80.4 - - - +
440A LYS* 1.3 51.0 + - + +
442A GLN* 2.7 30.0 + - - +
443A ILE* 2.7 29.8 + - + +
463A PHE* 5.6 4.7 - - + -
464A GLU* 4.9 20.0 - - + +
514A GLU* 6.1 3.1 - - + -
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Residues in contact with LYS 440 (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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436A GLU 3.3 19.2 + - - +
437A ALA* 3.9 10.0 + - - +
438A PHE 3.4 0.2 - - - -
439A ILE* 1.3 77.7 - - + +
441A GLU* 1.3 57.4 + - - +
443A ILE* 4.2 8.0 - - + +
444A LYS* 2.8 29.8 + - - +
513A LYS 5.8 0.7 - - - +
517A TYR* 3.4 61.8 + - + +
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Residues in contact with GLU 441 (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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437A ALA 3.2 14.1 + - - +
438A PHE* 3.6 12.6 - - + +
439A ILE 3.1 0.8 - - - -
440A LYS* 1.3 76.6 - - - +
442A GLN* 1.3 68.0 + - - +
444A LYS* 3.5 6.5 + - - +
445A LYS* 3.1 22.3 + - - +
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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
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415A THR* 4.8 2.6 + - - +
418A VAL* 3.5 23.7 - - + +
438A PHE* 3.1 53.8 + - + +
439A ILE* 2.7 10.5 + - - +
441A GLU* 1.3 79.6 - - - +
443A ILE* 1.3 64.6 - - - +
445A LYS* 3.2 8.6 + - - +
446A ALA* 2.9 21.8 + - - +
463A PHE* 3.7 32.3 - - + -
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Residues in contact with ILE 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ILE* 2.7 30.9 + - + +
440A LYS* 3.8 11.7 - - + +
442A GLN* 1.3 70.9 - - - +
444A LYS* 1.3 65.4 + - - +
446A ALA* 3.0 18.1 + - - +
447A ILE* 3.0 17.3 + - + +
460A HIS* 3.5 38.6 - - + +
463A PHE* 4.3 7.2 - - + -
464A GLU* 5.0 3.4 - - - +
514A GLU* 4.3 24.9 - - + +
517A TYR* 4.2 10.1 - - + -
518A ALA* 3.8 32.1 - - + -
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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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440A LYS 2.8 19.2 + - - +
441A GLU* 3.5 9.2 - - - +
442A GLN 3.2 0.2 - - - -
443A ILE* 1.3 78.5 - - - +
445A LYS* 1.3 61.7 + - - +
447A ILE* 3.4 3.3 + - - +
448A GLU* 3.3 20.1 + - - +
517A TYR* 4.0 13.0 - - - +
521A LEU* 3.7 19.3 - - + +
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Residues in contact with LYS 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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441A GLU 3.1 10.9 + - - +
442A GLN* 3.6 11.2 - - - +
444A LYS* 1.3 78.8 - - - +
446A ALA* 1.3 64.1 + - - +
448A GLU* 3.4 7.4 + - - +
449A LEU* 3.0 23.4 + - - +
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Residues in contact with ALA 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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412A PHE* 4.4 9.9 - - + -
442A GLN 2.9 13.8 + - - +
443A ILE* 3.0 11.2 + - - +
445A LYS* 1.3 76.5 - - - +
447A ILE* 1.3 64.7 + - + +
449A LEU* 3.2 8.8 + - - +
450A GLN* 3.1 38.1 + - - +
459A VAL 4.9 0.2 - - - +
460A HIS 4.5 6.5 - - - +
463A PHE* 3.8 24.2 - - + -
711A TRP* 5.8 2.7 - - + -
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Residues in contact with ILE 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 ILE* 3.0 20.5 + - + +
444A LYS 3.7 6.1 - - - +
446A ALA* 1.3 75.5 - - - +
448A GLU* 1.3 63.4 + - - +
450A GLN* 3.1 19.4 + - - +
451A GLU* 3.0 23.8 + - + +
458A LEU* 4.0 16.0 - - + +
459A VAL 4.2 8.1 - - - +
460A HIS* 4.8 0.7 - - - -
518A ALA* 4.0 31.4 - - + +
521A LEU* 4.3 21.8 - - + +
522A THR* 3.8 28.7 - - + -
526A VAL* 4.6 6.3 - - + -
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Residues in contact with GLU 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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444A LYS 3.3 10.0 + - - +
445A LYS* 3.7 10.5 - - - +
446A ALA 3.3 0.2 - - - -
447A ILE* 1.3 79.2 - - - +
449A LEU* 1.3 58.3 + - - +
451A GLU* 3.4 7.6 + - - +
452A GLU* 3.0 29.1 + - - +
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Residues in contact with LEU 449 (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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412A PHE* 6.0 2.0 - - + -
445A LYS 3.0 13.4 + - - +
446A ALA* 3.2 10.5 + - - +
448A GLU* 1.3 76.7 - - - +
450A GLN* 1.3 65.8 + - + +
452A GLU* 3.4 7.3 + - + +
453A ILE* 3.1 43.5 + - + +
711A TRP* 3.5 38.4 - - + -
715A ILE* 5.4 10.8 - - + -
718A LEU* 5.8 4.3 - - + -
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Residues in contact with GLN 450 (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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408A THR* 4.4 1.2 + - - -
412A PHE* 3.4 33.4 - - + -
446A ALA* 3.1 24.6 + - - +
447A ILE* 3.1 13.3 + - - +
449A LEU* 1.3 76.5 - - + +
451A GLU* 1.3 66.8 + - - +
453A ILE* 3.4 3.8 + - - +
454A GLY 3.0 17.7 + - - -
455A LEU* 3.1 33.5 + - + +
458A LEU* 3.5 28.1 - - + +
459A VAL* 2.8 43.3 + - - +
718A LEU* 6.0 1.6 - - + -
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Residues in contact with GLU 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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447A ILE* 3.0 18.6 + - + +
448A GLU* 3.7 7.6 - - - +
449A LEU 3.3 0.2 - - - -
450A GLN* 1.3 77.2 - - - +
452A GLU* 1.3 61.1 + - - +
454A GLY* 3.2 12.8 + - - -
458A LEU* 5.1 4.2 - - + +
522A THR* 6.0 2.0 - - - +
524A LYS* 4.3 21.8 + - + +
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Residues in contact with GLU 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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448A GLU 3.0 18.9 + - - +
449A LEU* 3.7 10.5 - - + +
450A GLN 3.3 0.2 - - - -
451A GLU* 1.3 79.1 - - - +
453A ILE* 1.3 62.3 + - + +
454A GLY* 4.6 0.2 - - - -
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Residues in contact with ILE 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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449A LEU* 3.1 35.8 + - + +
450A GLN* 4.1 5.2 - - - +
451A GLU 3.3 0.2 - - - -
452A GLU* 1.3 77.4 - - + +
454A GLY* 1.3 58.5 + - - +
455A LEU* 4.8 4.0 - - + +
715A ILE* 3.6 32.1 - - + +
718A LEU* 3.7 22.9 - - + +
719A ARG* 3.6 28.6 - - + +
722A VAL* 3.4 34.5 - - + +
726A LYS* 5.4 1.6 + - - -
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Residues in contact with GLY 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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406A THR* 3.7 4.7 + - - -
450A GLN 3.0 3.8 + - - -
451A GLU 3.2 12.1 + - - -
452A GLU 4.6 0.4 - - - -
453A ILE* 1.3 79.5 - - - +
455A LEU* 1.3 67.1 + - - +
456A ASP* 3.8 6.8 + - - +
524A LYS* 4.5 4.7 - - - -
722A VAL* 3.5 21.1 - - - +
726A LYS* 5.7 4.1 - - - -
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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
------------------------------------------------------------
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