Contacts of the helix formed by residues 436 - 451 (chain A) in PDB entry 5UDJ
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 ASP 436 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429A LYS* 3.8 17.2 + - - +
430A LEU* 3.9 0.8 - - + +
433A LYS* 3.4 40.9 + - + +
434A ALA 3.4 1.4 + - - -
435A LEU* 1.3 74.4 - - - +
437A LEU* 1.3 65.2 + - - +
438A GLU* 3.2 15.1 + - - +
439A SER* 2.5 32.4 + - - +
440A LEU* 3.0 25.2 + - - +
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Residues in contact with LEU 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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435A LEU 3.3 6.3 + - - +
436A ASP* 1.3 73.6 + - - +
438A GLU* 1.3 70.1 + - + +
440A LEU* 3.1 12.1 + - - +
441A SER* 3.1 27.8 + - - +
463A ALA* 3.0 33.4 - - + +
466A LEU* 4.2 10.3 - - + -
467A ALA* 3.8 30.7 - - + +
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Residues in contact with GLU 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ILE* 4.1 16.3 - - - +
429A LYS* 4.3 10.1 + - - -
436A ASP* 3.2 10.3 + - - +
437A LEU* 1.3 83.6 - - + +
439A SER* 1.3 59.1 + - - +
441A SER* 3.0 9.0 + - - +
442A LEU* 3.0 47.0 + - + +
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Residues in contact with SER 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A VAL* 3.1 27.1 - - - +
429A LYS* 3.1 24.5 + - - +
430A LEU* 3.7 24.8 - - - +
436A ASP* 2.5 29.4 + - - -
437A LEU 3.3 0.2 - - - -
438A GLU* 1.3 75.9 - - - +
440A LEU* 1.3 65.8 + - - +
442A LEU* 4.4 4.0 - - - -
443A LEU* 3.0 20.4 + - - +
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Residues in contact with LEU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 3.7 21.8 - - + -
434A ALA 4.0 12.6 - - - +
435A LEU* 4.5 1.1 - - + -
436A ASP 3.0 20.5 + - - +
437A LEU 3.1 6.5 + - - +
439A SER* 1.3 77.7 - - - +
441A SER* 1.3 58.5 + - - +
443A LEU* 3.4 3.5 + - - +
444A GLY 3.0 21.7 + - - -
459A TYR* 3.4 42.2 - - + +
462A ARG* 3.9 26.9 - - + -
463A ALA* 3.8 13.5 - - + -
466A LEU* 3.7 30.1 - - + -
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Residues in contact with SER 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A LEU* 3.1 16.2 + - - +
438A GLU* 3.0 18.5 + - - +
440A LEU* 1.3 75.5 - - - +
442A LEU* 1.3 60.0 + - - +
444A GLY* 3.3 1.3 + - - +
445A PHE* 2.9 26.0 + - - +
459A TYR 4.7 1.1 - - - -
460A TYR* 3.9 26.5 - - - -
463A ALA* 4.0 14.5 - - - +
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Residues in contact with LEU 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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399A ILE* 3.9 21.5 - - + -
403A LEU* 4.2 31.9 - - + -
422A LEU* 4.7 7.4 - - + -
426A VAL* 4.0 24.5 - - + -
429A LYS* 5.8 0.2 - - - +
438A GLU* 3.0 45.2 + - + +
439A SER* 3.9 6.7 - - - +
441A SER* 1.3 77.2 + - - +
443A LEU* 1.3 58.3 + - - +
445A PHE* 3.2 11.7 + - + +
446A VAL* 2.9 32.8 + - - +
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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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423A LYS* 4.3 16.8 - - + +
426A VAL* 4.1 11.8 - - + +
427A LEU* 4.0 31.0 - - + -
430A LEU* 3.9 16.6 - - + -
439A SER 3.0 18.1 + - - +
440A LEU 3.7 4.7 - - - +
442A LEU* 1.3 73.6 - - - +
444A GLY* 1.3 66.2 + - - +
446A VAL* 3.3 7.7 + - + +
447A TYR* 3.0 47.0 + - + +
459A TYR* 3.5 38.6 - - + +
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Residues in contact with GLY 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 LEU 3.0 14.0 + - - -
441A SER 3.3 3.6 + - - -
443A LEU* 1.3 77.2 - - - +
445A PHE* 1.3 55.6 + - - +
447A TYR* 3.3 0.7 + - - -
448A LYS* 2.9 27.2 + - - +
456A ALA* 3.3 32.6 - - - +
459A TYR* 3.9 7.2 - - - +
460A TYR* 3.4 11.0 - - - -
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Residues in contact with PHE 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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403A LEU* 3.7 30.3 - - + -
406A ILE* 4.3 11.4 - - + -
422A LEU* 4.4 10.8 - - + -
441A SER 2.9 13.6 + - - +
442A LEU* 3.2 17.7 + - + +
444A GLY* 1.3 75.2 - - - +
446A VAL* 1.3 66.5 + - - +
448A LYS* 3.1 18.4 + - - +
449A LEU* 2.9 62.9 + - + +
460A TYR* 3.3 19.8 + - - +
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Residues in contact with VAL 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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419A ILE* 4.3 14.1 - - + +
422A LEU* 3.9 32.1 - - + -
423A LYS* 3.8 46.4 - - + +
426A VAL* 5.9 0.9 - - + -
442A LEU 2.9 17.9 + - - +
443A LEU* 3.3 12.8 + - + +
445A PHE* 1.3 79.2 - - + +
447A TYR* 1.3 64.5 + - + +
449A LEU* 3.1 9.7 + - + +
450A GLU* 3.0 31.7 + - - +
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Residues in contact with TYR 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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423A LYS* 3.5 30.8 - - - -
427A LEU* 4.8 5.7 - - - +
443A LEU* 3.0 42.7 + - + +
444A GLY* 3.8 3.4 - - - +
446A VAL* 1.3 76.3 - - + +
448A LYS* 1.3 62.7 + - - +
450A GLU* 3.2 16.6 + - - +
451A GLY 3.0 17.8 + - - -
452A ASN* 3.0 22.6 + - + +
455A GLU* 3.4 32.2 - - + -
456A ALA 4.0 13.2 - - - +
459A TYR* 3.3 40.4 + + - -
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Residues in contact with LYS 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 GLY 2.9 17.5 + - - +
445A PHE* 3.1 23.5 + - - +
447A TYR* 1.3 76.9 - - - +
449A LEU* 1.3 67.6 + - + +
451A GLY* 3.1 12.8 + - - -
453A MET* 3.9 28.1 - - + +
456A ALA* 3.6 12.7 - - + +
460A TYR* 3.0 33.2 + - + +
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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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406A ILE* 3.5 31.6 - - + -
415A ARG* 4.3 15.0 + - - +
419A ILE* 4.1 30.6 - - + +
445A PHE* 2.9 48.7 + - + +
446A VAL* 3.7 7.9 - - + +
448A LYS* 1.3 83.2 - - + +
450A GLU* 1.3 61.0 + - - +
451A GLY 3.6 0.2 + - - -
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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
----------------------------------------------------------
419A ILE* 4.3 14.5 - - + +
420A ASN* 4.2 13.3 - - - +
423A LYS* 3.1 39.6 + - - +
446A VAL* 3.0 23.0 + - - +
447A TYR* 3.6 19.7 - - - +
448A LYS 3.2 0.2 - - - -
449A LEU* 1.3 79.2 - - - +
451A GLY* 1.3 56.0 + - - +
452A ASN* 3.7 16.0 + - - +
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Residues in contact with GLY 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 TYR 3.0 3.2 + - - -
448A LYS 3.1 10.9 + - - -
449A LEU 3.3 0.2 - - - -
450A GLU* 1.3 78.3 - - - +
452A ASN* 1.3 60.1 + - - +
453A MET* 3.0 27.4 + - - +
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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