Contacts of the helix formed by residues 431 - 446 (chain A) in PDB entry 5Y36
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 431 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427A GLU 4.0 9.8 - - - +
428A ASP 5.9 0.9 - - - -
429A PHE 3.9 6.3 - - - +
430A TYR* 1.3 84.4 - - + +
432A PHE* 1.3 76.3 + - + +
433A LEU 3.3 0.2 - - - -
434A LYS* 3.4 25.6 + - + +
435A ASP* 4.0 9.4 + - - +
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Residues in contact with PHE 432 (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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89A GLU* 4.7 26.5 - - + +
93A VAL* 5.5 13.7 - - + -
430A TYR* 3.1 13.9 - + + -
431A PRO* 1.3 94.2 - - + +
433A LEU* 1.3 57.4 + - + +
435A ASP* 3.4 10.4 + - - +
436A ASN* 3.1 33.1 + - - +
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Residues in contact with LEU 433 (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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86A PHE* 3.9 29.4 - - + -
151A LEU* 6.3 3.1 - - + -
154A ILE* 5.3 9.6 - - + -
158A LEU* 5.3 2.5 - - + -
422A ILE 5.1 0.7 - - - +
423A LEU* 3.9 39.0 - - + +
426A GLN* 3.4 40.6 - - + +
427A GLU* 4.7 6.0 - - + +
430A TYR* 3.3 23.1 + - + +
431A PRO 3.3 0.6 - - - -
432A PHE* 1.3 76.1 - - + +
434A LYS* 1.4 58.9 + - - +
436A ASN* 4.4 3.6 - - + +
437A ARG* 2.9 33.8 + - - +
440A ILE* 5.0 1.8 - - + -
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Residues in contact with LYS 434 (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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424A ARG* 5.7 1.1 - - - +
427A GLU* 3.5 56.4 + - + +
428A ASP* 3.8 14.6 + - - -
431A PRO* 3.4 17.9 + - + +
433A LEU* 1.4 77.1 - - - +
435A ASP* 1.3 65.0 + - - +
437A ARG* 4.2 14.0 + - - +
438A GLU* 5.0 1.9 + - - +
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Residues in contact with ASP 435 (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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431A PRO 4.0 8.8 + - - +
432A PHE* 3.4 10.5 + - - +
433A LEU 3.3 0.4 - - - -
434A LYS* 1.3 81.0 - - - +
436A ASN* 1.4 66.2 + - - +
438A GLU* 4.2 13.3 + - - +
439A LYS* 4.9 5.5 + - - +
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Residues in contact with ASN 436 (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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85A ILE* 4.5 15.5 - - + +
86A PHE* 4.7 6.3 - - + -
89A GLU* 2.8 38.6 + - - +
432A PHE* 3.1 20.1 + - - +
433A LEU* 3.5 4.2 + - - +
435A ASP* 1.4 76.8 - - - +
437A ARG* 1.4 64.5 + - - +
438A GLU 3.3 2.9 - - - -
439A LYS* 3.1 20.3 + - + +
440A ILE* 3.0 37.9 + - + +
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Residues in contact with ARG 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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420A HIS* 5.6 2.7 - - - +
423A LEU* 4.1 23.1 - - + -
424A ARG* 5.5 2.2 - - - +
427A GLU* 3.4 24.8 + - - -
433A LEU 2.9 19.0 + - - +
434A LYS* 4.3 10.3 + - - +
435A ASP 3.5 1.0 - - - -
436A ASN* 1.4 73.8 - - - +
438A GLU* 1.4 57.9 + - - +
440A ILE* 3.7 9.8 - - - +
441A GLU* 2.8 80.9 + - + +
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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
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434A LYS 5.0 2.1 + - - +
435A ASP 4.2 10.6 + - - +
436A ASN 3.3 0.6 - - - -
437A ARG* 1.4 80.9 - - - +
439A LYS* 1.4 63.6 + - + +
441A GLU* 4.0 7.5 - - - +
442A LYS* 3.2 58.5 + - - +
476A TRP* 3.5 24.4 - - + -
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Residues in contact with LYS 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 5.2 13.0 - - + +
435A ASP 5.3 5.2 - - - +
436A ASN* 3.1 21.5 + - + +
438A GLU* 1.4 78.0 - - + +
440A ILE* 1.3 62.2 + - + +
442A LYS* 3.5 8.0 + - - +
443A ILE* 3.2 26.1 + - - +
476A TRP* 3.8 56.5 - - + +
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Residues in contact with ILE 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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82A LEU* 5.0 7.9 - - + -
85A ILE* 4.5 17.9 - - + -
86A PHE* 3.6 33.4 - - + -
158A LEU* 5.5 6.1 - - + -
423A LEU* 3.8 30.5 - - + -
433A LEU* 5.0 0.9 - - + -
436A ASN* 3.0 31.4 + - + +
437A ARG* 3.3 6.0 + - - +
439A LYS* 1.3 72.3 - - + +
441A GLU* 1.3 59.2 + - - +
443A ILE* 3.2 9.7 - - + +
444A LEU* 3.0 53.4 + - + +
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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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416A LEU* 4.7 0.9 - - - +
420A HIS* 3.9 36.1 - - + +
423A LEU* 4.9 4.9 - - + -
437A ARG* 2.8 68.6 + - + +
438A GLU* 4.0 5.8 - - - +
440A ILE* 1.3 70.8 - - - +
442A LYS* 1.3 56.7 + - + +
444A LEU* 3.5 8.7 + - + +
445A THR* 3.0 34.1 + - - -
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Residues in contact with LYS 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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438A GLU* 3.2 50.7 + - + +
439A LYS* 3.7 8.1 - - - +
440A ILE 3.3 0.2 - - - -
441A GLU* 1.3 77.4 - - + +
443A ILE* 1.3 57.4 + - - +
445A THR* 3.3 5.3 + - - -
446A PHE* 2.8 31.0 + - - +
475A PRO* 6.2 5.8 - - + -
476A TRP* 3.8 19.5 - - + -
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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
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78A ARG* 2.6 46.8 + - - +
81A TYR* 3.9 36.3 - - + -
82A LEU* 5.9 3.8 - - + +
85A ILE* 4.6 14.4 - - + -
162A ILE* 4.7 9.3 - - + +
165A ARG* 3.9 0.3 + - - -
439A LYS 3.2 12.2 + - - +
440A ILE* 3.2 18.6 - - + +
442A LYS* 1.3 74.3 - - - +
444A LEU* 1.4 69.0 + - + +
445A THR 3.7 0.2 + - - -
446A PHE* 3.8 18.4 - - + +
474A THR* 5.9 2.9 - - - +
475A PRO* 5.9 5.8 - - + -
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Residues in contact with LEU 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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82A LEU* 6.6 0.4 - - + -
158A LEU 5.9 0.2 - - - +
161A MET 4.2 7.2 - - - +
162A ILE* 3.7 25.4 - - + -
165A ARG* 2.9 31.0 + - + +
412A HIS* 4.9 7.1 - - - +
416A LEU* 3.5 25.9 - - + +
419A LEU* 3.5 42.8 - - + -
420A HIS* 5.6 1.1 - - + -
423A LEU* 5.2 2.2 - - + -
440A ILE* 3.0 47.9 + - + +
441A GLU* 3.7 6.7 - - + +
443A ILE* 1.4 76.5 - - + +
445A THR* 1.4 56.8 + - - +
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Residues in contact with THR 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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165A ARG* 3.6 0.6 + - - -
168A PHE* 3.3 39.4 - - + -
412A HIS* 5.0 2.2 - - + +
416A LEU* 4.0 19.6 - - + +
441A GLU* 3.0 18.4 + - - +
442A LYS* 3.7 5.2 - - - -
444A LEU* 1.4 77.5 - - - +
446A PHE* 1.3 64.1 + - - +
447A ARG 3.8 0.5 + - - -
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Residues in contact with PHE 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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78A ARG* 3.0 26.8 + - - -
81A TYR* 6.0 4.9 - + - -
165A ARG* 2.9 22.7 + - - -
442A LYS 2.8 21.9 + - - +
443A ILE* 3.8 24.9 - - + +
444A LEU 3.6 1.0 - - - -
445A THR* 1.3 72.0 - - - +
447A ARG* 1.4 71.0 + - - +
448A ILE* 3.6 36.1 - - + -
449A PRO* 5.9 1.3 - - + -
455A LEU* 5.3 9.4 - - + -
475A PRO* 3.4 35.0 - - + -
17B C 4.7 3.6 - - - +
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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