Contacts of the helix formed by residues 432 - 447 (chain A) in PDB entry 2ADS
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 432 (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* 4.9 2.0 - - + +
430A VAL 4.1 3.1 - - - +
431A ASP* 1.3 85.4 - - + +
433A TYR* 1.3 71.8 + - + +
435A SER* 2.8 32.4 + - - -
436A PHE* 4.4 3.2 - - - -
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Residues in contact with TYR 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ARG* 2.9 26.9 + - - -
431A ASP* 2.7 40.0 - - + +
432A PRO* 1.3 88.1 - - + +
434A LYS* 1.3 65.9 + - - +
436A PHE* 2.8 25.3 + - + +
437A LEU* 3.0 31.6 + - + +
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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
----------------------------------------------------------
399A THR* 2.9 35.2 + - - +
400A ARG* 3.6 24.0 - - + +
402A GLU* 3.3 24.7 + - - -
403A ALA* 5.5 2.0 - - - +
428A PRO 4.0 3.8 + - - -
429A LYS* 3.8 27.1 - - + +
430A VAL* 4.8 2.0 - - + +
431A ASP* 3.0 37.8 + - - +
432A PRO 3.1 0.2 + - - -
433A TYR* 1.3 77.5 - - + +
435A SER* 1.3 57.1 + - - +
437A LEU* 3.4 12.1 + - + +
438A LEU* 2.9 40.1 + - + +
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Residues in contact with SER 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LEU* 5.5 0.3 - - - +
425A GLU 4.8 8.1 - - - -
426A GLU* 5.4 5.8 - - - -
429A LYS* 4.0 23.3 - - - +
432A PRO 2.8 19.9 + - - -
434A LYS* 1.3 76.5 - - - +
436A PHE* 1.3 72.0 + - - +
438A LEU* 3.4 4.3 + - - +
439A TYR* 2.9 28.9 + - - +
457A LEU* 4.7 17.1 - - - +
459A ARG* 5.8 1.0 + - - -
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Residues in contact with PHE 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A PRO 4.4 4.9 - - - -
433A TYR* 2.8 13.7 + - - +
435A SER* 1.3 91.4 + - - +
437A LEU* 1.3 66.3 + - + +
439A TYR* 3.5 7.5 + - - +
440A ASP* 3.1 34.3 + - - +
457A LEU* 5.4 7.4 - - + -
459A ARG* 4.4 20.0 - - - -
1G A 3.7 31.0 - + - -
15M G 3.6 27.8 - - - -
16M G 4.1 28.7 - - - -
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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
----------------------------------------------------------
400A ARG* 6.0 0.7 - - - +
433A TYR* 3.0 38.4 + - + +
434A LYS* 3.6 11.9 - - + +
436A PHE* 1.3 79.0 - - + +
438A LEU* 1.3 56.6 + - + +
440A ASP* 3.5 11.1 - - - +
441A PHE* 2.8 30.4 + - + +
444A ARG* 3.7 9.9 + - - +
691A ARG* 4.6 21.1 - - - +
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Residues in contact with LEU 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A GLU* 3.5 38.6 - - + +
403A ALA* 5.1 13.2 - - + +
406A LYS* 3.8 28.3 - - + +
424A LEU* 4.5 4.5 - - + -
429A LYS* 3.7 14.4 - - - -
434A LYS* 2.9 34.4 + - + +
435A SER* 3.8 5.4 - - - +
437A LEU* 1.3 73.3 - - + +
439A TYR* 1.3 66.9 + - - +
441A PHE* 3.7 14.5 - - + +
442A VAL* 2.9 30.6 + - - +
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Residues in contact with TYR 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LEU* 4.1 11.1 - - - +
435A SER 2.9 17.8 + - - +
436A PHE* 3.5 6.5 - - - +
438A LEU* 1.3 76.1 - - - +
440A ASP* 1.3 76.6 + - - +
442A VAL* 3.4 2.3 + - - +
443A LYS* 3.1 44.8 + - + +
455A VAL* 3.7 22.4 - - + +
457A LEU* 4.3 12.1 - - + -
688A LEU* 6.4 0.4 - - + -
1G A 3.0 106.9 + + + -
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Residues in contact with ASP 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A PHE* 3.1 23.1 + - - +
437A LEU* 3.5 9.3 - - - +
439A TYR* 1.3 94.3 - - - +
441A PHE* 1.3 58.0 + - - +
443A LYS* 3.4 6.4 + - - +
444A ARG* 2.9 50.6 + - - +
687A LYS* 4.9 7.8 + - - -
688A LEU* 3.2 29.6 - - + +
691A ARG* 5.8 1.4 + - - -
1G A 4.8 4.5 + - - +
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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
----------------------------------------------------------
406A LYS* 6.1 2.9 - - + -
407A LEU* 3.5 39.0 - - + -
410A VAL* 5.8 2.9 - - + -
437A LEU 2.8 21.4 + - - +
438A LEU* 3.3 19.5 + - + +
440A ASP* 1.3 70.6 - - - +
442A VAL* 1.3 67.4 + - + +
444A ARG* 3.0 24.8 + - + +
445A GLU* 2.9 51.7 + - + +
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Residues in contact with VAL 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A LYS* 3.9 28.5 - - + +
410A VAL* 4.9 14.4 - - + -
422A VAL* 4.4 15.3 - - + -
424A LEU* 4.2 17.0 - - + -
438A LEU* 2.9 20.2 + - + +
439A TYR 3.8 3.4 - - - +
441A PHE* 1.3 76.5 - - + +
443A LYS* 1.3 64.1 - - - +
445A GLU 3.2 0.2 + - - -
446A LEU* 2.8 46.2 + - + +
455A VAL* 3.7 24.2 - - + -
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Residues in contact with LYS 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A TYR* 3.1 38.3 + - + +
440A ASP* 3.5 9.6 - - - +
442A VAL* 1.3 76.1 - - - +
444A ARG* 1.3 63.6 + - - +
446A LEU* 3.6 4.5 + - - +
447A LEU* 3.1 33.4 + - + +
453A SER* 3.0 40.3 + - - +
455A VAL* 4.1 15.7 - - + -
688A LEU* 4.3 15.3 - - + -
704A TYR* 4.1 4.9 + - + -
705A TRP* 5.3 1.4 + - - +
706A LEU* 3.8 14.8 + - - -
1G A 2.9 29.9 + - - -
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Residues in contact with ARG 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A LEU* 3.7 12.5 + - - +
440A ASP* 2.9 33.3 + - - +
441A PHE* 3.0 40.2 + - + +
443A LYS* 1.3 78.0 - - - +
445A GLU* 1.3 65.8 + - - +
447A LEU* 3.1 29.1 + - - +
448A LYS* 3.7 6.5 - - - +
688A LEU* 3.7 27.9 + - + +
689A MSE 3.7 29.2 - - + +
691A ARG* 4.9 4.2 - - - +
692A GLY* 3.7 27.1 - - - +
696A ILE* 5.5 3.5 - - + +
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Residues in contact with GLU 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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407A LEU* 5.2 0.6 - - + +
410A VAL* 3.5 28.1 - - + +
411A ILE* 3.6 26.9 - - + +
441A PHE* 2.9 49.7 + - + +
444A ARG* 1.3 74.7 - - - +
446A LEU* 1.3 63.3 + - - +
447A LEU 2.8 6.5 - - - -
448A LYS* 3.0 59.2 + - - +
449A LYS* 4.0 8.1 + - - +
694A GLU* 5.3 0.5 - - - +
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Residues in contact with LEU 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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410A VAL* 4.1 14.6 - - + +
413A LYS* 3.6 25.6 - - + +
420A VAL* 4.3 13.0 - - + -
422A VAL* 4.4 5.6 - - + -
442A VAL* 2.8 39.4 + - + +
443A LYS 3.8 3.8 - - - +
445A GLU* 1.3 74.3 - - - +
447A LEU* 1.3 57.5 + - - +
448A LYS 3.0 1.0 + - - -
449A LYS* 3.2 7.1 + - + -
451A ILE* 3.4 42.5 + - + +
453A SER* 3.6 36.1 - - - -
455A VAL* 4.6 1.1 - - + -
698A LYS* 3.0 15.4 + - - -
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Residues in contact with LEU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LYS* 3.1 22.9 + - + +
444A ARG* 3.1 20.3 + - - +
445A GLU 2.8 0.6 - - - -
446A LEU* 1.3 76.2 - - + +
448A LYS* 1.3 58.6 + - - +
451A ILE 6.0 1.3 - - - +
453A SER* 5.5 2.9 - - - +
531A TYR* 4.3 11.4 - - + +
533A LEU* 4.9 3.6 - - + -
685A ILE* 5.4 3.6 - - + -
688A LEU* 5.9 1.3 - - + -
689A MSE 3.9 24.4 - - + +
696A ILE* 5.3 6.2 - - - +
698A LYS* 3.1 25.5 - - + +
704A TYR* 2.9 63.5 - - + +
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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
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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