Contacts of the helix formed by residues 433 - 447 (chain A) in PDB entry 4PKO
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 ASN 433 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ASP* 3.4 21.3 + - - +
432A GLN* 1.3 79.4 + - + +
434A GLU* 1.3 66.1 + - - +
435A ASP* 4.0 17.6 + - - +
436A GLN* 3.0 37.2 + - - +
437A ASN* 3.1 24.8 + - - +
34B LYS* 5.9 1.8 - - - +
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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
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433A ASN* 1.3 76.6 - - - +
435A ASP* 1.3 66.3 + - - +
437A ASN* 3.0 41.2 + - - +
438A VAL* 3.2 19.6 + - + +
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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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111A MET* 3.3 27.7 - - + +
112A ASN* 3.4 32.1 + - - +
115A ASP* 4.0 19.5 - - + +
116A LEU* 3.4 14.1 - - + +
433A ASN* 3.3 13.7 + - - +
434A GLU* 1.3 79.9 - - - +
436A GLN* 1.3 58.8 + - - +
438A VAL* 3.2 8.1 + - - +
439A GLY 3.0 21.1 + - - -
34B LYS* 5.5 2.6 + - - -
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Residues in contact with GLN 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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115A ASP* 3.2 43.4 + - + +
118A ARG* 4.1 20.6 - - - +
119A GLY* 3.8 9.8 - - - +
122A LYS* 6.1 0.3 - - - +
431A GLY* 3.7 5.0 - - - -
432A GLN* 2.7 54.6 + - - +
433A ASN* 3.0 28.1 + - - +
435A ASP* 1.3 73.9 - - - +
437A ASN* 1.3 67.4 + - - +
439A GLY* 3.1 2.3 + - - +
440A ILE* 2.9 29.7 + - - +
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Residues in contact with ASN 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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429A LEU 5.9 0.2 - - - -
430A ARG* 3.3 29.0 - - - +
431A GLY* 3.0 26.4 + - - +
433A ASN 3.1 12.2 + - - -
434A GLU* 3.0 40.6 + - - +
436A GLN* 1.3 76.3 - - - +
438A VAL* 1.3 56.5 + - - +
440A ILE* 3.3 7.9 + - - +
441A LYS* 3.0 33.3 + - + +
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Residues in contact with VAL 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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106A ALA* 4.5 5.2 - - + -
111A MET* 4.2 30.3 - - + -
116A LEU* 4.2 9.9 - - + -
434A GLU* 3.2 24.4 + - + +
435A ASP* 3.2 9.1 + - - +
437A ASN* 1.3 73.8 - - - +
439A GLY* 1.3 56.2 + - - +
441A LYS* 3.6 5.8 - - - -
442A VAL* 2.6 56.9 + - + +
445A ARG* 5.2 5.8 - - - +
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Residues in contact with GLY 439 (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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116A LEU* 3.7 31.1 - - - +
120A ILE* 3.1 31.0 - - - +
435A ASP 3.0 11.4 + - - -
436A GLN 3.1 4.8 + - - -
438A VAL* 1.3 77.4 - - - +
440A ILE* 1.3 60.6 + - - +
442A VAL* 3.6 2.8 + - - +
443A ALA 3.4 10.2 + - - -
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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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119A GLY* 3.2 21.8 - - - +
122A LYS* 4.5 6.3 - - + -
123A ALA* 3.9 18.5 - - + +
429A LEU* 3.8 33.9 - - + +
430A ARG* 3.2 42.6 - - - +
431A GLY* 3.3 8.5 - - - +
436A GLN 2.9 14.4 + - - +
437A ASN* 3.5 7.9 - - - +
439A GLY* 1.3 76.9 - - - +
441A LYS* 1.3 69.7 + - + +
443A ALA* 3.3 6.2 + - - +
444A LEU* 3.3 25.6 + - + +
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Residues in contact with LYS 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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426A LEU 4.1 2.6 + - - -
427A ALA* 2.6 36.4 + - - +
429A LEU 3.3 10.0 + - - +
430A ARG* 2.9 24.7 - - - +
437A ASN* 3.0 20.6 + - + +
438A VAL* 3.7 7.0 - - + +
440A ILE* 1.3 76.4 - - + +
442A VAL* 1.3 65.6 + - - +
443A ALA 3.1 2.0 - - - -
444A LEU* 3.9 16.0 - - + +
445A ARG* 3.0 37.8 + - - +
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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
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99A ILE* 4.0 17.3 - - - +
102A GLU* 3.8 36.4 - - + +
103A GLY* 4.1 6.7 - - - +
106A ALA* 5.0 3.8 - - + -
116A LEU* 5.3 2.2 - - + -
120A ILE* 4.7 11.4 - - + -
438A VAL* 2.6 45.8 + - + +
439A GLY* 3.9 8.3 - - - +
440A ILE 3.4 0.2 - - - -
441A LYS* 1.3 73.1 - - - +
443A ALA* 1.3 61.8 + - - +
445A ARG* 3.6 21.1 + - - +
446A ALA* 3.3 19.9 + - - +
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Residues in contact with ALA 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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99A ILE* 5.4 6.6 - - + +
120A ILE* 3.9 24.0 - - + +
123A ALA* 4.0 15.3 - - + -
124A VAL* 5.1 5.4 - - + -
439A GLY 3.4 10.3 + - - +
440A ILE 3.3 10.7 + - - +
441A LYS 3.1 0.2 - - - -
442A VAL* 1.3 79.1 - - - +
444A LEU* 1.3 65.2 + - + +
446A ALA* 3.1 13.7 + - - +
447A MET* 3.1 22.7 + - + +
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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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123A ALA* 4.6 9.2 - - + -
423A ALA* 3.6 33.7 - - + +
426A LEU* 3.8 45.3 - - + +
427A ALA* 4.1 8.1 - - + -
440A ILE* 3.3 17.8 + - + +
441A LYS* 3.3 22.4 + - + +
443A ALA* 1.3 76.5 - - - +
445A ARG* 1.3 63.6 + - - +
447A MET* 3.1 37.3 + - - +
448A GLU* 3.9 7.8 + - - +
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Residues in contact with ARG 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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102A GLU* 3.1 46.7 + - + +
438A VAL* 5.1 4.6 + - - +
441A LYS* 3.0 22.9 + - - +
442A VAL* 3.7 30.5 - - - +
444A LEU* 1.3 76.6 - - - +
446A ALA* 1.3 59.8 + - - +
447A MET 3.5 0.2 + - - -
448A GLU* 3.6 29.3 + - - +
449A ALA* 4.3 1.4 + - - +
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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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95A LEU* 3.3 12.3 - - + +
98A ALA* 3.7 26.6 - - + +
99A ILE* 3.7 27.1 - - + +
102A GLU* 6.2 1.3 - - + +
442A VAL 3.3 11.5 + - - +
443A ALA 3.1 9.6 + - - +
444A LEU 3.1 1.0 - - - -
445A ARG* 1.3 75.9 - - - +
447A MET* 1.3 57.9 + - + +
448A GLU 3.1 5.4 - - - -
449A ALA* 3.0 26.4 + - - +
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Residues in contact with MET 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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95A LEU* 4.0 7.6 - - + -
123A ALA 5.9 0.9 - - - +
124A VAL* 6.4 1.6 - - - -
127A ALA* 3.8 17.0 - - + -
419A LEU* 3.4 47.3 - - + +
420A ILE* 3.9 9.1 - - - +
422A VAL* 3.2 31.6 - - + -
423A ALA* 3.9 16.2 - - + -
443A ALA* 3.1 19.5 - - - +
444A LEU* 3.1 23.8 + - - +
446A ALA* 1.3 77.9 - - + +
448A GLU* 1.3 60.8 + - - +
449A ALA 3.3 0.2 - - - -
450A PRO* 3.3 10.6 - - - +
504A LEU* 4.2 23.1 - - + -
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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
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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