Contacts of the helix formed by residues 434 - 449 (chain A) in PDB entry 3OPY
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 434 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431A SER* 2.8 19.5 + - - +
433A SER* 1.4 93.8 + - - +
435A TRP* 1.4 59.4 + - - +
436A LYS 3.3 2.9 - - - +
437A ASP* 3.5 26.0 - - + +
438A ASP* 3.0 27.9 + - - +
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Residues in contact with TRP 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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422A TYR* 4.4 3.8 + - - +
424A PHE* 3.7 28.0 - + - -
430A PRO* 3.5 27.4 - - + -
431A SER 3.3 24.9 + - - +
432A GLU* 3.8 16.3 + - - -
433A SER 4.0 0.2 - - - -
434A ASN* 1.4 74.5 - - - +
436A LYS* 1.3 83.1 + - + +
438A ASP* 3.4 5.5 + - - +
439A LEU* 2.9 51.0 + - + +
464A ASP* 4.4 7.8 + - + -
470A ILE* 3.7 42.3 - - + +
474A GLU* 3.9 21.0 + - + -
475A VAL* 4.1 7.4 - - + -
478A VAL* 3.8 20.6 - - + -
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Residues in contact with LYS 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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432A GLU 6.0 0.7 - - - +
434A ASN* 3.3 0.4 - - - -
435A TRP* 1.3 117.8 - - + +
437A ASP* 1.3 62.1 + - - +
439A LEU* 3.4 3.5 + - - +
440A LYS* 3.1 38.6 + - - +
474A GLU* 5.4 9.1 + - - +
478A VAL* 3.4 29.8 - - + +
481A GLU* 5.4 5.2 - - - +
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Residues in contact with ASP 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 SER 4.6 1.9 - - - +
434A ASN* 3.5 32.8 + - + +
435A TRP 3.3 0.2 - - - -
436A LYS* 1.3 80.4 - - - +
438A ASP* 1.3 57.9 + - - +
440A LYS* 3.7 24.0 + - - +
441A LYS* 3.2 24.6 + - - +
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Residues in contact with ASP 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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422A TYR* 3.4 24.4 + - - +
430A PRO* 5.6 1.1 - - + +
434A ASN 3.0 18.6 + - - +
435A TRP* 3.4 6.3 + - - +
437A ASP* 1.3 72.9 - - - +
439A LEU* 1.4 65.6 + - - +
441A LYS* 3.3 8.6 + - - +
442A VAL* 3.1 32.3 + - - +
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Residues in contact with LEU 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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422A TYR* 3.8 39.0 - - + -
424A PHE* 4.1 4.5 - - + -
435A TRP* 2.9 36.4 + - + +
436A LYS 3.4 6.7 - - - +
438A ASP* 1.4 75.7 - - - +
440A LYS* 1.3 62.3 + - - +
442A VAL* 3.5 1.4 + - - +
443A CYS* 3.1 47.9 + - - -
456A VAL* 3.9 10.8 - - + -
475A VAL* 3.7 27.6 - - + +
478A VAL* 4.0 17.7 - - + -
479A LEU* 3.9 6.7 - - + -
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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 LYS* 3.1 17.1 + - - +
437A ASP* 3.7 25.4 + - - +
439A LEU* 1.3 78.8 - - - +
441A LYS* 1.4 64.4 + - - +
443A CYS* 3.5 3.6 + - - +
444A LEU* 3.0 31.1 + - + +
478A VAL* 3.8 17.0 - - + +
479A LEU* 6.0 2.5 - - + -
481A GLU* 3.0 41.9 + - - +
482A ILE* 3.4 38.6 - - + +
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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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437A ASP 3.2 12.6 + - - +
438A ASP* 3.3 17.2 + - - +
440A LYS* 1.4 78.4 - - - +
442A VAL* 1.4 54.4 + - + +
444A LEU* 3.3 3.8 + - - +
445A ARG* 2.9 38.8 + - - +
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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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421A ASP* 3.4 28.9 - - + +
422A TYR* 4.1 20.0 - - + -
438A ASP* 3.1 29.8 + - - +
439A LEU 3.8 3.8 - - - +
441A LYS* 1.4 73.5 - - + +
443A CYS* 1.3 62.9 + - - +
445A ARG* 3.4 24.7 + - - +
446A HIS* 3.1 40.7 + - + +
584A SER* 4.2 6.1 - - - +
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Residues in contact with CYS 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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421A ASP* 4.0 21.3 - - - +
422A TYR* 5.1 0.2 - - - -
439A LEU* 3.1 43.0 + - - +
440A LYS* 3.9 4.0 - - - +
442A VAL* 1.3 76.1 - - - +
444A LEU* 1.3 59.3 + - + +
446A HIS* 3.2 5.9 + - - +
447A ARG* 2.9 32.7 + - + +
454A THR* 3.7 28.3 - - + -
456A VAL* 4.5 2.0 - - - -
479A LEU* 3.8 12.6 - - + -
482A ILE* 5.6 2.2 - - + -
484A LEU* 5.4 5.2 - - + -
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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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440A LYS* 3.0 24.3 + - + +
441A LYS* 3.9 2.9 - - - +
443A CYS* 1.3 73.7 - - - +
445A ARG* 1.4 59.3 + - - +
447A ARG* 3.6 16.6 - - + +
448A GLU* 2.9 29.6 + - - +
482A ILE* 3.6 50.7 - - + +
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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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441A LYS* 2.9 16.1 + - - +
442A VAL* 3.4 32.0 - - - +
443A CYS 3.2 0.2 - - - -
444A LEU* 1.4 75.3 - - - +
446A HIS* 1.4 72.2 + - - +
448A GLU* 3.2 10.7 - - + +
449A LYS* 3.2 20.4 + - - +
584A SER* 2.6 37.2 + - - -
585A LYS* 3.6 6.5 - - - +
587A ASP* 3.3 33.9 - - + +
588A ASP* 3.5 25.0 + - - +
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Residues in contact with HIS 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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421A ASP* 3.4 34.7 + - + +
442A VAL* 3.1 35.7 + - + +
443A CYS 3.2 5.3 + - - +
445A ARG* 1.4 81.3 - - - +
447A ARG* 1.3 60.9 + - - +
449A LYS* 3.0 18.7 + - - +
450A GLY 3.2 1.2 + - - -
451A ARG* 3.1 35.0 + - + +
583A VAL 5.3 0.7 - - - -
584A SER* 3.1 37.1 + - - -
587A ASP* 3.1 25.8 + - - -
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Residues in contact with ARG 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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394A HIS* 2.7 32.9 + - - -
395A SER* 3.6 5.1 + - - +
396A ARG 3.4 16.4 + - - +
443A CYS 2.9 20.4 + - - +
444A LEU* 3.6 19.1 - - + +
445A ARG 3.4 0.2 - - - -
446A HIS* 1.3 74.7 - - - +
448A GLU* 1.3 60.7 + - - +
450A GLY 3.3 5.5 + - - -
451A ARG* 3.3 13.5 + - + +
452A ARG* 2.8 75.8 + - - +
454A THR* 3.5 23.3 + - + +
482A ILE* 6.0 0.2 - - - -
484A LEU* 3.5 27.2 - - - +
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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 LEU 2.9 14.3 + - - +
445A ARG* 3.2 14.4 - - - +
447A ARG* 1.3 76.1 - - - +
449A LYS* 1.4 63.7 + - + +
450A GLY* 3.2 5.1 + - - -
452A ARG* 5.2 1.0 + - - -
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Residues in contact with LYS 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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445A ARG* 3.2 4.4 + - + +
446A HIS* 3.0 8.4 + - - +
448A GLU* 1.4 81.8 - - + +
450A GLY* 1.3 55.2 + - - +
451A ARG 3.8 0.9 - - - -
587A ASP* 3.5 38.9 + - + +
652A TRP* 3.6 61.9 - - + +
653A ILE* 4.7 6.8 + - - +
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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