Contacts of the helix formed by residues 436 - 452 (chain A) in PDB entry 5OQN
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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384A GLU* 5.6 6.8 - - - +
385A ALA* 5.1 9.7 + - + +
386A SER* 4.8 6.8 + - - -
433A ASP* 4.9 4.0 + - - +
434A TYR* 3.5 13.5 - - - +
435A SER* 1.3 83.6 + - - +
437A GLU* 1.3 60.1 + - - +
438A VAL* 2.6 40.6 + - - +
439A GLY* 2.7 17.5 + - - +
440A ARG* 3.5 14.0 + - - +
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Residues in contact with GLU 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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434A TYR 5.0 2.3 - - - +
435A SER 3.3 6.1 + - - +
436A ASP* 1.3 76.0 + - - +
438A VAL* 1.3 65.5 + - + +
439A GLY 3.2 1.8 - - - -
440A ARG* 2.0 48.7 + - - +
441A ARG* 3.0 50.6 + - - +
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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
----------------------------------------------------------
386A SER* 4.6 12.8 - - - +
436A ASP* 2.6 15.1 + - - +
437A GLU* 1.3 74.8 - - + +
439A GLY* 1.3 56.4 + - - +
441A ARG* 4.1 5.0 - - - +
442A SER* 2.9 33.7 + - - -
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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
----------------------------------------------------------
385A ALA* 3.8 16.3 - - - +
386A SER* 3.6 31.3 + - - -
434A TYR* 4.9 0.2 - - - -
436A ASP* 2.7 19.9 + - - -
438A VAL* 1.3 73.2 - - - +
440A ARG* 1.3 61.6 + - - +
442A SER* 3.3 1.0 + - - -
443A MET* 3.0 26.3 + - - +
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Residues in contact with ARG 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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434A TYR* 4.3 30.5 - - + -
436A ASP 3.5 16.7 + - - +
437A GLU* 2.0 46.7 + - - +
439A GLY* 1.3 76.1 - - - +
441A ARG* 1.3 75.1 + - - +
443A MET* 3.9 1.5 - - - +
444A LEU* 2.9 48.0 + - - +
471A LEU* 3.5 47.5 + - + +
472A SER* 5.5 1.2 - - - +
473A ILE* 4.6 18.7 - - - +
477A ASP* 5.6 1.6 + - - -
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Residues in contact with ARG 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 GLU* 3.0 39.8 + - - +
438A VAL* 4.1 5.6 - - - +
440A ARG* 1.3 93.0 - - - +
442A SER* 1.3 61.8 + - - +
444A LEU* 3.6 14.1 - - + +
445A THR* 2.9 27.2 + - - -
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Residues in contact with SER 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A SER* 4.4 7.7 + - - -
389A SER* 2.8 25.5 + - - -
438A VAL* 2.9 22.6 + - - -
439A GLY* 3.5 6.3 - - - -
440A ARG 3.2 0.2 - - - -
441A ARG* 1.3 72.9 - - - +
443A MET* 1.3 66.9 + - - +
445A THR* 3.0 18.1 + - - -
446A VAL* 3.2 13.9 + - - +
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Residues in contact with MET 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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385A ALA* 4.1 17.5 - - - +
388A LEU* 4.3 13.2 - - + -
389A SER* 4.0 15.5 - - - -
392A LEU* 3.6 29.2 - - - -
429A ALA* 3.7 18.2 - - + -
432A TYR* 5.2 2.0 - - + -
434A TYR* 3.1 32.1 - - + +
439A GLY 3.0 13.3 + - - +
440A ARG* 3.9 3.1 - - - +
442A SER* 1.3 77.2 + - - +
444A LEU* 1.3 54.7 + - - +
446A VAL* 2.5 34.0 + - - +
447A VAL* 3.0 13.9 + - + +
467A VAL* 4.4 11.4 - - + -
471A LEU* 4.1 11.9 - - + -
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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 ARG* 2.9 34.7 + - - +
441A ARG* 3.6 14.4 - - + +
443A MET* 1.3 75.0 - - - +
445A THR* 1.3 59.3 + - - +
447A VAL* 3.2 4.8 - - - +
448A ARG* 3.0 43.0 + - + +
468A MET* 4.2 14.4 - - + +
471A LEU* 3.3 32.8 - - + +
472A SER 5.5 1.1 - - - +
481A MET* 3.7 40.2 - - + -
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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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441A ARG 2.9 14.8 + - - -
442A SER* 3.0 10.9 + - - -
444A LEU* 1.3 78.0 - - - +
446A VAL* 1.3 58.6 + - - +
448A ARG* 4.2 6.1 - - - +
449A ASN* 2.6 43.2 + - - +
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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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389A SER* 3.9 19.7 - - - +
392A LEU* 4.4 8.5 - - + -
393A ASN* 3.3 50.4 - - + +
396A ILE* 3.8 11.0 - - + +
442A SER* 3.2 17.9 - - - +
443A MET* 2.5 26.4 + - + +
445A THR* 1.3 71.4 - - - +
447A VAL* 1.3 59.3 + - + +
449A ASN* 3.5 3.6 + - - +
450A MET* 2.9 27.9 + - - +
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Residues in contact with VAL 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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392A LEU* 5.2 8.5 - - + -
443A MET* 3.0 13.2 + - + +
444A LEU* 3.2 20.9 - - - +
446A VAL* 1.3 74.6 - - + +
448A ARG* 1.3 61.5 + - + +
450A MET* 2.9 22.3 + - + -
451A LEU* 2.5 42.1 + - + +
464A GLY 4.5 6.5 - - - +
467A VAL* 3.9 29.8 - - + -
468A MET* 4.2 27.1 - - + -
471A LEU* 4.5 3.4 - - + -
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Residues in contact with ARG 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* 3.0 33.7 + - + +
445A THR* 4.5 2.9 - - - +
447A VAL* 1.3 78.4 - - + +
449A ASN* 1.3 63.5 + - - +
451A LEU* 5.0 0.2 - - - -
452A ALA* 3.2 27.2 + - - +
468A MET* 4.4 14.8 - - - -
481A MET* 3.2 43.7 - - + +
484A GLU* 3.7 21.0 + - - -
485A ILE* 4.2 24.7 - - + +
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Residues in contact with ASN 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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393A ASN* 5.8 2.0 - - - +
396A ILE* 5.4 1.2 - - - +
401A HIS* 5.2 7.1 - - + -
445A THR* 2.6 42.6 + - - +
446A VAL* 3.5 4.5 + - - +
447A VAL 3.2 0.4 - - - -
448A ARG* 1.3 79.7 - - - +
450A MET* 1.3 59.6 - - - +
452A ALA* 4.1 6.9 - - - +
453A LEU* 3.6 19.8 + - - +
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Residues in contact with MET 450 (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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392A LEU* 5.4 3.1 - - + -
396A ILE* 3.8 33.4 - - + -
400A TYR* 6.2 0.2 - - - -
422A ILE* 4.3 19.5 - - - -
426A SER* 5.0 8.3 - - - +
446A VAL 2.9 17.5 + - - +
447A VAL* 2.9 18.7 + - + +
449A ASN* 1.3 77.1 - - - +
451A LEU* 1.3 71.8 + - + +
452A ALA 3.2 1.1 - - - -
453A LEU* 3.0 26.7 + - + +
456A LEU* 3.5 26.6 - - + +
460A LEU* 4.2 10.8 - - + +
463A ILE* 5.5 0.7 - - + -
464A GLY* 3.7 30.7 - - - +
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Residues in contact with LEU 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 VAL 2.5 24.3 + - - +
450A MET* 1.3 73.7 - - + +
452A ALA* 1.3 58.2 + - - +
456A LEU* 4.1 15.9 - - + -
461A ILE* 4.1 11.2 - - + +
464A GLY* 3.8 33.2 - - - +
465A ILE* 3.8 29.6 - - + +
468A MET* 3.7 30.3 - - + -
485A ILE* 3.7 23.6 - - + +
489A ILE* 3.9 0.7 - - - +
581A ARG* 2.9 36.3 + - - +
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Residues in contact with ALA 452 (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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448A ARG 3.2 19.8 + - - +
449A ASN* 4.4 7.9 - - - +
450A MET 3.2 0.8 - - - -
451A LEU* 1.3 74.2 - - - +
453A LEU* 1.3 66.1 + - - +
454A THR* 3.4 6.8 + - - +
485A ILE* 3.7 16.7 - - + +
488A ASP* 6.4 2.2 - - + -
489A ILE* 3.9 15.8 - - + +
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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