Contacts of the helix formed by residues 427 - 442 (chain A) in PDB entry 2YPT
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 LYS 427 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A GLU 5.4 1.8 - - - +
330A LEU* 5.0 7.2 - - + +
331A ALA* 3.6 28.4 - - + +
334A GLY* 6.3 1.3 - - - -
422A ALA* 3.2 13.9 + - + +
425A LEU* 4.8 12.3 - - + +
426A GLY* 1.3 76.7 - - - +
428A ALA* 1.3 56.5 + - - +
429A LYS 3.5 2.0 - - - -
430A ASP* 4.0 9.9 - - + +
431A LEU* 3.0 29.8 + - - +
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Residues in contact with ALA 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ALA 3.9 1.6 + - - -
423A LYS* 3.8 30.7 - - + +
426A GLY 3.2 5.2 - - - +
427A LYS* 1.3 74.0 - - - +
429A LYS* 1.3 59.9 + - - +
431A LEU* 3.5 2.0 + - - +
432A TYR* 3.1 28.6 + - - +
469A LEU* 4.0 30.4 - - + +
472A MET 5.3 4.9 - - - -
50D HIS* 4.4 5.4 + - + -
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Residues in contact with LYS 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A GLY 4.7 2.8 + - - +
427A LYS* 3.5 0.4 - - - +
428A ALA* 1.3 77.8 - - - +
430A ASP* 1.3 59.9 + - - +
432A TYR* 3.6 4.0 - - - +
433A SER* 3.4 21.3 + - - -
50D HIS* 4.3 23.5 + - + +
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Residues in contact with ASP 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A GLU* 3.5 33.0 - - + +
328A GLU* 3.5 11.3 - - + +
331A ALA* 3.7 10.3 - - + -
427A LYS* 3.6 12.4 + - + +
428A ALA 3.3 0.4 - - - -
429A LYS* 1.3 77.6 - - - +
431A LEU* 1.4 58.8 + - - +
433A SER* 3.6 4.1 + - - -
434A ALA* 3.1 26.3 + - - +
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Residues in contact with LEU 431 (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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331A ALA* 3.5 21.0 - - + +
332A VAL* 5.3 0.9 - - + +
335A HIS* 6.2 1.1 - - + -
419A ASP* 5.9 2.2 - - - +
422A ALA* 4.8 8.1 - - + -
427A LYS 3.0 19.4 + - - +
428A ALA 3.9 4.0 - - - +
429A LYS 3.4 0.2 - - - -
430A ASP* 1.4 73.9 - - - +
432A TYR* 1.4 56.2 + - - +
434A ALA* 3.5 5.5 - - - +
435A LEU* 2.9 44.2 + - + +
469A LEU* 4.5 18.6 - - + -
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Residues in contact with TYR 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ALA 3.1 18.4 + - - +
429A LYS 3.6 7.0 - - - +
431A LEU* 1.4 75.8 - - - +
433A SER* 1.3 62.4 + - - +
436A ILE* 3.4 42.3 + - + +
466A LEU* 3.3 63.5 - - + +
469A LEU* 4.3 10.5 - - + +
470A LYS* 3.7 20.2 - - + +
49D THR* 3.5 39.8 + - + -
50D HIS* 3.4 24.9 - + - +
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Residues in contact with SER 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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328A GLU* 3.1 22.8 + - - +
429A LYS 3.4 13.2 + - - -
430A ASP* 3.8 6.1 - - - -
431A LEU 3.3 0.2 - - - -
432A TYR* 1.3 80.4 - - - +
434A ALA* 1.4 59.0 + - - +
436A ILE* 3.6 6.8 + - - +
437A LYS* 3.1 24.6 + - - +
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Residues in contact with ALA 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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324A CYS* 4.2 6.1 - - - -
328A GLU* 3.4 24.0 + - + +
332A VAL* 3.8 27.6 - - + -
430A ASP 3.1 18.5 + - - +
431A LEU* 3.3 8.0 + - - +
433A SER* 1.4 73.5 - - - +
435A LEU* 1.4 54.0 + - + +
437A LYS* 3.2 2.6 + - - +
438A LEU* 2.8 40.6 + - - +
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Residues in contact with LEU 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A VAL* 5.6 4.5 - - + -
335A HIS* 6.3 1.3 - - + -
419A ASP* 4.8 4.9 - - - +
431A LEU* 2.9 28.1 + - + +
432A TYR 4.1 4.9 - - - +
434A ALA* 1.4 72.3 - - + +
436A ILE* 1.3 57.4 + - - +
438A LEU* 4.0 12.4 - - + +
439A ASN* 3.1 26.7 + - - +
462A LEU* 3.4 21.3 - - + +
465A ARG* 3.5 61.9 - - + +
466A LEU* 4.3 6.3 - - + -
469A LEU* 4.2 17.9 - - + -
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Residues in contact with ILE 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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57A GLN* 4.8 4.9 - - + +
58A ILE* 3.4 37.6 - - + +
432A TYR* 3.4 43.6 + - + +
433A SER* 3.9 8.1 - - - +
434A ALA 3.3 0.4 - - - -
435A LEU* 1.3 72.6 - - - +
437A LYS* 1.4 61.3 + - - +
439A ASN* 3.1 10.0 + - - +
440A LYS* 2.9 28.5 + - + +
462A LEU* 4.5 6.1 - - + -
466A LEU* 3.7 26.7 - - + -
49D THR* 5.9 1.1 - - + -
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Residues in contact with LYS 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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322A GLN 4.9 10.3 - - - +
323A GLY 3.3 25.6 - - - +
324A CYS* 4.1 6.7 - - - -
328A GLU* 3.8 12.8 - - - +
433A SER 3.1 19.5 + - - +
434A ALA 3.2 4.0 + - - +
436A ILE* 1.4 78.3 - - - +
438A LEU* 1.4 54.5 + - - +
440A LYS* 3.5 13.8 + - + +
441A ASP* 2.8 61.9 + - - +
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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
----------------------------------------------------------
264A SER* 3.7 32.5 - - - +
265A ASN* 6.0 1.1 - - - -
283A LEU* 3.7 21.1 - - + -
324A CYS* 4.0 16.6 - - - -
332A VAL* 4.1 26.7 - - + -
434A ALA 2.8 23.7 + - - +
435A LEU* 4.1 11.0 - - + +
437A LYS* 1.4 69.7 - - - +
439A ASN* 1.4 60.0 + - - +
441A ASP* 3.4 7.5 + - - +
442A ASN* 3.1 40.5 + - - +
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Residues in contact with ASN 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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58A ILE* 5.3 6.5 + - - +
59A MET* 5.4 7.9 - - - +
435A LEU 3.1 15.3 + - - +
436A ILE* 3.3 10.3 + - - +
438A LEU* 1.4 76.1 - - - +
440A LYS* 1.4 60.3 + - - +
442A ASN* 3.4 3.5 + - - +
443A LEU 2.9 9.7 + - - -
444A GLY* 2.9 63.0 + - - +
445A PHE 4.9 2.1 - - - +
446A PRO* 5.0 6.5 - - - +
462A LEU* 3.6 33.8 - - + +
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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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58A ILE 5.4 6.7 - - - +
59A MET* 6.1 1.1 - - + -
63A THR* 4.3 26.4 - - + +
436A ILE* 2.9 13.2 + - + +
437A LYS* 3.7 21.3 - - + +
438A LEU 3.4 0.2 - - - -
439A ASN* 1.4 77.6 - - - +
441A ASP* 1.3 61.8 + - - +
443A LEU* 3.5 12.0 + - - +
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Residues in contact with ASP 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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155A PHE* 3.3 17.8 - - - -
262A SER* 4.3 9.5 - - - +
264A SER* 3.8 21.1 + - - +
322A GLN 4.0 10.7 + - - +
323A GLY* 3.4 30.2 - - - +
437A LYS* 2.8 46.2 + - - +
438A LEU* 3.5 12.0 - - - +
440A LYS* 1.3 76.8 - - - +
442A ASN* 1.4 59.5 + - - +
443A LEU 3.4 1.3 + - - -
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Residues in contact with ASN 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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70A TYR* 3.7 13.2 - - - -
71A GLN* 4.6 1.4 + - - -
74A LYS* 5.6 0.2 + - - -
155A PHE* 3.7 10.6 - - - -
263A HIS* 3.4 21.5 - - + +
264A SER* 2.9 46.7 + - - -
438A LEU* 3.1 23.1 + - - +
439A ASN* 3.4 3.1 + - - +
441A ASP* 1.4 76.1 - - - +
443A LEU* 1.4 69.0 + - - +
444A GLY* 3.3 4.3 + - - +
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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
------------------------------------------------------------
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