Contacts of the helix formed by residues 427 - 440 (chain A) in PDB entry 1T94
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
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Residue Dist Surf HB Arom Phob DC
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425A ILE* 4.4 1.0 - - - +
426A ASN* 1.3 111.2 + - - +
428A ALA* 1.3 65.4 + - - +
429A GLU* 3.2 14.8 - - + +
430A GLU* 2.9 28.8 + - + +
431A GLN* 3.1 10.8 + - - +
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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
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426A ASN 3.6 5.1 + - - -
427A LYS* 1.3 65.6 - - - +
429A GLU* 1.3 75.0 + - - +
431A GLN* 2.9 24.9 + - - +
432A TYR* 2.9 24.7 + - + -
496A ILE* 3.8 28.3 - - + -
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Residues in contact with GLU 429 (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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427A LYS* 3.6 21.6 - - + +
428A ALA* 1.3 81.3 + - - +
430A GLU* 1.3 62.5 + - + +
432A TYR* 3.2 6.6 + - - +
433A SER* 3.0 25.7 + - - -
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Residues in contact with GLU 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A ILE* 3.7 35.7 - - + +
427A LYS* 2.9 21.9 + - + +
429A GLU* 1.3 80.8 - - + +
431A GLN* 1.3 60.6 + - - +
433A SER* 3.6 8.1 + - - -
434A LEU* 3.3 24.9 + - - +
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Residues in contact with GLN 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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425A ILE* 3.6 23.9 + - + -
426A ASN* 3.9 3.9 - - - +
427A LYS 3.3 11.2 - - - +
428A ALA* 2.9 24.6 + - - +
430A GLU* 1.3 78.0 - - - +
432A TYR* 1.3 56.7 + - - +
434A LEU* 3.6 3.4 - - - +
435A CYS* 3.2 19.9 + - - +
492A LEU* 3.6 8.5 - - + +
496A ILE* 3.5 22.8 - - + +
504A LEU* 2.7 43.3 + - - +
506A LEU* 3.6 14.1 - - + +
509A MET* 3.2 27.9 - - + +
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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
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428A ALA* 2.9 28.0 + - + +
429A GLU* 3.2 5.8 + - - +
431A GLN* 1.3 73.0 - - - +
433A SER* 1.3 60.5 + - - +
434A LEU 3.0 2.0 - - - -
435A CYS* 2.8 21.0 + - - +
436A GLN* 2.8 10.6 + - - +
485A PHE* 3.7 12.0 - + + -
489A LYS* 3.7 44.0 - - + -
492A LEU* 3.7 17.7 - - + -
493A LYS* 2.8 39.1 - - + +
496A ILE* 3.4 24.2 - - + +
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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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429A GLU 3.0 16.4 + - - -
430A GLU* 3.6 9.9 + - - -
432A TYR* 1.3 77.6 - - - +
434A LEU* 1.3 58.7 + - - +
436A GLN* 3.3 14.9 + - - +
437A GLU* 2.9 32.5 + - - +
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Residues in contact with LEU 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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420A ARG* 3.8 33.9 - - + +
422A PHE* 3.8 33.2 - - + -
425A ILE* 4.2 15.3 - - + -
430A GLU 3.3 20.3 + - - +
431A GLN* 3.6 4.5 - - - +
432A TYR 3.0 0.6 - - - -
433A SER* 1.3 76.8 + - - +
435A CYS* 1.3 62.3 + - - +
436A GLN 3.1 0.2 - - - -
437A GLU* 3.3 16.8 + - + +
438A LEU* 3.0 39.7 + - + +
509A MET* 4.1 22.9 - - + -
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Residues in contact with CYS 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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431A GLN 3.2 12.1 + - - +
432A TYR* 2.8 11.4 + - - +
434A LEU* 1.3 79.7 - - - +
436A GLN* 1.3 55.8 + - - +
438A LEU* 3.6 4.2 - - - +
439A CYS* 2.9 36.6 + - - -
458A ILE* 4.7 3.8 - - - -
485A PHE* 3.8 9.6 - - + -
488A ALA* 3.2 43.5 - - - -
489A LYS 4.4 0.2 - - - -
492A LEU* 3.9 15.7 - - + -
509A MET* 3.8 17.0 - - - -
511A VAL* 4.7 6.5 - - - -
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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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432A TYR 2.8 6.2 + - - +
433A SER* 3.5 16.0 - - - +
434A LEU 3.1 0.2 - - - -
435A CYS* 1.3 74.2 - - - +
437A GLU* 1.3 57.9 + - - +
438A LEU 2.9 8.6 + - - -
439A CYS* 4.0 1.6 - - - +
440A SER* 3.1 25.6 + - - -
485A PHE* 3.4 45.2 - - + -
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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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420A ARG* 4.0 11.1 + - - -
433A SER* 2.9 22.7 + - - +
434A LEU* 3.5 28.9 - - + +
436A GLN* 1.3 75.3 - - - +
438A LEU* 1.3 57.5 + - - +
440A SER* 4.0 8.8 - - - -
441A GLU* 3.7 18.5 + - - +
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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
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418A VAL* 3.3 32.0 - - + +
419A GLU 4.6 0.4 - - - +
420A ARG* 4.5 19.3 - - + -
434A LEU* 3.0 21.8 - - + +
435A CYS 3.6 4.7 - - - +
436A GLN 2.9 0.2 - - - -
437A GLU* 1.3 80.4 - - + +
439A CYS* 1.3 59.1 + - - +
440A SER 3.0 4.5 - - - -
441A GLU* 3.0 28.9 + - - +
442A LEU* 3.5 10.7 + - - +
509A MET* 3.6 42.0 - - + +
510A GLY* 4.2 2.9 - - - -
511A VAL* 3.8 25.0 - - + +
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Residues in contact with CYS 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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435A CYS* 2.9 26.8 + - - +
436A GLN* 4.1 4.0 - - + +
438A LEU* 1.3 76.5 - - - +
440A SER* 1.3 57.4 + - - +
442A LEU* 3.2 11.6 - - - +
484A ILE* 3.1 51.7 - - + +
485A PHE* 3.5 35.9 - - + +
488A ALA* 3.6 17.3 - - - -
511A VAL* 4.4 7.9 - - - -
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Residues in contact with SER 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 GLN* 3.1 19.1 + - - -
437A GLU* 4.2 8.5 - - - -
438A LEU 3.0 0.4 - - - -
439A CYS* 1.3 76.3 - - - +
441A GLU* 1.3 57.8 + - - +
442A LEU 2.8 10.6 + - - -
443A ALA* 3.2 16.3 + - - +
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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
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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