Contacts of the helix formed by residues 430 - 440 (chain A) in PDB entry 2P6U
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 THR 430 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428A ALA* 4.1 1.7 - - - +
429A LYS* 1.3 83.6 - - + +
431A LEU* 1.3 64.7 + - - +
432A GLU* 3.2 16.9 + - - +
433A GLU* 2.9 37.9 + - - +
434A LEU* 3.1 20.1 + - - +
472A ALA 5.7 2.5 - - - +
473A HIS* 4.8 8.1 - - + +
474A LEU* 4.0 11.2 - - - +
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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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430A THR* 1.3 71.6 - - - +
432A GLU* 1.3 68.6 + - - +
434A LEU* 3.1 18.4 + - + -
435A GLU* 2.8 55.6 + - + +
452A SER 4.8 0.2 - - - +
455A LEU* 4.0 23.8 - - + +
456A GLU* 3.8 35.9 - - + +
459A VAL* 4.2 8.3 - - + -
474A LEU* 4.0 10.9 - - + +
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Residues in contact with GLU 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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430A THR* 3.2 15.0 + - - +
431A LEU* 1.3 81.6 + - - +
433A GLU* 1.3 51.7 + - - +
435A GLU* 2.6 39.2 + - - +
436A ASP* 2.8 22.2 + - - +
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Residues in contact with GLU 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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168A ARG* 4.6 7.2 + - - +
427A TYR 4.0 6.1 - - - +
428A ALA* 3.2 13.6 - - - +
429A LYS* 2.9 45.4 + - - +
430A THR* 2.9 35.3 + - - +
432A GLU* 1.3 75.8 - - + +
434A LEU* 1.3 61.8 + - - +
436A ASP* 3.6 18.6 - - + +
437A PHE* 3.2 16.6 + - - +
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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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419A SER* 4.4 11.9 - - - -
422A ILE* 4.2 18.8 - - + -
423A ILE* 4.4 12.8 - - + -
428A ALA* 3.3 16.6 - - + -
430A THR 3.1 12.2 + - - +
431A LEU* 3.1 19.9 + - + +
432A GLU 2.9 1.0 + - - -
433A GLU* 1.3 78.0 - - - +
435A GLU* 1.3 64.7 + - - +
437A PHE* 3.1 13.4 + - - +
438A PHE* 3.2 32.3 + - + -
455A LEU* 3.7 20.0 - - + -
459A VAL* 3.4 33.4 - - + -
474A LEU* 5.3 1.6 - - + -
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Residues in contact with GLU 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 LEU* 2.8 55.2 + - + +
432A GLU* 2.6 15.5 + - - +
434A LEU* 1.3 78.5 - - - +
436A ASP* 1.3 62.3 + - - +
438A PHE* 3.5 3.3 + - - +
439A ALA* 3.1 20.3 + - - +
451A LEU 6.3 0.2 - - - +
452A SER* 2.7 46.6 + - - +
455A LEU* 3.9 13.2 - - + -
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Residues in contact with ASP 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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168A ARG* 3.2 16.5 + - - +
432A GLU* 2.8 17.1 + - - +
433A GLU* 3.8 19.0 + - + +
434A LEU 3.2 0.2 - - - -
435A GLU* 1.3 76.3 - - - +
437A PHE* 1.3 68.6 + - - +
439A ALA* 2.8 23.2 + - - +
440A ASP* 3.2 4.2 - - - +
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Residues in contact with PHE 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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161A ILE* 4.0 19.3 - - + -
164A THR* 3.5 29.9 - - + +
165A LYS* 3.5 32.8 - - + -
168A ARG* 3.0 33.3 - - - +
422A ILE* 3.4 40.8 - - + -
427A TYR* 4.0 21.5 - + + -
428A ALA* 5.0 0.4 - - + -
433A GLU 3.2 11.7 + - - +
434A LEU* 3.1 12.9 + - - +
436A ASP* 1.3 78.3 - - - +
438A PHE* 1.3 64.0 + + + +
440A ASP* 2.8 28.4 + - - +
441A THR* 3.9 3.1 + - - -
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Residues in contact with PHE 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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161A ILE* 4.3 9.0 - - + -
409A LEU* 3.4 35.2 - - + +
415A LEU* 3.2 40.4 - - + -
418A HIS* 4.5 2.9 - - + -
419A SER* 4.1 18.4 - - - -
422A ILE* 3.4 31.9 - - + -
434A LEU* 3.2 20.9 + - + +
435A GLU 3.9 7.0 - - - +
437A PHE* 1.3 80.1 - + - +
439A ALA* 1.3 57.1 + - - +
441A THR* 2.7 29.4 + - - -
443A PHE* 5.4 2.8 - - - -
444A PHE* 3.7 6.8 + - - +
451A LEU* 4.3 13.4 - - + +
455A LEU* 3.8 17.9 - - + -
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Residues in contact with ALA 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 GLU 3.1 11.7 + - - +
436A ASP* 2.8 20.5 + - - +
438A PHE* 1.3 74.4 - - - +
440A ASP* 1.3 59.4 + - - +
441A THR 3.0 6.1 + - - +
444A PHE* 2.8 54.9 - - + +
445A LYS 4.5 0.3 + - - -
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Residues in contact with ASP 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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164A THR* 3.8 20.4 + - + -
168A ARG* 3.0 36.7 + - - +
191A TRP* 3.0 21.1 + - - -
436A ASP* 3.2 8.5 - - - +
437A PHE 2.8 9.0 + - - +
439A ALA* 1.3 78.7 - - - +
441A THR* 1.3 59.4 + - - +
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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