Contacts of the helix formed by residues 437 - 452 (chain A) in PDB entry 2XOA
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 PRO 437 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410A LEU* 4.0 16.2 - - + -
413A GLN* 3.3 42.2 - - + +
414A PHE* 4.1 24.9 - - + -
436A LEU* 1.3 85.7 - - + +
438A ILE* 1.3 63.1 + - - +
439A GLU* 3.4 2.9 - - - -
440A ALA* 3.3 8.2 + - + -
441A VAL* 2.9 26.0 + - + +
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Residues in contact with ILE 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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414A PHE* 4.6 5.4 - - + -
436A LEU* 2.8 59.6 + - + +
437A PRO* 1.3 72.2 - - - +
439A GLU* 1.3 68.5 + - + +
441A VAL* 3.8 4.7 - - - +
442A ILE* 3.0 34.1 + - + +
511A ALA* 4.6 18.4 - - + +
514A SER* 3.4 33.0 - - - +
518A ILE* 4.0 15.7 - - + -
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Residues in contact with GLU 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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46A LEU* 6.0 2.3 - - - +
437A PRO 3.4 0.8 - - - -
438A ILE* 1.3 83.6 - - - +
440A ALA* 1.3 57.0 + - + +
442A ILE* 3.5 6.4 + - - +
443A LEU* 3.1 26.9 + - - +
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Residues in contact with ALA 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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43A GLY 3.7 18.9 - - - +
44A ASN* 5.3 7.2 - - + +
410A LEU* 3.8 23.8 - - + -
437A PRO* 3.3 11.6 + - + +
438A ILE 3.2 0.6 - - - -
439A GLU* 1.3 74.8 - - + +
441A VAL* 1.3 57.0 + - - +
442A ILE 3.1 1.1 - - - -
443A LEU* 3.1 2.4 + - - +
444A SER* 2.7 36.6 + - - -
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Residues in contact with VAL 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A LEU* 3.9 22.1 - - + +
411A TYR* 4.4 9.9 - - + -
414A PHE* 3.7 40.8 - - + -
437A PRO* 2.9 20.9 + - + +
438A ILE* 3.8 3.8 - - - +
440A ALA* 1.3 75.6 - - - +
442A ILE* 1.3 62.9 + - - +
444A SER* 3.6 1.8 - - - -
445A LEU* 2.9 44.8 + - + +
518A ILE* 4.0 25.1 - - + -
522A LEU* 6.1 0.7 - - + -
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Residues in contact with ILE 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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438A ILE* 3.0 38.4 + - + +
439A GLU* 3.8 6.7 - - - +
441A VAL* 1.3 77.4 - - - +
443A LEU* 1.3 58.0 + - - +
445A LEU* 3.3 2.8 + - - +
446A GLN* 2.8 45.4 + - - +
514A SER* 4.0 13.5 - - - +
517A GLU* 3.8 35.4 - - - +
518A ILE* 3.7 19.5 - - + -
521A LEU* 3.8 14.3 - - + +
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Residues in contact with LEU 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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43A GLY 3.6 22.9 - - - +
44A ASN* 3.8 7.2 - - - +
45A ARG* 3.6 39.7 - - + +
439A GLU 3.1 15.9 + - - +
440A ALA 3.1 1.0 + - - -
442A ILE* 1.3 77.5 - - - +
444A SER* 1.3 57.9 + - - +
446A GLN* 3.2 20.4 + - + +
447A ASP* 2.8 49.1 + - - +
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Residues in contact with SER 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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43A GLY* 3.7 17.6 - - - +
407A THR* 4.6 5.9 + - - +
410A LEU* 3.5 20.4 - - - +
411A TYR* 2.7 30.8 + - - -
440A ALA 2.7 21.4 + - - -
441A VAL 3.6 3.1 - - - -
443A LEU* 1.3 71.2 - - - +
445A LEU* 1.3 56.5 + - - +
447A ASP* 3.0 5.1 + - - +
448A LEU* 2.8 36.7 + - - +
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Residues in contact with LEU 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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411A TYR* 2.8 39.5 - - + +
441A VAL* 2.9 41.4 + - + +
442A ILE* 3.5 6.7 - - - +
444A SER* 1.3 76.7 + - - +
446A GLN* 1.3 63.6 + - - +
448A LEU* 3.3 2.6 + - - +
449A ILE* 2.9 31.2 + - + +
518A ILE* 4.2 5.8 - - + -
521A LEU* 3.8 34.3 - - + +
522A LEU* 4.1 28.5 - - + +
525A LEU* 4.1 17.0 - - + -
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Residues in contact with GLN 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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442A ILE* 2.8 39.7 + - + +
443A LEU* 3.7 24.7 - - + +
445A LEU* 1.3 74.3 - - - +
447A ASP* 1.3 63.2 + - - +
449A ILE* 3.5 9.4 + - - +
450A GLY* 3.2 17.5 + - - -
517A GLU* 4.2 9.9 + - - -
521A LEU* 4.2 16.3 - - + +
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Residues in contact with ASP 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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42A PHE* 3.3 22.5 - - + -
43A GLY 2.8 29.5 + - - +
45A ARG* 2.8 35.7 + - - -
116A MET* 5.3 0.3 - - - +
443A LEU* 2.8 21.2 + - - +
444A SER* 3.3 5.2 - - - +
446A GLN* 1.3 74.8 - - - +
448A LEU* 1.3 67.5 + - + +
450A GLY* 3.1 3.9 + - - -
451A TYR* 2.9 22.0 + - - +
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Residues in contact with LEU 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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42A PHE* 5.9 4.7 - - + -
403A MET* 5.0 9.2 - - + -
407A THR* 3.7 29.2 - - + +
411A TYR* 3.7 22.2 - - - +
444A SER* 2.8 20.9 + - - +
445A LEU 4.0 2.2 - - - +
447A ASP* 1.3 75.5 - - + +
449A ILE* 1.3 64.5 + - - +
451A TYR* 3.0 11.9 + - + -
452A PHE* 2.9 36.2 + - + -
478A PHE* 4.0 32.3 - - + -
525A LEU* 3.9 26.2 - - + -
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Residues in contact with ILE 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 LEU* 2.9 24.0 + - + +
446A GLN* 3.8 6.3 - - - +
448A LEU* 1.3 77.6 - - - +
450A GLY* 1.3 62.4 + - - +
452A PHE* 3.4 3.1 + - - +
453A GLU* 3.2 19.6 + - - +
521A LEU* 3.6 47.1 - - + +
524A GLU* 3.7 32.3 - - + +
525A LEU* 4.1 25.1 - - + +
528A SER* 4.5 13.2 + - - +
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Residues in contact with GLY 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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446A GLN 3.2 10.6 + - - -
447A ASP 3.1 6.7 + - - -
449A ILE* 1.3 77.2 - - - +
451A TYR* 1.3 61.6 + - - +
453A GLU* 3.3 28.0 + - - +
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Residues in contact with TYR 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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42A PHE* 5.6 6.7 - + + -
396A GLU* 4.4 2.6 + - - +
399A GLN* 4.2 5.3 + - - -
400A ALA* 3.6 21.0 + - - +
403A MET* 3.3 34.7 - - + +
447A ASP 2.9 13.7 + - - +
448A LEU* 3.0 17.0 + - + +
450A GLY* 1.3 75.7 - - - +
452A PHE* 1.3 78.5 + + - +
453A GLU 3.4 2.2 + - - +
474A ARG* 2.6 79.1 + - + +
478A PHE* 3.7 23.1 - + - -
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Residues in contact with PHE 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 LEU* 2.9 27.4 + - + +
449A ILE 3.7 2.2 - - - +
451A TYR* 1.3 98.9 - + - +
453A GLU* 1.3 65.2 + - - +
454A PRO* 3.4 6.5 - - - +
471A LEU* 3.6 20.1 - - + +
474A ARG* 3.8 7.2 - - + -
475A GLN* 3.8 40.4 - - + -
478A PHE* 3.6 39.3 - + - -
525A LEU* 3.9 19.1 - - + -
528A SER* 3.8 33.3 - - - +
529A LEU* 3.5 18.8 - - + -
531A ARG* 5.8 0.7 + - - +
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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