Contacts of the helix formed by residues 432 - 446 (chain A) in PDB entry 4D10
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 432 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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426A ALA* 4.0 1.8 - - - -
431A THR* 1.3 81.6 + - - +
433A VAL* 1.3 62.0 + - - +
434A ALA* 4.5 4.2 - - - +
435A ALA* 3.3 20.8 + - - +
436A LEU* 2.8 30.5 + - - +
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Residues in contact with VAL 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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422A MET* 4.0 27.4 - - + +
423A HIS* 3.8 29.4 - - + +
426A ALA* 4.0 17.3 - - + -
432A THR* 1.3 74.2 - - - +
434A ALA* 1.3 57.7 + - - +
436A LEU* 3.4 2.8 + - + +
437A GLU* 2.8 28.3 + - - +
458A LYS* 3.8 35.4 - - + -
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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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432A THR* 3.3 3.7 - - - +
433A VAL* 1.3 75.4 - - - +
435A ALA* 1.3 61.2 + - - +
437A GLU* 3.2 9.1 + - - +
438A ASP* 2.9 36.5 + - - +
458A LYS* 5.0 8.7 - - - +
325C ARG* 5.2 0.2 + - - -
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Residues in contact with ALA 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 THR* 3.4 17.0 - - - +
432A THR* 3.3 22.3 + - - +
434A ALA* 1.3 74.5 - - - +
436A LEU* 1.3 60.0 + - - +
438A ASP* 3.5 9.9 + - - +
439A GLU* 3.0 38.4 + - - +
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Residues in contact with LEU 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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410A LEU* 4.3 18.2 - - + -
422A MET* 3.5 37.9 - - + +
425A MET* 3.8 39.3 - - + +
426A ALA* 3.8 2.2 - - + +
429A PHE* 4.4 3.1 - - + -
431A THR* 3.9 17.0 + - + -
432A THR 2.8 20.2 + - - +
433A VAL* 3.5 5.2 - - - +
435A ALA* 1.3 72.3 - - - +
437A GLU* 1.3 54.5 + - - +
439A GLU* 3.7 10.6 + - + +
440A LEU* 2.8 60.4 + - + +
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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
----------------------------------------------------------
422A MET* 3.8 11.5 - - + +
433A VAL 2.8 13.8 + - - +
434A ALA* 3.3 12.6 - - - +
436A LEU* 1.3 77.0 - - - +
438A ASP* 1.3 53.7 + - - +
440A LEU* 3.6 2.6 + - - +
441A THR* 2.8 37.4 + - - -
453A VAL* 3.8 19.6 - - + +
455A SER* 3.3 24.1 - - - -
458A LYS* 2.8 36.0 + - - +
314C PHE* 3.3 23.9 - - + -
317C LEU* 4.7 0.3 - - - +
321C ASP* 4.2 10.2 - - - +
325C ARG* 3.9 9.0 + - - +
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Residues in contact with ASP 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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434A ALA* 2.9 26.5 + - - +
435A ALA* 3.7 10.5 - - - +
437A GLU* 1.3 71.9 - - - +
439A GLU* 1.3 61.0 + - + +
441A THR* 3.2 5.9 + - - -
442A GLN* 3.0 28.1 + - - +
325C ARG* 2.7 38.3 + - - +
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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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406A ARG* 3.0 34.2 + - - -
410A LEU* 4.5 12.1 - - + +
431A THR* 3.8 17.1 + - - +
435A ALA* 3.0 32.2 + - - +
436A LEU* 3.7 10.8 + - - +
438A ASP* 1.3 75.9 - - + +
440A LEU* 1.3 56.8 + - + +
442A GLN* 3.4 7.7 + - - +
443A LEU* 2.9 38.7 + - + +
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Residues in contact with LEU 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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410A LEU* 4.7 3.8 - - + -
422A MET* 3.9 15.0 - - + -
425A MET* 4.0 17.3 - - + -
436A LEU* 2.8 49.2 + - + +
437A GLU 3.9 3.1 - - - +
439A GLU* 1.3 69.3 - - - +
441A THR* 1.3 61.4 + - - +
443A LEU* 3.0 17.1 + - + +
444A ILE* 2.8 38.3 + - + +
449A ILE* 4.7 15.9 - - + -
453A VAL* 4.5 9.2 - - + -
460A LEU* 3.8 36.1 - - + -
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Residues in contact with THR 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A GLU 2.8 21.2 + - - -
438A ASP* 3.2 8.2 + - - -
440A LEU* 1.3 77.2 - - - +
442A GLN* 1.3 56.4 + - - +
444A ILE* 3.3 2.4 + - - -
445A LEU* 3.0 44.0 + - + +
453A VAL* 4.4 4.3 - - - +
310C LEU* 6.3 0.2 - - + -
313C THR* 3.5 33.4 - - + +
314C PHE* 3.4 29.0 - - + -
325C ARG* 4.6 10.1 - - - +
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Residues in contact with GLN 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 ASP 3.0 13.3 + - - +
439A GLU* 3.5 10.8 - - - +
441A THR* 1.3 77.4 - - - +
443A LEU* 1.3 60.4 + - + +
445A LEU* 3.5 17.0 + - - +
446A GLU* 3.4 34.3 + - - +
447A GLY 4.3 1.6 + - - -
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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
----------------------------------------------------------
407A ASN* 4.2 31.0 - - + +
410A LEU* 3.7 38.4 - - + -
411A ILE* 4.4 15.0 - - + -
439A GLU* 2.9 24.4 + - + +
440A LEU* 3.0 16.1 + - + +
442A GLN* 1.3 75.6 - - + +
444A ILE* 1.3 60.0 + - - +
447A GLY* 3.1 40.1 + - - +
449A ILE* 3.8 25.9 + - + -
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Residues in contact with ILE 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 LEU* 2.8 25.8 + - + +
441A THR* 3.9 6.3 - - - +
443A LEU* 1.3 73.9 - - - +
445A LEU* 1.3 64.4 + - - +
446A GLU* 3.3 4.1 + - - -
447A GLY 4.4 1.9 - - - +
449A ILE* 3.5 33.4 - - + +
450A SER* 5.1 0.7 - - - -
451A ALA* 3.3 37.2 - - + +
452A ARG* 4.0 3.8 - - - +
453A VAL* 3.8 27.8 - - + -
460A LEU* 4.4 3.8 - - + -
312C LYS 3.4 21.1 - - - +
313C THR* 4.0 9.6 - - + +
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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
----------------------------------------------------------
441A THR* 3.0 39.7 + - + +
442A GLN* 3.8 18.8 - - - +
443A LEU 3.5 0.2 - - - -
444A ILE* 1.3 77.9 - - - +
446A GLU* 1.3 74.8 + - + +
309C ARG* 4.4 40.4 - - + +
312C LYS* 4.8 21.8 + - + +
313C THR* 3.5 16.4 - - + -
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Residues in contact with GLU 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A GLN* 3.4 24.5 + - - +
444A ILE 4.3 0.7 - - - -
445A LEU* 1.3 90.8 - - + +
447A GLY* 1.3 68.5 - - - +
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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