Contacts of the helix formed by residues 434 - 444 (chain A) in PDB entry 3UON
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 434 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A LEU* 4.0 16.8 - - + +
36A VAL* 3.9 28.0 - - + +
37A THR* 2.5 32.9 + - - +
77A MET* 3.4 17.0 - - - +
431A ILE* 2.6 24.1 + - - -
433A SER* 1.3 71.8 - - - +
435A ILE* 1.3 59.7 + - + -
436A ASN 3.2 4.5 - - - -
437A PRO* 3.3 17.0 - - - +
438A ALA* 4.3 4.9 + - - +
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Residues in contact with ILE 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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395A ALA* 3.8 26.2 - - + -
398A ILE* 5.9 0.7 - - + -
399A THR* 4.4 11.7 - - + -
431A ILE* 3.0 22.6 + - + +
432A ASN* 3.7 24.7 - - - +
434A THR* 1.3 79.9 - - + +
436A ASN* 1.3 63.1 + - - +
437A PRO 3.6 0.4 - - - -
438A ALA* 3.3 13.6 - - + +
439A CYS* 3.1 28.6 + - - -
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Residues in contact with ASN 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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41A ASN* 5.0 0.4 - - - +
65A LEU* 4.0 14.3 - - - +
69A ASP* 2.6 30.9 + - - +
392A ILE* 4.1 15.7 - - - +
395A ALA* 4.7 4.7 - - - +
432A ASN* 2.9 33.2 + - - +
433A SER 4.3 0.7 - - - +
434A THR 3.2 0.2 - - - -
435A ILE* 1.3 76.8 - - - +
437A PRO* 1.3 73.6 - - + +
439A CYS* 3.0 16.6 + - - +
440A TYR* 3.1 41.8 + - + +
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Residues in contact with PRO 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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37A THR* 5.2 0.4 - - - +
40A GLY* 3.8 31.2 - - - +
41A ASN* 3.8 16.8 - - - +
44A VAL* 3.7 16.2 - - + -
433A SER 3.8 7.9 - - - +
434A THR 3.3 15.9 - - - +
436A ASN* 1.3 95.9 - - + +
438A ALA* 1.3 60.2 + - - +
440A TYR* 3.3 17.0 + - + +
441A ALA* 3.2 22.9 + - - +
451A PHE* 3.9 8.2 - - + -
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Residues in contact with ALA 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 THR 4.3 2.8 + - - +
435A ILE* 3.3 23.7 + - + +
436A ASN 3.1 0.2 - - - -
437A PRO* 1.3 80.7 - - - +
439A CYS* 1.3 57.7 + - - +
441A ALA* 3.3 7.0 + - - +
442A LEU* 3.0 41.2 + - + +
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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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388A THR* 5.5 2.0 - - + +
391A ALA* 4.0 36.1 - - + -
392A ILE* 4.5 7.6 - - + -
395A ALA* 4.9 10.1 - - - -
435A ILE* 3.1 27.8 + - - -
436A ASN* 3.0 11.1 + - - +
438A ALA* 1.3 75.5 - - - +
440A TYR* 1.3 61.9 + - + +
442A LEU* 4.4 7.2 - - - +
443A CYS* 2.8 41.3 + - - +
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Residues in contact with TYR 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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41A ASN* 5.5 1.1 + - - -
44A VAL* 3.7 40.2 - - + -
62A LEU* 3.9 37.0 + - + +
65A LEU* 3.6 33.1 - - - +
66A ALA* 4.9 3.8 + - + -
69A ASP* 4.8 0.3 + - - -
388A THR* 4.1 11.4 - - + -
392A ILE* 3.3 22.4 - - + -
436A ASN* 3.1 33.2 + - + +
437A PRO* 3.3 7.8 + - + +
439A CYS* 1.3 76.8 - - - +
441A ALA* 1.3 58.0 + - - +
444A ASN* 2.9 37.4 + - - +
447A PHE* 3.6 23.9 - + + +
451A PHE* 4.9 1.8 - - + -
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Residues in contact with ALA 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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437A PRO 3.2 9.4 + - - +
438A ALA* 3.6 10.1 - - - +
439A CYS 3.2 0.2 - - - -
440A TYR* 1.3 81.9 - - - +
442A LEU* 1.3 61.0 + - + +
444A ASN 3.1 17.4 - - - +
445A ALA* 4.5 0.9 + - - -
447A PHE* 4.3 0.6 - - - +
448A LYS* 3.3 42.6 - - + +
451A PHE* 3.9 16.2 - - + -
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Residues in contact with LEU 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 ALA* 3.0 27.7 + - + +
439A CYS* 4.0 6.5 - - - +
441A ALA* 1.3 82.7 - - + +
443A CYS* 1.3 65.7 + - - +
444A ASN 3.3 1.1 + - - -
448A LYS* 4.8 13.2 - - - +
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Residues in contact with CYS 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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384A LYS* 4.2 4.3 - - - -
387A ARG* 3.3 56.0 + - + +
388A THR* 3.6 27.0 + - - +
391A ALA* 3.9 20.0 - - - -
439A CYS* 2.8 21.9 + - - +
442A LEU* 1.3 78.6 - - - +
444A ASN* 1.3 60.1 + - - +
445A ALA 4.3 0.2 - - - -
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Residues in contact with ASN 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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54A LEU* 4.6 7.5 - - - +
59A ASN* 5.2 5.9 + - - +
384A LYS* 3.5 30.9 - - + +
388A THR* 4.5 8.6 + - - +
440A TYR* 2.9 23.5 + - - +
441A ALA 3.1 11.3 - - - +
442A LEU 3.3 0.6 - - - -
443A CYS* 1.3 81.3 - - - +
445A ALA* 1.3 63.0 + - - +
446A THR* 2.7 40.7 + - - -
447A PHE* 3.3 22.4 + - + -
448A LYS 3.4 8.1 + - - -
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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