Contacts of the helix formed by residues 437 - 445 (chain A) in PDB entry 1Q6Z
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 ALA 437 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A ALA* 5.5 0.2 - - - -
49A CYS* 3.6 18.0 - - + -
53A ILE* 4.7 2.5 - - + -
407A LEU* 3.8 9.9 - - + -
408A PRO* 3.7 31.2 - - + -
411A ILE* 3.1 18.9 - - + +
434A SER 3.1 15.6 + - - +
436A SER* 1.3 79.2 + - - +
438A LEU* 1.3 62.3 + - - +
440A THR* 2.9 19.4 + - - +
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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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407A LEU* 3.9 15.8 - - + +
411A ILE* 4.4 3.1 - - - -
435A ILE* 3.2 40.0 + - + +
436A SER 3.0 0.6 - - - -
437A ALA* 1.3 77.6 - - - +
439A TRP* 1.3 62.4 + - - +
441A ALA* 3.1 15.2 + - - +
442A ALA 3.2 9.0 + - - -
450A PHE* 3.7 39.0 - - + -
486A LEU 4.4 5.6 - - - +
487A ALA* 4.2 25.1 - - - +
490A TYR* 3.9 13.2 - - + -
492A VAL* 3.6 17.8 - - + +
518A LEU* 4.3 15.0 - - + -
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Residues in contact with TRP 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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43A LEU* 3.7 44.6 - - + -
45A LEU* 3.5 33.9 - - + -
436A SER 3.1 13.7 + - - +
437A ALA 3.0 1.0 + - - -
438A LEU* 1.3 79.3 - - - +
440A THR* 1.3 66.6 + - - +
442A ALA* 3.2 1.9 + - - +
443A GLN* 2.8 77.3 + - + +
444A TYR* 5.0 2.5 - + - -
489A GLY 5.6 0.2 - - - -
490A TYR* 3.6 38.2 - + + +
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Residues in contact with THR 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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42A ILE* 3.7 17.0 - - + -
43A LEU 2.8 26.8 + - - +
44A ALA* 3.4 17.5 - - - +
45A LEU 4.7 0.5 + - - -
53A ILE* 3.8 15.5 - - + -
411A ILE* 4.3 10.1 - - + -
436A SER 5.0 0.2 + - - -
437A ALA* 2.9 12.2 + - - -
439A TRP* 1.3 85.7 - - - +
441A ALA* 1.3 63.2 + - - +
444A TYR* 3.1 40.0 + - + +
446A ILE* 4.3 2.1 - - + +
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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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411A ILE* 3.8 24.7 - - + +
437A ALA 3.7 2.4 + - - -
438A LEU 3.1 10.6 + - - +
440A THR* 1.3 79.8 - - - +
442A ALA* 1.3 55.7 + - - +
445A ASN* 3.0 10.0 + - - -
446A ILE* 2.9 49.8 + - - +
448A THR* 5.2 0.2 - - - +
450A PHE* 4.4 7.2 - - + -
492A VAL* 5.0 0.2 - - + -
516A PRO* 3.7 17.9 - - + +
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Residues in contact with ALA 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 LEU 3.2 5.1 + - - +
439A TRP 3.2 5.5 + - - +
441A ALA* 1.3 78.7 - - - +
443A GLN* 1.3 72.4 + - + +
445A ASN* 3.3 13.2 + - - +
490A TYR 3.3 26.0 - - - +
491A GLY* 3.6 21.3 - - - +
492A VAL* 4.1 2.7 - - + -
516A PRO* 4.0 9.8 - - - +
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Residues in contact with GLN 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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439A TRP* 2.8 74.7 + - + +
440A THR 3.4 3.1 + - - +
442A ALA* 1.3 79.7 + - - +
444A TYR* 1.3 75.4 + - + +
445A ASN* 5.3 0.5 - - - +
490A TYR 5.6 0.2 + - - -
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Residues in contact with TYR 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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40A ARG* 5.4 4.3 - - + -
41A TYR* 3.3 21.4 + - - -
42A ILE* 4.0 19.3 - - + -
43A LEU* 3.0 49.8 + - + +
415A LEU* 6.0 0.7 - - + -
439A TRP* 5.0 2.3 - + - -
440A THR* 3.1 29.0 + - + +
443A GLN* 1.3 90.4 - - + +
445A ASN* 1.3 69.6 + - - +
446A ILE* 3.3 19.1 - - + +
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Residues in contact with ASN 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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441A ALA 3.0 9.0 + - - -
442A ALA 3.3 10.2 + - - +
443A GLN 3.4 0.8 - - - +
444A TYR* 1.3 81.3 - - - +
446A ILE* 1.3 60.4 + - - +
447A PRO* 3.4 10.8 - - - +
514A LYS* 3.3 20.8 + - - +
515A GLY* 3.4 21.1 - - - -
516A PRO* 3.7 4.5 - - - +
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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