Contacts of the helix formed by residues 437 - 444 (chain D) in PDB entry 4K9P
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44D ALA* 5.6 0.7 - - - -
45D LEU 6.0 0.2 - - - +
49D CYS* 3.6 16.2 - - + -
53D ILE* 4.8 2.9 - - + -
407D LEU* 3.8 10.3 - - + -
408D PRO* 3.7 31.4 - - + -
411D ILE* 3.1 18.5 - - + +
434D SER 3.1 15.7 + - - +
436D SER* 1.3 81.1 + - - +
438D LEU* 1.3 62.0 + - - +
440D THR* 2.8 20.6 + - - +
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Residues in contact with LEU 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407D LEU* 4.0 10.8 - - + +
411D ILE* 4.5 4.0 - - - -
435D ILE* 3.2 38.7 + - + +
436D SER 3.0 0.6 - - - -
437D ALA* 1.3 78.1 - - - +
439D TRP* 1.3 61.4 - - - +
441D ALA* 3.1 14.7 + - - +
442D ALA 3.1 9.4 + - - -
450D PHE* 3.7 43.5 - - + -
486D LEU* 4.6 3.6 - - + +
487D ALA* 4.1 26.5 - - + +
490D TYR* 4.0 11.4 - - + -
492D VAL* 3.6 19.3 - - + +
518D LEU* 4.3 15.9 - - + -
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Residues in contact with TRP 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477B ASP 3.9 6.5 - - - -
478B VAL* 3.7 15.9 - - + -
479B PRO* 2.8 27.8 + - + -
480B GLY 3.7 9.4 - - - -
481B ILE* 3.5 24.2 - - + +
43D LEU* 3.7 45.3 - - + -
45D LEU* 3.6 26.9 - - + -
436D SER 3.0 13.2 + - - +
437D ALA 2.9 0.6 + - - -
438D LEU* 1.3 78.9 - - - +
440D THR* 1.3 66.7 + - - +
442D ALA* 3.4 1.2 + - - +
443D GLN* 2.9 62.2 + - + +
444D TYR* 4.8 3.6 - + - -
490D TYR* 3.6 30.2 - + + +
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Residues in contact with THR 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ILE* 3.9 12.3 - - + -
43D LEU 2.7 26.8 + - - +
44D ALA* 3.4 16.6 - - - +
45D LEU 4.6 0.7 + - - -
53D ILE* 3.9 22.2 - - + +
411D ILE* 4.4 10.3 - - + -
436D SER 5.0 0.2 + - - -
437D ALA* 2.8 12.4 + - - -
439D TRP* 1.3 85.7 - - - +
441D ALA* 1.3 63.9 + - - +
444D TYR* 3.0 40.0 + - + +
446D ILE* 4.3 1.7 - - + +
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Residues in contact with ALA 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411D ILE* 3.6 25.7 - - + +
437D ALA 3.5 2.0 + - - -
438D LEU 3.1 10.7 + - - +
440D THR* 1.3 78.8 - - - +
442D ALA* 1.3 62.0 + - - +
445D ASN* 3.2 4.0 + - - -
446D ILE* 2.9 49.5 + - - +
450D PHE* 4.3 8.3 - - + -
492D VAL* 5.0 0.4 - - + -
516D PRO* 3.8 15.8 - - + +
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Residues in contact with ALA 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438D LEU 3.1 6.5 + - - +
439D TRP 3.8 3.1 - - - +
441D ALA* 1.3 81.3 - - - +
443D GLN* 1.3 67.9 + - + +
444D TYR 3.4 0.5 + - - -
445D ASN* 3.4 15.2 + - - +
490D TYR 3.5 19.7 - - - +
491D GLY* 3.4 28.7 - - - +
492D VAL* 4.0 3.4 - - + -
516D PRO* 4.0 10.5 - - + +
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Residues in contact with GLN 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479B PRO* 3.2 36.5 + - - +
480B GLY* 4.3 5.9 + - - -
439D TRP* 2.9 57.7 + - + +
442D ALA* 1.3 82.7 - - - +
444D TYR* 1.3 80.0 + - + +
445D ASN* 3.4 8.7 + - - -
490D TYR 5.7 0.2 + - - -
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Residues in contact with TYR 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B GLY* 5.8 0.3 - - - -
40D ARG* 6.0 0.9 - - + -
41D TYR* 3.4 19.9 + - - -
42D ILE* 3.8 19.1 - - + -
43D LEU* 2.9 52.5 + - + +
415D LEU* 5.7 2.6 - - + +
439D TRP* 4.8 3.4 - + - -
440D THR* 3.0 35.1 + - + +
443D GLN* 1.3 88.9 - - + +
445D ASN* 1.3 78.8 + - - +
446D ILE* 3.2 21.0 + - + +
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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