Contacts of the helix formed by residues 437 - 445 (chain X) in PDB entry 3F6E
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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44X ALA* 5.5 0.7 - - - -
49X CYS* 3.7 16.2 - - + -
53X ILE* 4.8 2.5 - - + -
407X LEU* 3.7 12.8 - - + -
408X PRO* 3.7 30.5 - - + -
411X ILE* 3.1 19.2 - - + +
434X SER 3.1 15.4 + - - +
436X SER* 1.3 78.8 + - - +
438X LEU* 1.3 64.4 + - - +
439X TRP 3.0 0.2 - - - -
440X THR* 3.0 20.1 + - - +
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Residues in contact with LEU 438 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407X LEU* 3.8 18.2 - - + +
411X ILE* 4.5 2.7 - - - -
435X ILE* 3.1 40.5 + - + +
436X SER 3.0 1.0 - - - -
437X ALA* 1.3 78.1 - - - +
439X TRP* 1.3 61.9 - - - +
441X ALA* 3.2 5.1 + - - +
442X ALA 3.1 16.8 + - - -
450X PHE* 3.7 36.1 - - + -
486X LEU 4.4 3.6 - - - +
487X ALA* 4.1 26.9 - - - +
490X TYR* 3.9 11.9 - - + -
492X VAL* 3.4 22.1 - - + +
518X LEU* 4.2 15.3 - - + -
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Residues in contact with TRP 439 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43X LEU* 3.6 43.3 - - + -
45X LEU* 3.6 37.0 - - + +
436X SER 3.1 13.5 + - - +
437X ALA 3.0 1.0 - - - -
438X LEU* 1.3 78.9 - - - +
440X THR* 1.3 67.7 + - - +
442X ALA* 3.2 1.7 + - - +
443X GLN* 2.8 72.1 + - + +
444X TYR* 5.2 2.2 - + - -
489X GLY 5.5 0.7 - - - -
490X TYR* 3.6 40.9 - + + +
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Residues in contact with THR 440 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42X ILE* 3.7 17.0 - - + -
43X LEU 2.7 27.2 + - - +
44X ALA* 3.3 16.8 - - - +
45X LEU 4.7 0.5 + - - -
53X ILE* 3.9 15.5 - - + -
411X ILE* 4.3 10.3 - - + -
436X SER 5.0 0.2 + - - -
437X ALA* 3.0 12.7 + - - -
439X TRP* 1.3 86.6 - - - +
441X ALA* 1.3 63.4 + - - +
444X TYR* 3.1 40.5 + - + +
446X ILE* 4.3 1.7 - - + +
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Residues in contact with ALA 441 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411X ILE* 3.8 26.6 - - + +
437X ALA 3.6 2.4 + - - -
438X LEU 3.2 9.8 + - - +
440X THR* 1.3 77.9 - - - +
442X ALA* 1.3 57.6 + - - +
445X ASN* 2.9 11.3 + - - -
446X ILE* 2.9 48.4 + - - +
450X PHE* 4.2 9.6 - - + -
516X PRO* 3.6 16.9 - - + +
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Residues in contact with ALA 442 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438X LEU 3.1 5.8 + - - +
439X TRP 3.2 4.0 + - - +
441X ALA* 1.3 76.7 - - - +
443X GLN* 1.3 70.8 + - + +
445X ASN* 3.2 14.6 + - - +
490X TYR 3.2 27.8 - - - +
491X GLY* 3.6 23.3 - - - +
492X VAL* 3.9 5.6 - - + -
516X PRO* 3.9 10.5 - - - +
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Residues in contact with GLN 443 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439X TRP* 2.8 73.4 + - + +
440X THR 4.1 2.7 - - - +
442X ALA* 1.3 78.1 - - - +
444X TYR* 1.3 75.4 + - + +
445X ASN* 3.4 0.7 - - - +
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Residues in contact with TYR 444 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41X TYR* 3.3 19.5 + - - -
42X ILE* 4.0 20.2 - - + -
43X LEU* 3.0 50.8 + - + +
415X LEU* 6.1 0.4 - - + -
439X TRP* 5.2 2.2 - + - -
440X THR* 3.1 30.3 + - + +
443X GLN* 1.3 87.7 - - + +
445X ASN* 1.3 69.1 + - - +
446X ILE* 3.5 24.3 + - + +
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Residues in contact with ASN 445 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441X ALA 2.9 10.4 + - - -
442X ALA 3.2 11.0 + - - +
443X GLN 3.4 1.1 - - - +
444X TYR* 1.3 80.6 - - - +
446X ILE* 1.3 59.8 + - - +
447X PRO* 3.3 11.3 - - - +
514X LYS* 3.0 24.5 + - - +
515X GLY* 3.3 19.3 - - - -
516X PRO* 3.5 5.0 - - - +
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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