Contacts of the helix formed by residues 439 - 451 (chain E) in PDB entry 5UQ9
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 PRO 439 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438E LEU* 1.3 89.1 - - + +
440E ALA* 1.3 62.8 + - - +
441E SER* 3.1 5.2 - - - +
442E LEU* 3.2 13.3 + - - +
196F GLN* 6.0 2.7 - - - +
199F CYS* 3.4 42.5 - - + +
200F GLU* 5.4 1.3 - - + -
202F TYR* 3.8 24.7 - - + -
203F HIS* 3.6 40.8 - - + +
206F LYS* 5.6 2.9 - - - +
419F PRO* 5.6 1.1 - - + +
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Residues in contact with ALA 440 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438E LEU* 2.9 6.8 + - + +
439E PRO* 1.3 75.7 - - - +
441E SER* 1.3 64.5 + - - +
442E LEU 3.1 0.4 - - - -
443E ILE* 3.0 26.2 + - + +
444E GLN* 3.3 14.6 + - - +
256F ASP* 3.9 15.7 - - + +
258F ALA* 4.4 8.2 - - + +
291F SER* 3.5 33.9 - - - +
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Residues in contact with SER 441 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438E LEU 3.8 7.0 + - - -
439E PRO* 4.4 2.6 - - - +
440E ALA* 1.3 78.9 - - - +
442E LEU* 1.3 58.9 + - - +
444E GLN* 3.3 3.8 + - - +
445E ALA* 3.0 22.9 + - - +
202F TYR* 5.5 2.9 + - - -
251F LEU* 3.4 21.2 + - - +
252F PRO* 5.7 0.3 - - - +
254F ILE* 3.3 36.9 - - - +
255F ARG 3.9 13.0 - - - -
256F ASP* 3.7 11.3 - - - +
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Residues in contact with LEU 442 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439E PRO 3.2 12.0 + - - +
440E ALA 3.1 0.6 - - - -
441E SER* 1.3 80.6 + - - +
443E ILE* 1.3 58.7 + - - +
445E ALA 3.3 0.3 + - - -
446E GLN* 2.8 51.0 + - + +
198F ILE* 4.3 4.5 - - + -
199F CYS* 4.1 10.3 - - - -
202F TYR* 3.9 36.6 - - + -
236F THR* 3.8 31.6 - - + +
239F ILE* 3.9 18.6 - - + -
240F LEU* 4.9 1.8 - - + -
251F LEU* 3.7 27.8 - - + -
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Residues in contact with ILE 443 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439E PRO 4.0 0.4 + - - -
440E ALA* 3.0 16.6 + - + +
442E LEU* 1.3 78.0 - - - +
444E GLN* 1.3 53.5 + - - +
446E GLN* 3.0 15.3 + - - +
447E ARG* 2.6 57.3 + - + +
192F TYR 5.8 0.4 - - - +
195F MET* 4.0 12.8 - - + -
196F GLN* 3.9 29.8 - - + +
199F CYS* 3.5 20.6 - - - -
258F ALA* 4.0 19.1 - - + -
288F ARG* 4.1 26.2 - - + +
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Residues in contact with GLN 444 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440E ALA 3.3 11.4 + - - +
441E SER 3.3 7.2 + - - +
442E LEU 3.3 0.2 - - - -
443E ILE* 1.3 76.5 - - - +
445E ALA* 1.3 57.9 + - - +
447E ARG* 2.9 30.3 + - - +
448E ASP* 2.9 31.7 + - - +
454E THR 4.0 11.1 + - - +
455E TYR* 4.0 21.0 - - + +
456E GLU* 4.4 10.5 + - - +
464E PHE* 6.1 1.2 - - - -
254F ILE* 4.1 6.1 - - + -
255F ARG 4.2 8.7 - - - +
257F SER 2.3 37.0 + - - +
258F ALA* 3.8 8.7 - - - -
259F GLY* 3.2 14.9 - - - +
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Residues in contact with ALA 445 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441E SER 3.0 10.7 + - - +
442E LEU 3.6 8.1 - - - +
444E GLN* 1.3 76.2 - - - +
446E GLN* 1.3 57.3 + - - +
448E ASP* 3.8 1.5 - - - -
449E TYR* 3.0 27.4 + - - +
455E TYR* 5.3 0.4 - - - -
469E TRP* 3.8 17.7 - - + -
239F ILE* 3.4 31.5 - - + +
251F LEU* 3.9 2.7 - - + -
254F ILE* 3.6 25.0 - - + +
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Residues in contact with GLN 446 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442E LEU* 2.8 37.0 + - + +
443E ILE* 3.0 12.9 + - - +
445E ALA* 1.3 75.0 - - - +
447E ARG* 1.3 60.5 + - - +
449E TYR* 2.8 20.1 + - - +
450E PHE* 2.9 20.8 + - + -
195F MET* 3.3 37.0 + - + +
198F ILE* 4.1 15.0 - - - +
199F CYS* 5.3 0.2 - - - -
232F LEU* 4.7 8.2 + - + +
235F ILE* 4.1 13.7 - - + -
236F THR* 2.7 27.7 + - - +
239F ILE* 3.8 16.4 - - + -
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Residues in contact with ARG 447 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443E ILE* 2.6 38.6 + - - +
444E GLN* 2.9 27.4 + - - +
446E GLN* 1.3 72.2 - - - +
448E ASP* 1.3 57.7 + - - +
450E PHE* 3.6 14.4 - - + -
451E GLY* 3.2 18.2 + - - -
453E HIS* 3.2 60.0 + - + +
454E THR 4.5 0.4 + - - +
195F MET* 3.8 15.0 - - + -
259F GLY* 3.9 18.5 + - - +
261F LYS* 3.4 36.8 - - - +
288F ARG* 3.9 22.7 - - - +
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Residues in contact with ASP 448 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444E GLN 2.9 18.3 + - - +
445E ALA 4.0 4.0 - - - +
447E ARG* 1.3 74.6 - - - +
449E TYR* 1.3 65.5 + - - +
452E ALA* 3.4 13.9 + - - -
453E HIS* 3.7 7.5 - - - +
454E THR* 3.2 26.7 + - - +
455E TYR* 3.4 23.3 - - + -
466E HIS* 3.4 25.0 + - - -
467E THR 3.4 15.9 + - - +
469E TRP* 2.7 27.1 + - - +
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Residues in contact with TYR 449 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445E ALA 3.0 14.7 + - - +
446E GLN* 2.8 15.8 + - - +
448E ASP* 1.3 81.2 - - - +
450E PHE* 1.3 66.6 + - + +
452E ALA 4.5 1.0 + - - -
466E HIS* 5.8 0.5 - - - -
469E TRP* 3.4 49.1 + + + +
231F PHE* 4.5 7.7 - + - -
235F ILE* 3.4 48.9 - - + +
238F ASN* 4.6 18.7 + - + +
239F ILE* 4.0 15.0 - - + -
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Residues in contact with PHE 450 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446E GLN* 2.9 31.4 - - + -
447E ARG* 3.6 19.3 - - + -
449E TYR* 1.3 84.0 - - + +
451E GLY* 1.3 63.4 + - - +
452E ALA 3.8 0.2 - - - -
453E HIS* 4.2 16.8 - + - -
191F GLU* 4.1 21.8 - - - -
195F MET* 4.1 14.4 - - + -
231F PHE* 4.4 13.7 - - + -
232F LEU* 4.7 0.7 - - + -
235F ILE* 3.9 13.5 - - + -
367F ILE* 3.6 48.1 - - + +
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Residues in contact with GLY 451 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447E ARG 3.2 9.1 + - - -
450E PHE* 1.3 87.1 - - - +
452E ALA* 1.3 72.7 + - - +
453E HIS* 3.2 24.1 + - - -
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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