Contacts of the helix formed by residues 439 - 452 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E GLN* 5.4 5.4 - - - +
199E CYS* 3.2 55.1 - - + +
200E GLU* 4.7 1.6 - - + +
202E TYR* 3.7 26.0 - - + -
203E HIS* 3.7 28.3 - - + +
206E LYS* 5.9 1.5 - - - +
419E PRO* 5.5 2.2 - - + +
438F LEU* 1.3 90.1 - - + +
440F ALA* 1.3 57.6 + - - +
441F SER* 3.1 4.3 - - - +
442F LEU* 3.0 17.8 + - - +
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Residues in contact with ALA 440 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E GLN* 5.8 2.9 - - - +
199E CYS* 4.9 0.2 - - - -
256E ASP* 4.3 9.0 - - - +
258E ALA* 4.2 12.4 - - + +
287E ALA 5.4 1.6 - - - +
288E ARG* 5.9 0.2 - - - -
291E SER* 3.5 34.8 - - - +
438F LEU* 2.8 8.2 + - + +
439F PRO* 1.3 75.5 - - - +
441F SER* 1.3 60.7 + - - +
442F LEU 3.1 0.2 - - - -
443F ILE* 3.0 33.6 + - + +
444F GLN* 3.4 9.9 + - - +
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Residues in contact with SER 441 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E TYR* 5.6 0.9 - - - -
251E LEU* 4.0 19.2 + - - +
254E ILE* 3.4 36.5 - - - +
255E ARG 3.9 11.2 - - - -
256E ASP* 3.7 13.8 - - - +
437F MET* 5.6 4.2 - - - +
438F LEU 3.7 10.2 + - - -
439F PRO* 4.3 2.8 - - - +
440F ALA* 1.3 78.1 - - - +
442F LEU* 1.3 63.1 + - - +
444F GLN* 3.4 4.9 + - - +
445F ALA* 3.1 21.7 + - - +
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Residues in contact with LEU 442 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E ILE* 3.9 24.7 - - + -
199E CYS* 3.7 15.3 - - - -
202E TYR* 4.0 31.0 - - + -
236E THR* 4.3 13.2 - - + -
239E ILE* 4.3 15.9 - - + -
240E LEU* 5.0 5.4 - - + -
251E LEU* 3.9 25.3 - - + +
439F PRO 3.0 15.1 + - - +
441F SER* 1.3 79.8 + - - +
443F ILE* 1.3 57.1 + - - +
445F ALA 3.4 0.3 + - - -
446F GLN* 2.9 51.5 + - + +
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Residues in contact with ILE 443 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E TYR 5.5 0.2 - - - +
195E MET* 3.5 46.0 - - + +
196E GLN* 4.1 11.7 - - + +
199E CYS* 3.5 25.1 - - - -
258E ALA* 4.1 14.6 - - + -
288E ARG* 3.8 28.9 - - + +
440F ALA* 3.0 21.4 + - + +
442F LEU* 1.3 77.4 - - - +
444F GLN* 1.3 59.4 + - - +
446F GLN* 3.1 6.4 + - - +
447F ARG* 2.8 40.8 + - - +
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Residues in contact with GLN 444 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254E ILE* 4.2 4.7 - - + -
255E ARG 4.3 9.4 - - - +
257E SER 3.2 24.9 + - - +
258E ALA* 3.3 4.0 - - - +
259E GLY* 2.9 27.3 + - - +
440F ALA 3.4 10.4 + - - +
441F SER 3.8 6.3 - - - +
442F LEU 3.4 0.2 - - - -
443F ILE* 1.3 75.5 - - - +
445F ALA* 1.3 57.7 + - - +
447F ARG* 3.4 22.9 + - - +
448F ASP* 2.9 30.8 + - - +
453F HIS* 6.1 0.4 - - - +
454F THR 3.8 18.8 + - - +
455F TYR* 4.0 24.7 - - + +
456F GLU* 5.5 1.8 - - - +
464F PHE* 5.0 9.1 - - - -
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Residues in contact with ALA 445 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E ILE* 3.2 37.9 - - + +
251E LEU* 3.8 4.9 - - + -
254E ILE* 3.8 20.8 - - + +
441F SER 3.1 14.0 + - - +
442F LEU* 3.7 7.4 - - - +
443F ILE 3.2 0.2 - - - -
444F GLN* 1.3 75.8 - - - +
446F GLN* 1.3 57.4 + - - +
448F ASP* 3.4 3.4 + - - +
449F TYR* 2.9 23.0 + - - +
455F TYR* 5.3 0.4 - - - -
469F TRP* 4.0 12.9 + - + -
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Residues in contact with GLN 446 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E MET* 3.3 41.9 + - + +
198E ILE* 3.7 25.1 - - - +
232E LEU* 4.6 4.8 + - + +
235E ILE* 4.5 12.3 - - + -
236E THR* 2.8 28.1 + - - +
239E ILE* 3.8 11.7 - - + -
442F LEU* 2.9 37.5 + - + +
443F ILE* 3.5 7.9 - - - +
445F ALA* 1.3 73.7 - - - +
447F ARG* 1.3 66.5 + - - +
449F TYR* 3.0 13.6 + - - +
450F PHE* 3.0 22.0 - - + -
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Residues in contact with ARG 447 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E GLU* 5.7 0.2 - - - +
195E MET* 3.8 14.8 - - + -
259E GLY* 3.1 36.8 + - - -
260E GLN 3.9 1.0 - - - +
261E LYS* 4.8 6.1 - - - +
288E ARG* 4.1 3.8 - - - +
443F ILE* 2.8 31.3 + - - +
444F GLN* 3.6 23.1 + - - +
446F GLN* 1.3 71.7 - - - +
448F ASP* 1.3 56.3 + - - +
450F PHE* 3.8 13.2 - - + -
451F GLY* 2.9 29.1 + - - -
452F ALA 3.2 4.5 + - - -
453F HIS* 3.5 44.0 + - + +
454F THR 5.8 0.2 - - - +
501F 8HS 2.8 40.9 + - - +
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Residues in contact with ASP 448 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444F GLN 2.9 18.1 + - - +
445F ALA* 3.8 4.5 - - - +
447F ARG* 1.3 74.8 - - - +
449F TYR* 1.3 67.2 + - - +
452F ALA* 3.2 20.3 + - - +
453F HIS* 3.9 4.0 - - - +
454F THR* 3.8 13.1 + - - +
455F TYR* 2.8 38.8 - - + -
466F HIS* 2.5 36.9 + - - -
467F THR 3.4 12.0 + - - -
469F TRP* 3.5 11.4 + - - +
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Residues in contact with TYR 449 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E PHE* 4.7 7.0 - + - -
234E GLU* 5.4 1.0 + - - -
235E ILE* 3.4 37.1 - - + +
238E ASN* 3.4 37.0 + - + +
239E ILE* 3.5 23.6 - - + -
445F ALA 2.9 14.5 + - - +
446F GLN* 3.0 10.7 + - - +
448F ASP* 1.3 80.9 - - - +
450F PHE* 1.3 65.7 + - + +
466F HIS* 5.6 0.9 - - - -
469F TRP* 3.5 45.9 + - + +
470F THR* 4.4 14.1 + - - -
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Residues in contact with PHE 450 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E GLY 4.8 1.5 - - - +
131E GLY* 3.9 3.3 - - - -
132E GLU* 3.8 24.8 + - - +
133E GLU* 5.0 5.8 + - - +
191E GLU* 3.2 22.0 - - - -
195E MET* 4.7 4.3 - - + -
231E PHE* 4.1 16.8 - - + -
232E LEU* 4.6 5.2 - - + -
235E ILE* 3.9 15.9 - - + -
367E ILE* 3.5 43.3 - - + -
446F GLN* 3.0 34.7 + - + -
447F ARG* 3.8 15.3 - - + -
449F TYR* 1.3 80.6 - - + +
451F GLY* 1.3 62.9 + - - +
452F ALA 3.8 0.7 - - - -
453F HIS* 4.8 2.2 - + - -
501F 8HS 3.5 32.3 - - - -
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Residues in contact with GLY 451 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E GLY* 5.0 2.2 - - - -
132E GLU* 4.4 10.1 - - - +
447F ARG 2.9 11.1 + - - -
450F PHE* 1.3 82.9 - - - +
452F ALA* 1.3 71.4 + - - +
453F HIS* 3.2 15.8 + - - -
501F 8HS 3.6 21.4 + - - -
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Residues in contact with ALA 452 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E GLU* 3.8 23.3 + - - +
447F ARG 3.2 3.8 + - - -
448F ASP* 3.2 19.9 + - - -
449F TYR 4.9 0.2 + - - -
450F PHE 3.8 0.6 - - - -
451F GLY* 1.3 79.7 - - - +
453F HIS* 1.3 57.7 + - - +
454F THR* 3.2 14.7 + - - +
466F HIS* 3.6 29.3 - - + +
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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