Contacts of the helix formed by residues 406 - 419 (chain D) in PDB entry 3UO9
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 ASP 406 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404D GLY 3.5 3.9 + - - +
405D THR* 1.3 72.3 - - - +
407D MET* 1.3 67.5 + - - +
408D VAL* 3.6 11.8 + - - +
409D GLY* 3.2 21.2 + - - -
410D ILE* 2.9 24.0 + - - +
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Residues in contact with MET 407 (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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392D GLY* 3.5 27.8 - - - +
393D TYR* 3.6 50.7 - - + -
396D LYS* 4.2 22.2 - - + +
401D PHE* 3.6 24.6 - - + -
405D THR* 3.5 12.7 + - - +
406D ASP* 1.3 73.7 + - - +
408D VAL* 1.3 67.9 + - + +
410D ILE* 3.1 6.2 + - - +
411D LEU* 2.9 50.0 + - + +
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Residues in contact with VAL 408 (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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389D PHE* 4.9 17.4 - - + -
393D TYR* 4.2 13.0 - - - +
406D ASP* 3.3 9.2 + - - +
407D MET* 1.3 96.5 - - + +
409D GLY* 1.3 60.7 + - - +
411D LEU* 3.4 8.5 + - - +
412D ASP* 3.2 22.2 + - + +
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Residues in contact with GLY 409 (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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351D ASN* 3.0 30.1 + - - +
406D ASP* 3.2 23.0 + - - -
408D VAL* 1.3 77.5 - - - +
410D ILE* 1.3 64.4 + - - +
412D ASP* 3.4 4.7 + - - +
413D PHE 3.2 11.8 + - - -
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Residues in contact with ILE 410 (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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339D ILE* 3.7 34.1 - - + +
342D THR* 3.9 11.3 - - + +
343D SER* 3.6 29.2 - - - +
351D ASN* 5.4 1.1 - - - +
354D LYS* 3.8 24.2 - - - +
401D PHE* 4.5 3.8 - - + -
405D THR* 3.6 20.6 - - + -
406D ASP 2.9 17.4 + - - +
407D MET* 3.6 10.1 - - - +
409D GLY* 1.3 74.1 - - - +
411D LEU* 1.3 60.8 + - - +
413D PHE* 3.3 9.9 + - + +
414D TYR* 2.9 26.9 + - + +
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Residues in contact with LEU 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D ILE* 4.1 22.9 - - + -
388D ASN* 3.6 33.2 - - + +
389D PHE* 3.4 48.2 - - + -
392D GLY* 4.6 2.0 - - - -
407D MET* 2.9 33.3 + - - +
408D VAL* 3.5 9.6 - - - +
409D GLY 3.4 0.2 - - - -
410D ILE* 1.3 76.3 - - - +
412D ASP* 1.3 56.1 + - - +
414D TYR* 3.3 8.4 - - + +
415D PHE* 3.0 47.4 + - + -
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Residues in contact with ASP 412 (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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351D ASN* 4.0 8.1 - - - +
378D PHE* 3.6 10.5 - - - -
382D ARG* 3.0 44.3 + - - -
389D PHE* 6.1 0.7 - - - -
408D VAL* 3.2 13.3 + - - +
409D GLY* 3.4 12.3 - - - +
410D ILE 3.2 0.4 - - - -
411D LEU* 1.3 77.0 - - - +
413D PHE* 1.3 56.4 + - - +
415D PHE* 3.4 5.1 + - - -
416D GLN* 3.1 46.7 + - - +
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Residues in contact with PHE 413 (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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342D THR* 3.4 35.4 - - + -
345D ILE* 4.4 11.2 - - + -
351D ASN* 3.6 18.8 + - - +
354D LYS* 3.6 44.4 - - + -
355D PHE* 3.8 23.1 - + + -
358D VAL* 3.9 11.4 - - + -
409D GLY 3.2 4.2 + - - +
410D ILE* 3.5 12.1 - - + +
412D ASP* 1.3 75.5 - - - +
414D TYR* 1.3 58.1 + - - +
416D GLN* 3.1 20.0 + - - +
417D LEU* 2.9 58.7 + - + +
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Residues in contact with TYR 414 (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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289D LYS* 3.1 19.1 + - - -
292D LYS* 3.4 26.5 - - - -
335D ASN* 3.6 10.4 + - - -
338D ALA* 4.1 12.1 - - + -
339D ILE* 3.8 30.5 - - + -
342D THR* 3.7 17.5 - - + +
388D ASN* 3.9 15.9 - - - -
410D ILE* 2.9 16.4 + - + +
411D LEU* 3.3 17.0 - - + +
413D PHE* 1.3 71.8 - - - +
415D PHE* 1.3 79.3 + + - +
417D LEU* 3.2 5.8 + - - +
418D CYS* 3.1 39.9 + - - -
600D GLU 2.7 28.6 + - - -
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Residues in contact with PHE 415 (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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378D PHE* 3.7 19.0 - - + -
381D GLU* 3.9 38.1 - - + +
382D ARG* 3.8 23.8 - - + +
385D GLY* 4.2 6.1 - - - -
388D ASN* 3.8 33.9 - - + -
389D PHE* 3.8 33.9 - + - -
411D LEU* 3.0 35.3 + - + -
412D ASP* 3.7 5.8 - - - +
414D TYR* 1.3 87.7 - + - +
416D GLN* 1.3 61.0 + - - +
418D CYS* 3.6 6.4 + - - +
419D SER* 2.9 27.2 + - - -
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Residues in contact with GLN 416 (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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351D ASN* 4.6 15.2 + - - +
355D PHE* 3.7 35.8 - - + +
373D PHE* 3.4 28.2 - - + -
378D PHE* 3.7 26.2 - - + -
412D ASP* 3.1 44.3 + - - +
413D PHE* 3.1 14.0 + - - +
415D PHE* 1.3 76.5 - - - +
417D LEU* 1.3 61.4 + - - +
419D SER 3.1 9.7 + - - -
420D ILE* 3.5 7.6 + - - +
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Residues in contact with LEU 417 (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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284D LEU* 5.0 0.5 - - - +
288D VAL* 3.7 31.9 - - + +
292D LYS* 3.9 25.6 - - + +
342D THR* 4.0 17.7 - - + +
345D ILE* 5.7 1.6 - - + -
355D PHE* 4.5 4.7 - - + -
358D VAL* 3.6 33.7 - - + -
413D PHE* 2.9 51.2 + - + +
414D TYR* 3.2 4.0 + - - +
416D GLN* 1.3 72.5 - - - +
418D CYS* 1.3 66.8 + - - +
419D SER 3.4 0.3 + - - -
420D ILE* 3.5 29.4 + - + +
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Residues in contact with CYS 418 (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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283D CYS* 3.7 7.3 - - - +
285D GLN* 3.2 56.7 + - - +
288D VAL* 5.0 3.6 - - - -
289D LYS* 5.0 3.8 - - - -
292D LYS* 5.1 0.2 - - - -
381D GLU* 4.9 5.4 - - - -
414D TYR* 3.1 50.5 + - - -
415D PHE* 3.7 11.0 - - - +
417D LEU* 1.3 76.9 - - - +
419D SER* 1.3 58.3 + - - +
420D ILE 3.3 4.1 + - - -
600D GLU* 3.9 15.3 - - - +
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Residues in contact with SER 419 (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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283D CYS* 3.7 14.0 - - - -
373D PHE* 3.8 9.4 - - - -
374D SER 3.0 42.0 + - - -
377D THR* 3.6 11.2 - - - +
378D PHE* 3.2 20.0 + - - -
381D GLU* 4.2 2.6 - - - +
415D PHE 2.9 17.2 + - - -
416D GLN 3.1 9.1 + - - -
418D CYS* 1.3 75.2 - - - +
420D ILE* 1.3 62.0 + - - +
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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