Contacts of the helix formed by residues 439 - 450 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438G LEU* 1.3 91.6 - - + +
440G ALA* 1.3 57.2 + - - -
441G SER* 3.2 1.8 - - - +
442G LEU* 3.1 24.7 + - - +
196H GLN* 4.9 5.6 - - - +
199H CYS* 3.3 47.5 - - + +
200H GLU* 4.6 2.2 - - + +
202H TYR* 3.7 26.2 - - + -
203H HIS* 3.8 28.0 - - + +
419H PRO* 5.8 2.0 - - + +
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Residues in contact with ALA 440 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438G LEU* 2.9 6.4 + - + -
439G PRO* 1.3 76.8 - - - +
441G SER* 1.3 61.5 + - - +
442G LEU 3.1 0.2 - - - -
443G ILE* 3.0 15.3 + - + +
444G GLN* 2.9 29.3 + - - +
199H CYS* 5.2 0.2 - - - -
256H ASP* 3.6 25.6 - - + -
257H SER 4.4 2.9 - - - +
291H SER* 3.6 27.6 - - - +
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Residues in contact with SER 441 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437G MET* 4.7 5.9 - - - +
438G LEU 3.7 10.7 + - - -
439G PRO* 4.5 1.7 - - - +
440G ALA* 1.3 74.9 - - - +
442G LEU* 1.3 60.1 + - - +
444G GLN* 3.9 0.9 - - - +
445G ALA* 2.9 31.2 + - - +
202H TYR* 4.9 8.1 + - - -
251H LEU* 3.9 20.2 + - - +
254H ILE* 3.7 36.2 - - - +
255H ARG 4.4 7.4 - - - -
256H ASP* 3.7 10.8 - - - +
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Residues in contact with LEU 442 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439G PRO 3.1 16.8 + - - +
441G SER* 1.3 81.5 + - - +
443G ILE* 1.3 54.6 + - - +
445G ALA* 3.4 1.9 + - - +
446G GLN* 2.9 57.4 + - + +
198H ILE* 4.6 4.5 - - + -
199H CYS* 3.8 15.0 - - - -
202H TYR* 4.4 26.2 - - + -
236H THR* 3.9 15.9 - - + -
239H ILE* 3.5 28.3 - - + -
240H LEU* 3.6 21.8 - - + -
251H LEU* 4.4 1.7 - - + +
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Residues in contact with ILE 443 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439G PRO 3.6 0.6 + - - -
440G ALA* 3.0 18.1 + - + +
442G LEU* 1.3 79.1 - - - +
444G GLN* 1.3 69.3 + - + +
446G GLN* 3.3 7.3 + - - +
447G ARG* 2.9 33.9 + - - +
192H TYR 5.6 0.7 - - - +
195H MET* 3.7 25.0 - - + +
196H GLN* 4.4 18.6 - - + +
199H CYS* 3.5 23.6 - - - -
257H SER 5.2 3.4 - - - +
258H ALA* 6.1 1.3 - - + -
288H ARG* 3.5 46.9 - - + +
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Residues in contact with GLN 444 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440G ALA 2.9 16.5 + - - +
441G SER 4.0 2.9 - - - +
443G ILE* 1.3 78.4 - - + +
445G ALA* 1.3 60.5 + - - +
447G ARG* 3.8 14.2 - - - +
448G ASP* 2.8 31.2 + - - +
453G HIS* 4.2 5.4 - - - +
454G THR 4.7 8.7 + - - +
455G TYR* 4.2 22.3 - - + +
456G GLU* 5.9 2.8 + - - +
254H ILE* 4.2 7.0 - - + -
255H ARG 3.9 13.0 + - - +
257H SER* 2.3 45.1 + - - +
258H ALA* 3.9 6.7 + - - +
261H LYS* 5.2 10.1 + - - +
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Residues in contact with ALA 445 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441G SER 2.9 19.1 + - - +
442G LEU 3.8 0.4 - - - +
444G GLN* 1.3 74.2 - - - +
446G GLN* 1.3 55.4 + - - +
448G ASP* 4.0 5.1 - - - +
449G TYR* 2.7 37.7 + - - +
455G TYR* 5.4 0.9 - - - -
239H ILE* 3.6 31.9 - - + -
251H LEU* 4.3 2.2 - - + -
254H ILE* 4.0 20.8 - - + +
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Residues in contact with GLN 446 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442G LEU* 2.9 39.6 + - + +
443G ILE* 3.3 6.9 + - - +
445G ALA* 1.3 77.0 - - - +
447G ARG* 1.3 56.6 + - - +
449G TYR* 3.8 7.2 - - - +
450G PHE* 3.0 31.4 + - + +
195H MET* 3.3 36.9 - - + +
198H ILE* 4.5 6.5 - - - +
232H LEU* 3.5 20.8 + - + +
235H ILE* 4.9 8.8 - - + +
236H THR* 2.6 30.3 + - - +
239H ILE* 4.8 13.2 - - + -
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Residues in contact with ARG 447 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443G ILE* 2.9 21.2 + - - +
444G GLN* 3.9 13.9 - - - +
446G GLN* 1.3 74.9 - - - +
448G ASP* 1.3 65.0 + - - +
450G PHE* 3.2 20.3 + - + +
451G GLY 3.6 0.5 + - - -
452G ALA 3.9 0.3 + - - -
453G HIS* 2.9 67.9 + - + -
191H GLU* 4.7 13.6 + - - +
192H TYR* 4.0 14.8 + - - -
195H MET* 4.5 10.7 - - + +
261H LYS* 5.6 11.5 - - - +
262H GLY* 4.3 12.5 - - - -
288H ARG* 3.4 35.0 - - - +
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Residues in contact with ASP 448 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444G GLN 2.8 16.8 + - - +
445G ALA* 4.0 2.7 - - - +
447G ARG* 1.3 74.5 - - - +
449G TYR* 1.3 66.4 + - - +
450G PHE 3.0 4.3 + - - +
452G ALA 3.0 27.4 - - - +
453G HIS 3.2 12.3 + - - +
455G TYR* 3.1 24.1 - - + -
465G ILE 2.8 26.3 - - - +
466G HIS* 3.4 17.0 + - - -
467G THR* 3.0 28.7 + - - +
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Residues in contact with TYR 449 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445G ALA 2.7 23.9 + - - +
446G GLN* 3.9 5.2 - - - +
448G ASP* 1.3 74.8 + - - +
450G PHE* 1.3 63.6 + - - +
467G THR* 5.1 12.1 - - + -
235H ILE* 3.5 51.1 - - + +
238H ASN* 4.2 29.9 + - + +
239H ILE* 4.5 13.9 - - + -
242H PHE* 6.3 4.7 - + - -
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Residues in contact with PHE 450 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446G GLN 3.0 16.1 + - - +
447G ARG* 3.2 19.5 - - + +
448G ASP 3.0 1.9 - - - +
449G TYR* 1.3 85.8 - - - +
451G GLY* 1.3 70.3 + - - +
453G HIS* 4.8 5.6 - + + +
466G HIS* 5.2 0.9 - - - -
191H GLU* 4.4 3.8 - - - -
195H MET* 6.4 1.6 - - + -
231H PHE* 3.5 35.0 - + - -
232H LEU* 6.4 0.7 - - + -
235H ILE* 4.9 7.9 - - + -
366H CYS 5.1 0.9 - - - -
367H ILE* 3.3 52.5 - - + -
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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