Contacts of the helix formed by residues 439 - 452 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A GLN* 5.9 1.6 - - - +
199A CYS* 3.4 35.6 - - + +
200A GLU* 5.4 0.7 - - - -
202A TYR* 4.0 18.6 - - + -
203A HIS* 3.4 41.7 - - + +
419A PRO* 5.9 2.7 - - + +
438B LEU* 1.3 91.9 - - + +
440B ALA* 1.3 56.9 + - - +
441B SER* 3.1 6.7 - - - +
442B LEU* 2.9 27.1 + - - +
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Residues in contact with ALA 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A GLN* 5.9 1.8 - - - +
256A ASP* 4.0 13.5 - - + +
258A ALA* 4.1 9.4 - - + +
287A ALA 5.5 0.7 - - - +
288A ARG* 5.9 0.2 - - - -
291A SER* 3.4 36.1 - - - +
438B LEU* 3.0 4.9 + - + -
439B PRO* 1.3 76.3 - - - +
441B SER* 1.3 64.2 + - - +
442B LEU 3.1 0.4 - - - -
443B ILE* 3.0 26.3 + - + +
444B GLN* 3.1 15.9 + - - +
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Residues in contact with SER 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A TYR* 5.7 0.9 - - - -
251A LEU* 4.0 20.4 + - - +
254A ILE* 3.3 37.2 - - - +
255A ARG 3.6 17.9 - - - -
256A ASP* 3.5 9.9 - - - +
437B MET* 5.7 2.4 - - - +
438B LEU 3.9 7.6 + - - -
439B PRO* 4.2 2.4 + - - +
440B ALA* 1.3 77.8 - - - +
442B LEU* 1.3 58.0 + - - +
444B GLN* 3.3 4.9 + - - +
445B ALA* 3.0 26.0 + - - +
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Residues in contact with LEU 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ILE* 4.2 7.4 - - + -
199A CYS* 3.9 13.2 - - - -
202A TYR* 3.9 39.0 - - + -
236A THR* 4.1 24.2 - - + -
239A ILE* 4.2 14.8 - - + -
240A LEU* 4.9 1.8 - - + -
251A LEU* 3.6 27.1 - - + -
439B PRO 2.9 12.9 + - - +
441B SER* 1.3 79.8 + - - +
443B ILE* 1.3 59.1 + - - +
445B ALA* 3.3 4.0 + - - +
446B GLN* 3.0 49.9 + - + +
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Residues in contact with ILE 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A TYR 5.6 0.4 - - - +
195A MET* 3.7 31.1 - - + +
196A GLN* 3.5 36.6 - - + +
199A CYS* 3.5 18.8 - - - -
258A ALA* 3.8 21.5 - - + -
288A ARG* 4.0 24.2 - - + +
439B PRO 3.7 0.2 + - - -
440B ALA* 3.0 16.1 + - + +
442B LEU* 1.3 77.8 - - - +
444B GLN* 1.3 56.8 + - - +
446B GLN* 3.2 4.7 + - - +
447B ARG* 2.9 40.8 + - - +
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Residues in contact with GLN 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A ILE* 4.3 13.5 - - + -
255A ARG* 4.3 8.5 - - + +
257A SER 3.2 27.1 + - - +
258A ALA* 3.2 4.5 - - - +
259A GLY* 2.9 23.7 + - - +
440B ALA 3.1 12.6 + - - +
441B SER 3.6 7.9 - - - +
442B LEU 3.3 0.2 - - - -
443B ILE* 1.3 74.8 - - - +
445B ALA* 1.3 62.4 + - - +
447B ARG* 3.4 24.8 + - - +
448B ASP* 3.0 26.5 + - - +
453B HIS 5.4 0.4 + - - -
454B THR 4.1 18.3 + - - +
455B TYR* 4.3 13.5 - - + +
456B GLU* 5.4 1.6 + - - +
464B PHE* 5.7 5.9 - - - -
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Residues in contact with ALA 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ILE* 3.4 32.4 - - + +
251A LEU* 5.0 1.8 - - + -
254A ILE* 4.0 20.1 - - + +
441B SER 3.0 13.6 + - - +
442B LEU* 3.6 10.1 - - - +
443B ILE 3.3 0.2 - - - -
444B GLN* 1.3 75.8 - - - +
446B GLN* 1.3 58.6 + - - +
448B ASP* 3.8 3.3 - - - +
449B TYR* 2.9 28.1 + - - +
455B TYR* 5.6 0.4 - - - -
469B TRP* 4.1 13.2 - - + -
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Residues in contact with GLN 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A MET* 3.2 42.6 + - + +
198A ILE* 4.1 17.4 - - - +
199A CYS* 5.1 0.2 - - - -
232A LEU* 4.6 5.3 + - - -
235A ILE* 4.3 8.7 - - + -
236A THR* 3.0 26.0 + - - +
239A ILE* 3.8 16.6 - - + -
442B LEU* 3.0 36.0 + - + +
443B ILE* 3.2 7.1 + - - +
445B ALA* 1.3 74.2 - - - +
447B ARG* 1.3 60.9 + - - +
449B TYR* 2.8 18.3 + - - +
450B PHE* 3.0 28.4 + - + -
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Residues in contact with ARG 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A GLU* 5.7 0.4 - - - +
195A MET* 3.6 14.1 - - + -
259A GLY* 3.6 19.7 + - - -
260A GLN* 4.2 12.1 - - - +
261A LYS* 4.5 16.2 - - - +
288A ARG* 3.7 20.9 - - - +
443B ILE* 2.9 23.7 + - - +
444B GLN* 3.7 33.7 + - - +
446B GLN* 1.3 74.6 - - - +
448B ASP* 1.3 58.1 + - - +
450B PHE* 3.9 12.8 - - + -
451B GLY* 3.0 24.3 + - - -
452B ALA 3.1 4.9 + - - -
453B HIS* 3.1 58.3 + - + +
454B THR 5.1 0.4 + - - +
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Residues in contact with ASP 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B GLN 3.0 17.5 + - - +
445B ALA* 3.9 4.5 - - - +
447B ARG* 1.3 75.3 - - - +
449B TYR* 1.3 66.3 + - - +
452B ALA* 3.1 17.5 + - - -
453B HIS* 3.7 6.7 - - - +
454B THR* 3.4 22.8 + - - +
455B TYR* 2.9 33.7 - - + -
466B HIS* 2.5 35.1 + - - -
467B THR 3.3 11.1 + - - -
469B TRP* 3.4 9.0 + - - +
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Residues in contact with TYR 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A PHE* 4.7 6.7 - + - -
235A ILE* 3.4 35.4 - - + +
238A ASN* 3.5 31.4 + - + +
239A ILE* 3.5 31.6 - - + -
445B ALA 2.9 14.0 + - - +
446B GLN* 2.8 11.1 + - - +
448B ASP* 1.3 80.5 - - - +
450B PHE* 1.3 64.4 + - + +
452B ALA 4.6 0.5 + - - -
466B HIS* 5.6 0.9 - - - -
469B TRP* 3.5 48.9 + + + +
470B THR* 5.0 9.0 + - - -
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Residues in contact with PHE 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLY 4.8 1.6 - - - +
131A GLY* 3.5 21.3 - - - -
132A GLU* 4.1 4.3 + - - +
133A GLU 5.4 0.9 + - - -
191A GLU* 3.4 29.8 - - - -
195A MET* 4.2 8.5 - - - -
231A PHE* 4.2 22.4 - + + -
232A LEU* 4.1 15.0 - - + -
235A ILE* 3.7 16.4 - - + -
367A ILE* 3.5 29.2 - - + -
446B GLN* 3.0 36.3 - - + -
447B ARG* 3.9 15.3 - - + -
449B TYR* 1.3 82.1 - - + +
451B GLY* 1.3 66.0 + - - +
453B HIS* 4.8 9.4 - + - -
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Residues in contact with GLY 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A GLY* 4.9 6.3 - - - -
132A GLU* 4.4 11.7 - - - +
447B ARG 3.0 10.7 + - - -
450B PHE* 1.3 87.5 - - - +
452B ALA* 1.3 73.0 + - - +
453B HIS* 3.1 25.0 + - - -
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Residues in contact with ALA 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLU* 4.2 20.2 - - - +
447B ARG 3.1 2.8 + - - -
448B ASP* 3.1 21.8 + - - -
449B TYR 4.6 0.6 + - - +
450B PHE 3.8 0.8 - - - -
451B GLY* 1.3 79.4 - - - +
453B HIS* 1.3 56.9 + - - +
454B THR* 3.0 20.9 + - - +
466B HIS* 3.6 25.3 + - + +
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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