Contacts of the helix formed by residues 406 - 416 (chain B) in PDB entry 1UPX
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 ARG 406 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B GLN* 3.0 23.6 + - - +
399B CYS 2.9 25.9 + - - -
400B ASP* 3.6 5.1 + - - +
401B GLY* 3.2 46.3 - - - +
403B ALA* 2.9 19.3 + - + +
405B SER* 1.3 72.6 - - - +
407B SER* 1.3 60.9 + - - +
408B TYR 2.9 5.6 - - - -
409B TYR* 2.9 28.1 + - + +
410B THR 3.9 0.2 + - - -
431B ARG* 3.5 29.8 - - - +
484B ALA* 3.9 8.9 - - - +
485B TRP 2.8 24.7 + - - -
486B TYR* 4.0 7.9 - - - +
509B PRO* 3.6 32.4 - - + +
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Residues in contact with SER 407 (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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404B LYS 3.1 17.3 + - - -
405B SER* 3.1 3.3 + - - -
406B ARG* 1.3 76.5 - - - +
408B TYR* 1.3 63.8 + - - +
410B THR* 3.1 12.0 + - - -
411B ASP* 3.0 34.7 + - - -
431B ARG* 3.7 12.1 - - - +
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Residues in contact with TYR 408 (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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405B SER 3.0 18.6 + - - +
406B ARG* 4.3 1.8 - - - -
407B SER* 1.3 79.9 + - - +
409B TYR* 1.3 83.9 + + - +
411B ASP* 3.7 1.5 - - - +
412B PHE* 2.8 40.4 + + + +
482B ASN* 3.0 32.1 + - - -
532B ILE* 3.7 24.6 - - + +
533B THR 3.6 14.6 - - - -
534B SER 3.6 14.6 - - - -
535B PRO* 3.6 31.1 - - + +
538B ASP* 2.6 37.3 + - - +
542B PHE* 3.5 3.1 - - - -
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Residues in contact with TYR 409 (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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396B MET* 3.6 28.2 - - + +
406B ARG* 2.9 29.4 + - + +
408B TYR* 1.3 103.5 - + - +
410B THR* 1.3 58.0 + - - +
412B PHE* 4.3 0.4 - - - -
413B ALA* 3.0 28.9 + - - +
428B ALA* 5.7 0.7 - - + +
431B ARG* 4.0 17.7 - - + -
432B TYR* 4.1 8.0 - + + -
482B ASN* 4.0 22.9 - - - -
483B ILE 3.8 2.4 + - - -
484B ALA* 3.7 24.9 - - + -
508B GLY* 3.1 36.0 + - - -
509B PRO* 3.4 21.5 - - + +
532B ILE* 4.0 4.7 - - + +
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Residues in contact with THR 410 (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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406B ARG 3.9 0.4 + - - -
407B SER* 3.1 12.9 + - - -
409B TYR* 1.3 78.6 - - - +
411B ASP* 1.3 61.2 + - - +
413B ALA* 3.3 4.5 + - - +
414B GLU* 3.0 43.2 + - - +
431B ARG* 2.6 43.7 + - - +
435B LEU* 4.2 20.4 - - + -
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Residues in contact with ASP 411 (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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407B SER* 3.0 29.3 + - - +
410B THR* 1.3 78.1 - - - +
412B PHE* 1.3 62.2 + - - +
414B GLU* 3.4 13.7 + - - +
415B GLY* 2.9 26.3 + - - -
535B PRO* 3.7 26.9 - - + +
536B GLN* 5.1 2.1 - - - +
539B LEU* 4.6 0.9 - - - +
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Residues in contact with PHE 412 (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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394B VAL* 3.9 18.6 - - + -
396B MET* 3.7 19.1 - - + -
408B TYR* 2.8 40.1 + + + +
409B TYR* 3.8 6.3 - - - +
411B ASP* 1.3 73.0 - - - +
413B ALA* 1.3 61.9 + - - +
415B GLY 3.2 2.8 + - - -
416B LEU* 3.1 42.3 + - + +
480B VAL* 5.3 0.7 - - + -
482B ASN* 3.4 27.8 - - - -
535B PRO* 4.0 12.9 - - + +
538B ASP* 4.1 6.3 - - + -
539B LEU* 3.6 35.5 - - + +
542B PHE* 4.2 4.5 - + - -
543B PHE* 3.7 23.1 - + - -
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Residues in contact with ALA 413 (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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396B MET* 4.6 1.3 - - - -
409B TYR 3.0 18.7 + - - +
410B THR 3.6 4.9 - - - +
412B PHE* 1.3 78.3 - - - +
414B GLU* 1.3 61.2 + - - +
416B LEU* 3.4 28.9 + - - +
422B ILE* 3.7 15.5 - - + -
432B TYR* 3.6 27.6 - - + -
435B LEU* 4.3 4.5 - - + -
437B LEU* 4.3 14.5 - - + +
445B ARG* 4.6 2.8 + - - -
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Residues in contact with GLU 414 (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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410B THR* 3.0 27.5 + - - +
411B ASP* 3.9 12.9 - - - +
413B ALA* 1.3 76.1 - - - +
415B GLY* 1.3 58.7 + - - +
416B LEU 3.4 4.4 + - - +
435B LEU* 3.7 35.2 - - + +
436B ASN 5.7 0.2 + - - -
437B LEU* 4.4 12.6 - - + +
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Residues in contact with GLY 415 (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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411B ASP 2.9 15.4 + - - -
412B PHE 3.2 3.3 + - - -
414B GLU* 1.3 77.4 - - - +
416B LEU* 1.3 64.3 + - - +
417B PRO* 3.5 3.6 - - - +
536B GLN* 5.0 4.8 + - - -
539B LEU* 3.7 21.6 - - - +
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Residues in contact with LEU 416 (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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394B VAL* 3.9 14.1 - - + -
412B PHE* 3.1 26.6 + - + +
413B ALA* 3.4 13.8 + - - +
414B GLU 4.3 4.9 - - - +
415B GLY* 1.3 79.8 - - - +
417B PRO* 1.3 74.0 - - + +
418B LYS* 3.6 2.8 + - - +
420B THR* 3.4 16.6 - - - +
422B ILE* 3.6 37.5 - - + -
445B ARG* 3.8 13.0 + - - +
539B LEU* 3.6 12.1 - - + -
543B PHE* 3.4 33.9 - - + -
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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