Contacts of the helix formed by residues 406 - 416 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A GLN* 3.1 26.1 + - - +
399A CYS 2.9 25.3 + - - -
400A ASP* 3.6 7.4 + - - +
401A GLY* 3.2 41.8 - - - +
403A ALA* 3.0 18.4 + - + +
405A SER* 1.3 73.3 + - - +
407A SER* 1.3 60.8 + - - +
408A TYR 2.9 5.6 - - - -
409A TYR* 3.0 28.1 + - + -
431A ARG* 3.4 31.0 - - - +
484A ALA* 3.8 9.3 - - - +
485A TRP 2.8 24.5 + - - -
486A TYR* 4.0 11.3 - - - +
509A PRO* 3.6 29.5 - - + +
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Residues in contact with SER 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A LYS* 3.1 18.8 + - - +
405A SER* 3.1 3.7 + - - -
406A ARG* 1.3 75.9 - - - +
408A TYR* 1.3 64.2 + - - +
410A THR* 3.2 10.4 + - - -
411A ASP* 3.0 36.2 + - - -
431A ARG* 3.6 11.4 - - - +
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Residues in contact with TYR 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A SER 3.0 18.6 + - - +
406A ARG 4.4 0.2 - - - -
407A SER* 1.3 79.3 + - - +
409A TYR* 1.3 86.0 + + + +
411A ASP* 3.9 0.7 - - - +
412A PHE* 2.8 39.7 + + + +
482A ASN* 3.0 32.2 + - - -
532A ILE* 3.6 24.6 - - + +
533A THR 3.3 22.0 - - - -
535A PRO* 3.5 39.4 - - + +
538A ASP* 2.6 37.2 + - - +
542A PHE* 3.4 3.8 - - - -
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Residues in contact with TYR 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A MET* 3.7 27.9 - - + +
406A ARG* 3.0 31.6 + - + +
408A TYR* 1.3 99.2 - + - +
410A THR* 1.3 65.6 + - - +
412A PHE* 4.3 0.4 - - - -
413A ALA* 3.0 24.8 + - - +
428A ALA 5.6 0.4 - - - +
431A ARG* 4.0 19.5 - - + -
432A TYR* 4.0 5.0 - + + -
482A ASN* 4.0 21.5 - - - -
483A ILE 3.7 2.3 + - - -
484A ALA* 3.8 26.2 - - + -
508A GLY* 3.1 35.5 + - - -
509A PRO* 3.4 19.7 - - + +
532A ILE* 3.9 5.9 - - + +
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Residues in contact with THR 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A ARG 3.9 0.6 + - - -
407A SER* 3.2 12.8 + - - -
409A TYR* 1.3 78.1 - - - +
411A ASP* 1.3 64.3 + - - +
413A ALA* 3.3 4.5 + - - +
414A GLU* 2.9 29.6 + - + +
431A ARG* 2.7 44.8 + - - +
435A LEU* 4.0 21.1 - - + +
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Residues in contact with ASP 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A SER* 3.0 30.4 + - - +
408A TYR* 5.0 0.2 - - - -
410A THR* 1.3 81.8 - - - +
412A PHE* 1.3 60.0 + - - +
414A GLU* 3.8 5.8 - - - +
415A GLY* 2.9 27.4 + - - -
535A PRO* 3.7 26.8 - - + +
539A LEU* 4.3 2.6 - - - +
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Residues in contact with PHE 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A VAL* 4.0 19.1 - - + -
396A MET* 3.8 16.2 - - + -
408A TYR* 2.8 40.7 + + + +
409A TYR* 3.8 4.7 - - - +
411A ASP* 1.3 76.5 - - - +
413A ALA* 1.3 64.2 + - - +
415A GLY 3.2 0.5 + - - -
416A LEU* 3.0 43.3 + - + +
480A VAL* 5.3 0.7 - - + -
482A ASN* 3.4 26.2 - - - -
535A PRO* 3.8 13.1 - - + +
538A ASP 4.0 5.4 - - - -
539A LEU* 3.6 36.0 - - + +
542A PHE* 4.0 7.9 - + - -
543A PHE* 3.9 22.4 - + - -
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Residues in contact with ALA 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A MET* 4.5 1.6 - - - -
409A TYR 3.0 14.3 + - - +
410A THR 3.6 2.7 - - - +
412A PHE* 1.3 81.3 - - - +
414A GLU* 1.3 61.0 + - - +
415A GLY 3.3 0.2 + - - -
416A LEU* 3.3 26.1 + - - +
422A ILE* 3.8 15.3 - - + -
432A TYR* 3.4 35.4 - - + -
435A LEU* 4.2 3.4 - - + -
437A LEU* 4.1 14.9 - - + +
445A ARG* 4.6 2.1 + - - -
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Residues in contact with GLU 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A THR* 2.9 19.0 + - + +
411A ASP* 3.8 7.6 - - - +
413A ALA* 1.3 76.6 - - - +
415A GLY* 1.3 59.8 + - - +
416A LEU 3.6 4.7 + - - +
418A LYS* 5.3 8.5 + - - -
435A LEU* 3.9 27.2 - - + +
436A ASN 5.2 4.0 + - - +
437A LEU* 4.1 18.8 - - - +
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Residues in contact with GLY 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A ASP 2.9 17.7 + - - -
412A PHE 3.7 2.2 - - - -
413A ALA 3.2 0.2 - - - -
414A GLU* 1.3 73.9 - - - +
416A LEU* 1.3 66.0 + - - +
417A PRO* 3.4 4.7 - - - +
539A LEU* 3.7 20.9 - - - +
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Residues in contact with LEU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A VAL* 4.0 12.8 - - + -
396A MET* 4.5 0.7 - - - -
412A PHE* 3.0 31.0 + - + +
413A ALA* 3.3 11.3 + - - +
414A GLU 4.1 5.4 - - - +
415A GLY* 1.3 79.6 - - - +
417A PRO* 1.3 74.1 - - + +
418A LYS* 3.7 6.9 + - - +
420A THR* 3.4 21.5 - - - +
422A ILE* 3.7 36.3 - - + -
445A ARG* 3.7 11.7 + - - +
539A LEU* 3.6 13.5 - - + -
543A PHE* 3.5 31.0 - - + -
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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