Contacts of the helix formed by residues 410 - 423 (chain A) in PDB entry 1U9J
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 PHE 410 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406A PHE* 2.9 49.3 + + + +
409A ASP* 1.3 79.5 - - - +
411A GLU* 1.3 66.5 + - + +
413A ASN 3.4 0.7 + - - -
414A LEU* 2.9 54.3 + - + +
466A SER* 3.4 30.1 - - - +
469A LEU* 3.6 42.6 - - + -
470A LEU* 3.7 25.1 - - + +
473A VAL* 5.0 7.4 - - + -
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Residues in contact with GLU 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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406A PHE* 3.2 33.0 + - + +
407A GLU* 3.3 32.7 - - - +
410A PHE* 1.3 86.2 - - + +
412A GLU* 1.3 68.9 + - - +
414A LEU* 3.3 7.8 + - + +
415A ARG* 3.3 25.1 + - - +
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Residues in contact with GLU 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ILE* 2.8 38.3 - - + +
370A SER* 3.7 32.5 - - - +
404A ARG* 5.0 2.6 + - - +
407A GLU* 2.9 25.1 + - - +
408A LEU* 3.3 15.7 + - + +
410A PHE 3.5 0.2 - - - -
411A GLU* 1.3 77.2 - - - +
413A ASN* 1.3 61.6 + - - +
415A ARG* 3.3 34.7 + - - +
416A ILE* 3.5 16.5 + - - +
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Residues in contact with ASN 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ILE* 4.1 6.0 - - - +
388A PRO* 3.4 33.3 + - - +
390A VAL 3.1 25.7 + - - +
391A ALA* 4.8 1.1 - - - +
408A LEU 3.1 19.0 + - - +
409A ASP* 3.4 20.4 - - - +
410A PHE 3.4 1.2 + - - -
411A GLU 3.3 0.8 - - - -
412A GLU* 1.3 76.2 - - - +
414A LEU* 1.3 66.2 + - - +
416A ILE* 3.2 13.5 + - - +
417A ILE* 3.0 27.6 + - - +
429A PHE* 4.0 21.4 - - + -
467A LYS* 6.1 0.9 - - - -
470A LEU* 4.0 1.8 - - + -
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Residues in contact with LEU 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 PHE* 2.9 40.5 + - + +
411A GLU* 3.5 8.7 - - + +
412A GLU 3.2 0.2 - - - -
413A ASN* 1.3 79.1 - - - +
415A ARG* 1.3 61.6 + - + +
417A ILE* 3.2 13.0 + - + +
418A ARG* 2.9 63.7 + - + +
470A LEU* 4.1 11.6 - - + +
473A VAL* 3.8 30.1 - - + -
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Residues in contact with ARG 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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370A SER 5.8 1.4 + - - -
372A HIS 5.1 3.0 + - - -
373A SER* 3.1 29.0 - - - +
411A GLU 3.3 13.6 + - - +
412A GLU* 3.6 29.6 + - - +
413A ASN 3.2 0.6 - - - -
414A LEU* 1.3 78.9 - - + +
416A ILE* 1.3 57.2 + - + +
418A ARG* 3.2 12.8 + - - +
419A TYR* 3.0 64.2 + - + +
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Residues in contact with ILE 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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321A LEU* 3.7 36.1 - - + -
369A ILE* 3.8 33.9 - - + -
376A ILE* 4.3 13.9 - - + -
380A VAL* 4.7 7.0 - - + -
386A VAL* 4.2 10.1 - - + -
388A PRO* 4.0 16.6 - - + -
412A GLU 3.7 14.4 - - - +
413A ASN* 3.2 17.1 + - - +
415A ARG* 1.3 74.1 - - + +
417A ILE* 1.3 64.6 + - - +
419A TYR* 3.2 12.5 + - + +
420A CYS* 3.1 24.1 + - - -
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Residues in contact with ILE 417 (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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413A ASN 3.0 17.7 + - - +
414A LEU* 3.4 15.0 - - + +
416A ILE* 1.3 76.2 - - + +
418A ARG* 1.3 61.3 + - - +
420A CYS* 3.1 12.6 + - - +
421A VAL* 3.0 19.2 + - - +
427A ILE* 3.8 25.8 - - + -
429A PHE* 4.0 12.3 - - + -
470A LEU* 3.5 32.5 - - + -
473A VAL* 5.1 0.9 - - + -
474A ILE* 3.7 33.9 - - + +
477A TYR* 4.2 22.2 - - + -
483A LEU* 4.5 9.6 - - + +
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Residues in contact with ARG 418 (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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414A LEU* 2.9 50.4 + - + +
415A ARG* 3.6 12.6 - - - +
417A ILE* 1.3 74.3 - - - +
419A TYR* 1.3 61.4 + - + +
421A VAL* 3.4 9.0 + - + +
422A LYS* 2.9 29.5 + - - +
473A VAL* 5.8 1.6 - - - +
477A TYR* 3.0 34.8 + - + +
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Residues in contact with TYR 419 (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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372A HIS 5.0 0.4 + - - -
373A SER* 3.3 17.1 + - - -
376A ILE* 4.2 11.4 - - + -
377A GLU* 3.8 53.1 + - + -
380A VAL* 3.9 24.0 - - + -
415A ARG* 3.0 61.7 + - + -
416A ILE* 3.2 19.2 + - + +
418A ARG* 1.3 78.3 - - + +
420A CYS* 1.3 58.8 + - - +
422A LYS* 3.2 8.5 + - + -
423A TYR* 2.9 40.2 + + + +
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Residues in contact with CYS 420 (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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380A VAL* 4.2 9.4 - - - -
386A VAL* 3.9 37.9 - - - -
416A ILE* 3.1 16.3 + - - -
417A ILE* 3.1 10.4 + - - +
419A TYR* 1.3 81.0 - - - +
421A VAL* 1.3 56.5 + - - +
424A ARG* 2.9 8.8 + - - -
425A LYS* 2.9 42.3 + - - +
427A ILE* 3.9 22.7 - - + -
483A LEU* 4.1 10.9 - - + +
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Residues in contact with VAL 421 (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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417A ILE 3.0 18.8 + - - +
418A ARG* 3.7 13.2 - - + +
420A CYS* 1.3 72.5 - - - +
422A LYS* 1.3 71.1 - - - +
424A ARG* 3.3 15.7 + - - +
477A TYR* 3.9 32.5 - - + -
481A GLU* 3.6 33.3 - - + +
483A LEU* 4.0 25.3 - - + +
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Residues in contact with LYS 422 (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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377A GLU* 4.0 9.0 - - - +
418A ARG 2.9 19.0 + - - +
419A TYR* 3.2 9.4 + - + +
421A VAL* 1.3 84.0 - - - +
423A TYR* 1.3 98.7 + - + +
424A ARG* 3.6 11.8 + - - +
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Residues in contact with TYR 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLU* 2.6 48.8 + - + +
380A VAL* 4.5 4.3 - - + -
381A LYS* 3.7 44.6 - - + +
419A TYR* 2.9 32.9 + - + +
422A LYS* 1.3 105.5 - - + +
424A ARG* 1.3 73.3 + - - +
425A LYS* 3.4 30.9 + - + -
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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