Contacts of the helix formed by residues 440 - 451 (chain A) in PDB entry 3JUE
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 CYS 440 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420A CYS* 3.5 6.8 - - + -
423A CYS* 3.8 7.4 - - - -
425A GLU* 3.6 28.5 - - + -
428A PRO* 3.7 10.7 - - + +
429A GLU 4.8 0.4 - - - +
430A TRP* 4.0 2.9 - - - -
439A LEU* 1.3 75.1 - - - +
441A ILE* 1.3 57.1 + - - +
442A GLN* 3.7 11.0 - - - -
443A CYS* 3.4 13.9 - - - -
444A SER* 2.8 36.2 + - - -
506A LYS* 4.7 1.1 - - - -
999A ZN 2.4 35.4 - - - -
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Residues in contact with ILE 441 (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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429A GLU* 6.4 0.7 - - + -
430A TRP* 4.0 18.7 - - + +
440A CYS* 1.3 73.0 - - - +
442A GLN* 1.3 65.1 + - - +
444A SER* 2.9 19.2 + - - -
445A GLY* 3.1 8.3 + - - -
1135A SO4 3.2 24.5 + - - +
413B SER* 6.0 2.9 - - - +
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Residues in contact with GLN 442 (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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440A CYS* 3.3 10.2 - - - -
441A ILE* 1.3 83.3 - - - +
443A CYS* 1.3 61.8 + - - +
445A GLY* 3.3 2.4 + - - -
446A ILE* 3.2 31.8 + - + +
499A PRO 4.3 1.7 - - - +
501A CYS 3.9 6.1 + - - +
503A ARG* 3.7 35.9 + - + +
506A LYS* 2.9 41.8 + - + +
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Residues in contact with CYS 443 (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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420A CYS* 3.9 11.7 - - - -
422A ASP* 3.9 15.0 - - - +
423A CYS* 3.9 2.5 - - - -
439A LEU* 4.5 3.6 - - + -
440A CYS* 3.4 5.0 - - - +
442A GLN* 1.3 76.4 - - - +
444A SER* 1.3 60.6 + - - +
446A ILE* 3.2 3.7 + - - +
447A HIS* 2.9 34.6 + - - -
506A LYS* 3.9 22.0 - - - -
510A ILE* 3.8 26.7 - - + -
999A ZN 2.4 34.3 - - - -
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Residues in contact with SER 444 (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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430A TRP* 3.5 24.3 - - - -
439A LEU* 4.0 16.0 - - - +
440A CYS 2.8 23.2 + - - -
441A ILE 2.9 8.7 + - - -
443A CYS* 1.3 73.2 - - - +
445A GLY* 1.3 63.8 + - - +
447A HIS* 3.2 4.7 + - - +
448A ARG* 3.0 25.5 + - - +
457A VAL* 3.7 11.7 - - - +
1135A SO4 2.6 26.6 + - - -
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Residues in contact with GLY 445 (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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441A ILE 3.1 11.8 + - - -
442A GLN* 3.7 4.0 - - - -
443A CYS 3.3 0.2 - - - -
444A SER* 1.3 76.5 + - - +
446A ILE* 1.3 59.9 + - - +
448A ARG* 3.2 24.8 + - - +
503A ARG* 4.0 11.0 - - - -
1135A SO4 3.2 17.5 - - - -
409B ALA* 3.4 14.6 - - - +
413B SER* 4.7 5.8 - - - -
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Residues in contact with ILE 446 (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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442A GLN* 3.2 19.4 + - + +
443A CYS* 3.2 7.4 + - - +
445A GLY* 1.3 70.8 - - - +
447A HIS* 1.3 67.0 + - - +
448A ARG 3.0 1.6 - - - -
449A SER* 2.8 29.1 + - - -
450A LEU* 3.7 7.5 + - + +
503A ARG* 3.9 34.5 - - + +
506A LYS* 3.8 17.0 - - + -
507A GLU* 3.7 42.8 - - + +
510A ILE* 3.8 32.5 - - + -
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Residues in contact with HIS 447 (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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422A ASP* 2.6 31.6 - - - -
432A SER* 4.3 0.4 - - - -
435A LEU* 4.0 8.9 - - + +
437A VAL* 4.9 0.4 - - - +
439A LEU* 3.6 25.0 - - + +
443A CYS 2.9 26.4 + - - +
444A SER* 3.2 10.5 + - - +
446A ILE* 1.3 71.2 - - - +
448A ARG* 1.3 61.4 + - - +
450A LEU* 3.1 30.4 + - + +
451A GLY 4.0 2.9 + - - -
455A SER* 2.7 36.7 - - - +
457A VAL* 3.7 15.3 - - + +
510A ILE* 3.9 9.3 - - + +
514A TYR* 3.4 26.7 + + - -
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Residues in contact with ARG 448 (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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430A TRP* 3.2 23.2 - - - -
444A SER 3.0 16.1 + - - +
445A GLY* 3.3 13.9 - - - +
446A ILE 3.0 1.4 + - - -
447A HIS* 1.3 76.1 - - - +
449A SER* 1.3 60.6 + - - +
450A LEU 3.3 0.7 + - - -
451A GLY* 3.8 8.8 + - - -
455A SER 5.9 0.7 - - - -
457A VAL* 3.6 27.5 + - + +
1135A SO4 2.7 46.6 + - - -
408B VAL* 3.8 16.5 - - - +
409B ALA* 3.9 18.4 - - - +
412B GLN* 3.0 45.1 - - - +
418B ALA* 3.4 17.4 - - - +
427B ALA* 4.4 10.5 - - - +
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Residues in contact with SER 449 (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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445A GLY 3.6 1.8 + - - -
446A ILE* 2.8 21.9 + - - -
448A ARG* 1.3 79.3 - - - +
450A LEU* 1.3 63.9 + - - +
451A GLY 3.5 0.3 + - - -
503A ARG* 5.0 2.4 + - - -
404B VAL* 4.8 7.0 - - - +
405B GLY* 3.5 41.4 + - - -
406B HIS* 4.2 8.1 + - - -
409B ALA* 3.5 11.0 - - - +
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Residues in contact with LEU 450 (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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446A ILE* 3.9 12.8 - - + +
447A HIS* 3.1 31.1 + - + +
449A SER* 1.3 82.4 - - - +
451A GLY* 1.3 60.6 + - - +
453A HIS* 5.8 0.2 - - - +
454A PHE* 3.5 43.4 - - + -
455A SER* 4.5 4.5 - - - -
510A ILE* 4.0 22.9 - - + -
511A HIS* 4.7 13.0 - - + +
514A TYR* 4.6 13.0 - - + -
515A VAL* 3.9 20.6 - - + -
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Residues in contact with GLY 451 (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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447A HIS 4.0 1.8 + - - -
448A ARG 3.8 9.3 + - - -
449A SER 3.3 4.2 + - - -
450A LEU* 1.3 80.6 - - - +
452A VAL* 1.3 59.5 + - - -
453A HIS* 3.2 3.6 - - - -
454A PHE* 3.1 17.8 + - - -
455A SER* 3.1 16.2 + - - +
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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