Contacts of the helix formed by residues 442 - 454 (chain E) in PDB entry 5IIO
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 GLY 442 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440E HIS 3.7 0.4 + - - -
441E ARG* 1.3 71.7 - - - +
443E ILE* 1.3 63.4 + - - +
444E PHE* 3.6 2.0 - - - +
445E SER* 4.2 6.9 + - - -
446E ARG* 3.5 24.5 + - - +
471E GLN* 5.2 7.3 + - - +
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Residues in contact with ILE 443 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403E ALA* 5.0 4.7 - - + +
406E PHE* 3.9 27.8 - - + -
407E ASN* 4.6 6.1 - - + -
410E LEU* 4.0 28.9 - - + -
432E ILE* 5.1 2.5 - - + -
439E SER 3.3 25.4 - - - +
440E HIS* 3.4 15.6 + - - +
441E ARG 3.1 3.1 - - - +
442E GLY* 1.3 76.0 - - - +
444E PHE* 1.3 67.8 + - - +
446E ARG* 3.1 21.5 + - - +
447E LEU* 2.9 36.5 + - + +
493E VAL* 4.9 10.5 - - + -
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Residues in contact with PHE 444 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440E HIS 4.5 1.4 + - - -
442E GLY 5.3 0.2 - - - -
443E ILE* 1.3 78.6 - - - +
445E SER* 1.3 69.3 + - - +
447E LEU* 3.2 5.2 + - - +
448E LEU* 3.1 41.1 + - + +
463E SER 3.7 4.7 - - - -
464E GLN* 3.6 36.8 - - + -
471E GLN* 3.5 54.1 - - + +
472E LYS 3.5 24.0 - - - -
473E TYR* 3.6 24.9 - - + -
491E ILE* 3.8 11.4 - - + -
493E VAL* 3.9 22.4 - - + +
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Residues in contact with SER 445 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442E GLY 4.2 6.8 + - - -
443E ILE 3.2 0.8 + - - -
444E PHE* 1.3 87.4 - - - +
446E ARG* 1.3 60.9 + - - +
448E LEU* 3.6 6.8 + - - +
449E ASP* 3.2 32.0 + - - +
464E GLN* 5.6 4.7 - - - -
471E GLN* 5.2 1.5 + - - -
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Residues in contact with ARG 446 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406E PHE* 3.2 65.4 + - + +
441E ARG 5.8 0.8 + - - -
442E GLY 3.5 16.7 + - - +
443E ILE* 3.5 23.3 - - - +
445E SER* 1.3 76.8 - - - +
447E LEU* 1.3 64.8 + - - +
449E ASP* 3.7 12.3 - - + +
450E SER* 3.1 17.7 + - - -
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Residues in contact with LEU 447 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399E VAL* 3.9 11.4 - - + +
402E ALA* 3.7 16.4 - - + -
403E ALA* 3.6 31.9 - - + +
406E PHE* 3.8 9.4 - - + -
432E ILE* 3.7 30.7 - - + -
443E ILE* 2.9 27.5 + - + +
444E PHE* 3.5 8.7 - - + +
446E ARG* 1.3 78.6 - - - +
448E LEU* 1.3 57.3 + - + +
450E SER* 3.3 1.6 + - - -
451E LEU* 3.0 43.9 + - + +
491E ILE* 4.1 17.7 - - + -
493E VAL* 5.2 0.4 - - + -
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Residues in contact with LEU 448 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444E PHE* 3.1 36.1 + - + +
445E SER* 3.8 8.5 - - - +
446E ARG 3.3 0.2 - - - -
447E LEU* 1.3 75.3 - - + +
449E ASP* 1.3 56.2 + - - +
451E LEU* 3.3 2.5 + - + -
452E ARG* 2.7 56.3 + - - +
457E LEU* 3.6 14.7 - - + +
463E SER* 3.5 24.7 - - - +
473E TYR* 3.5 33.9 - - + -
491E ILE* 3.8 24.5 - - + -
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Residues in contact with ASP 449 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445E SER* 3.2 21.4 + - - +
446E ARG* 3.7 15.1 - - + +
447E LEU 3.3 0.4 - - - -
448E LEU* 1.3 77.2 - - - +
450E SER* 1.3 56.7 + - - +
452E ARG* 3.2 22.8 + - - +
453E GLN* 2.9 31.1 + - - +
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Residues in contact with SER 450 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402E ALA* 4.1 11.4 + - - +
406E PHE* 4.0 18.8 - - - -
446E ARG 3.1 14.9 + - - -
447E LEU 3.6 4.7 - - - -
448E LEU 3.3 0.2 - - - -
449E ASP* 1.3 79.8 - - - +
451E LEU* 1.3 62.1 + - - +
453E GLN* 3.3 6.8 + - - +
454E GLU* 3.1 39.3 + - - +
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Residues in contact with LEU 451 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398E THR* 3.9 11.0 - - + +
399E VAL* 4.3 12.1 - - + -
402E ALA* 3.6 24.5 - - + -
447E LEU* 3.0 34.2 + - + +
448E LEU* 3.7 3.6 - - + +
450E SER* 1.3 75.2 - - - +
452E ARG* 1.3 58.7 + - - +
454E GLU* 3.5 13.6 + - - +
456E PHE* 3.1 48.1 + - + +
457E LEU* 3.4 25.7 + - + -
491E ILE* 3.7 30.7 - - + -
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Residues in contact with ARG 452 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448E LEU* 2.7 46.7 + - - +
449E ASP* 3.4 30.4 + - - +
451E LEU* 1.3 78.5 - - - +
453E GLN* 1.3 61.2 + - - +
455E GLY* 3.1 14.4 + - - -
457E LEU* 4.1 26.9 - - + +
460E ASP* 2.8 36.5 + - - -
463E SER* 4.8 5.3 - - - -
473E TYR* 4.5 0.4 - - - -
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Residues in contact with GLN 453 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449E ASP 2.9 16.8 + - - +
450E SER* 3.8 6.5 - - - +
452E ARG* 1.3 73.1 - - - +
454E GLU* 1.3 58.5 + - + +
455E GLY* 2.9 10.0 + - - -
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Residues in contact with GLU 454 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398E THR* 4.1 21.9 - - - +
402E ALA* 4.2 10.9 - - - +
450E SER* 3.1 34.2 + - - +
451E LEU* 3.8 13.7 - - - +
452E ARG 3.3 0.4 - - - -
453E GLN* 1.3 75.1 - - + +
455E GLY* 1.3 57.8 + - - +
456E PHE* 3.2 8.4 + - + +
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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