Contacts of the helix formed by residues 443 - 454 (chain M) 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 ILE 443 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403M ALA* 4.9 4.9 - - + -
406M PHE* 3.8 21.3 - - + -
407M ASN* 4.6 6.1 - - + -
410M LEU* 3.9 29.6 - - + -
432M ILE* 5.3 2.9 - - + -
439M SER 3.5 24.9 - - - +
440M HIS* 3.5 16.0 + - - +
441M ARG 3.9 1.3 - - - +
442M GLY* 1.3 79.8 - - - +
444M PHE* 1.3 60.2 + - - +
445M SER 3.4 1.3 - - - -
446M ARG* 3.1 28.1 + - - +
447M LEU* 2.7 46.6 + - + +
493M VAL* 5.2 7.6 - - + -
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Residues in contact with PHE 444 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440M HIS 4.7 1.2 + - - -
443M ILE* 1.3 78.9 - - - +
445M SER* 1.3 68.7 + - - +
447M LEU* 3.3 4.7 + - - +
448M LEU* 3.1 38.7 + - + +
463M SER 3.6 16.4 - - - -
464M GLN* 3.6 33.2 - - + -
471M GLN* 3.6 47.6 - - + +
472M LYS 3.6 14.4 - - - -
473M TYR* 3.5 40.2 - - + -
491M ILE* 3.8 9.6 - - + -
493M VAL* 4.0 22.2 - - + +
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Residues in contact with SER 445 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A ARG* 3.8 14.5 - - - +
442A GLY* 3.5 36.0 + - - -
442M GLY* 5.2 2.4 - - - -
443M ILE 3.4 1.4 - - - +
444M PHE* 1.3 83.2 - - - +
446M ARG* 1.3 59.3 + - - +
448M LEU* 3.5 6.0 + - - +
449M ASP* 3.1 36.0 + - - +
452M ARG* 5.1 0.2 + - - -
464M GLN* 4.3 10.7 + - - -
471M GLN* 5.2 1.6 + - - +
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Residues in contact with ARG 446 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A GLY* 6.1 2.0 - - - +
446A ARG* 4.9 22.9 - - + +
406M PHE* 3.3 55.5 + - + +
441M ARG 5.7 0.4 + - - -
442M GLY 3.1 22.3 + - - +
443M ILE* 3.1 28.2 + - - +
445M SER* 1.3 76.1 - - - +
447M LEU* 1.3 61.8 + - - +
449M ASP* 3.4 8.5 + - - +
450M SER* 2.9 29.6 + - - -
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Residues in contact with LEU 447 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399M VAL* 3.9 11.0 - - + +
402M ALA* 3.6 17.7 - - + -
403M ALA* 3.5 32.8 - - + +
406M PHE* 3.9 6.5 - - + -
432M ILE* 3.6 30.5 - - + -
443M ILE* 2.7 30.9 + - + +
444M PHE* 3.6 4.9 - - - +
446M ARG* 1.3 74.4 - - - +
448M LEU* 1.3 59.7 + - + +
450M SER* 3.1 4.7 + - - -
451M LEU* 2.9 43.1 + - + +
491M ILE* 4.0 17.7 - - + -
493M VAL* 5.3 3.8 - - + -
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Residues in contact with LEU 448 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444M PHE* 3.1 38.5 + - + +
445M SER* 3.9 5.2 - - - +
447M LEU* 1.3 79.3 - - + +
449M ASP* 1.3 56.2 + - - +
451M LEU* 3.3 2.7 + - + +
452M ARG* 2.9 53.8 + - - +
457M LEU* 3.9 13.3 - - + +
463M SER 3.5 14.4 - - - +
473M TYR* 3.5 44.6 - - + -
491M ILE* 4.0 24.0 - - + -
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Residues in contact with ASP 449 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445M SER* 3.1 24.8 + - - +
446M ARG* 3.7 6.9 - - - +
448M LEU* 1.3 74.8 - - - +
450M SER* 1.3 64.2 + - - +
452M ARG* 3.3 24.6 + - - +
453M GLN* 3.1 41.1 + - - +
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Residues in contact with SER 450 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402M ALA* 4.0 18.3 + - - +
406M PHE* 4.1 18.9 - - - -
446M ARG 2.9 14.1 + - - -
447M LEU* 3.1 10.1 + - - -
449M ASP* 1.3 76.7 - - - +
451M LEU* 1.3 63.7 + - - +
453M GLN* 3.4 12.1 + - - +
454M GLU* 3.2 24.9 + - - +
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Residues in contact with LEU 451 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398M THR* 4.0 11.9 - - + +
399M VAL* 4.4 11.4 - - + -
402M ALA* 3.7 23.1 - - + -
447M LEU* 2.9 35.5 + - + +
448M LEU* 4.8 0.2 - - - -
450M SER* 1.3 75.1 - - - +
452M ARG* 1.3 59.4 + - - +
454M GLU* 3.6 13.0 + - - +
455M GLY 3.5 1.2 + - - -
456M PHE* 3.0 49.3 + - + +
457M LEU* 3.3 27.9 + - + -
491M ILE* 3.7 29.4 - - + -
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Residues in contact with ARG 452 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445M SER 5.1 0.2 + - - -
448M LEU* 2.9 48.2 + - - +
449M ASP* 3.3 29.0 + - - +
451M LEU* 1.3 74.1 - - - +
453M GLN* 1.3 58.9 + - + +
455M GLY* 2.7 24.6 + - - -
457M LEU* 4.2 24.3 - - + +
460M ASP* 2.6 37.0 + - - -
463M SER* 4.5 6.9 + - - -
473M TYR* 4.4 1.6 - - - -
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Residues in contact with GLN 453 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449M ASP* 3.1 29.2 + - - +
450M SER* 3.8 9.1 - - - +
452M ARG* 1.3 79.4 - - + +
454M GLU* 1.3 61.1 + - - +
455M GLY 3.2 0.9 + - - -
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Residues in contact with GLU 454 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398M THR* 3.7 23.6 - - - +
402M ALA* 4.8 6.8 - - - +
450M SER* 3.2 15.0 + - - +
451M LEU* 3.7 21.8 - - - +
452M ARG 3.1 0.8 - - - -
453M GLN* 1.3 77.2 - - - +
455M GLY* 1.3 58.9 + - - +
456M PHE* 3.1 10.1 - - + +
480M PRO* 5.4 9.1 - - + +
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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