Contacts of the strand formed by residues 470 - 477 (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 GLN 470 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465M GLU 3.6 0.2 - - - +
466M GLU* 3.6 4.3 - - - +
467M ASN* 2.8 42.8 + - + +
468M GLY 4.1 0.9 - - - +
469M GLN* 1.3 81.4 - - - +
471M GLN* 1.3 62.4 + - - +
472M LYS* 5.7 1.1 - - + -
492M ILE* 4.1 6.2 - - + +
493M VAL 3.4 6.3 - - - +
494M VAL* 3.4 30.2 - - + +
495M PRO* 4.3 0.2 - - + -
498M GLU* 2.8 32.3 + - - +
502M ALA* 4.1 2.4 - - - +
506M PHE* 4.0 10.2 - - - -
529M GLU* 3.0 47.7 + - - +
530M HIS* 3.6 6.2 + - + -
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Residues in contact with GLN 471 (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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471A GLN* 5.6 6.7 - - - +
440M HIS* 4.8 6.9 - - - +
441M ARG* 5.4 2.1 - - - -
442M GLY* 5.2 6.8 + - - +
444M PHE* 3.6 44.0 + - + +
445M SER* 5.2 2.0 + - - +
464M GLN* 3.6 20.4 - - - +
465M GLU 3.4 4.9 - - - +
466M GLU* 3.5 23.5 + - - +
469M GLN 4.7 6.3 - - - +
470M GLN* 1.3 73.9 - - - +
472M LYS* 1.3 62.0 + - - +
492M ILE* 3.3 5.2 - - - +
493M VAL* 2.9 47.1 + - + +
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Residues in contact with LYS 472 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444M PHE* 3.6 3.5 - - - -
462M VAL* 4.3 1.7 - - - +
464M GLN* 3.5 4.5 - - - -
465M GLU* 2.7 77.7 + - + +
470M GLN* 5.7 1.1 - - + -
471M GLN* 1.3 75.9 - - - +
473M TYR* 1.3 64.7 + - - +
474M LEU* 3.8 28.0 + - + -
490M ASP* 5.2 0.9 - - + -
491M ILE 3.4 2.5 - - - +
492M ILE* 3.9 28.7 - - + -
505M TYR* 5.4 1.8 - - - -
506M PHE* 4.2 13.0 - - + -
529M GLU* 5.2 6.5 + - - -
6O C 2.9 40.8 + - - +
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Residues in contact with TYR 473 (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* 3.5 20.2 - - + -
448M LEU* 3.5 26.7 - - + -
452M ARG* 4.4 0.4 - - - -
457M LEU* 3.7 33.5 - - + +
459M ASP 3.2 14.2 + - - -
460M ASP* 2.7 41.7 + - + -
462M VAL 3.7 6.7 - - - -
463M SER 3.5 15.9 - - - -
472M LYS* 1.3 73.3 - - - +
474M LEU* 1.3 67.1 + - - +
475M GLY* 3.4 23.9 - - - -
476M VAL 3.7 2.3 + - - -
489M LEU* 3.9 10.1 - - + -
490M ASP* 3.1 7.1 - - - +
491M ILE* 2.8 43.8 + - + +
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Residues in contact with LEU 474 (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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342M TRP* 4.2 13.7 - - + -
460M ASP 3.9 0.2 - - - -
461M LEU* 2.8 11.3 + - + -
462M VAL* 2.8 66.1 + - + +
465M GLU* 5.4 4.0 - - + +
472M LYS* 3.8 27.8 - - + +
473M TYR* 1.3 84.1 - - - +
475M GLY* 1.3 56.8 + - - +
488M ARG* 4.1 5.8 - - - +
490M ASP* 3.2 35.2 - - - +
5O A 5.9 0.7 - - - +
6O C 3.9 25.1 - - - -
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Residues in contact with GLY 475 (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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459M ASP 3.6 5.4 - - - -
461M LEU* 3.8 7.6 - - - -
473M TYR* 3.4 17.8 - - - -
474M LEU* 1.3 75.3 - - - +
476M VAL* 1.3 67.2 + - - +
488M ARG* 3.0 23.0 + - - +
489M LEU* 2.9 26.4 + - - -
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Residues in contact with VAL 476 (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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375M ILE* 3.9 13.5 - - + -
379M HIS* 4.0 4.7 - - + -
383M PHE* 3.6 27.6 - - + -
457M LEU* 3.3 10.2 - - - +
458M THR* 2.8 47.8 + - - +
459M ASP* 2.8 31.6 + - + +
461M LEU* 4.5 5.6 - - + -
473M TYR* 3.7 2.0 + - - -
475M GLY* 1.3 80.4 - - - +
477M CYS* 1.3 58.3 + - - +
486M HIS* 3.7 27.1 - - + -
487M ARG 3.6 4.0 - - - +
489M LEU* 5.1 0.2 - - - -
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Residues in contact with CYS 477 (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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395M ILE* 3.8 26.5 - - - -
456M PHE* 3.1 46.0 - - + +
457M LEU* 4.3 1.1 - - + -
458M THR* 4.6 1.3 - - - -
476M VAL* 1.3 76.5 - - - +
478M ARG* 1.3 61.3 + - - +
485M ARG 4.1 0.2 - - - +
486M HIS* 3.4 5.2 - - - -
487M ARG* 2.9 44.0 + - - +
489M LEU* 3.9 24.1 - - + +
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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