Contacts of the strand formed by residues 457 - 467 (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 LEU 457 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448M LEU* 3.9 28.5 - - + +
451M LEU* 3.3 29.3 + - + +
452M ARG* 4.2 25.2 - - + +
455M GLY* 4.1 7.6 - - - +
456M PHE* 1.3 85.4 - - + +
458M THR* 1.3 61.6 + - - +
460M ASP* 4.6 5.2 - - - +
473M TYR* 3.7 35.7 - - + +
476M VAL 3.3 9.9 - - - +
477M CYS* 4.3 1.1 - - + -
489M LEU* 3.9 27.4 - - + -
491M ILE* 5.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 458 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455M GLY 4.2 9.2 - - - +
456M PHE 4.0 4.0 - - - +
457M LEU* 1.3 76.9 - - - +
459M ASP* 1.3 86.7 + - - +
476M VAL* 2.8 16.0 + - - +
478M ARG* 3.9 28.5 - - + +
486M HIS* 3.0 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 459 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375M ILE* 3.9 18.3 - - + +
378M LYS* 2.8 35.1 + - - -
379M HIS* 3.0 19.6 + - - -
457M LEU 3.7 0.6 - - - -
458M THR* 1.3 105.7 + - - +
460M ASP* 1.3 64.6 + - - +
473M TYR* 3.2 6.8 + - - -
476M VAL* 2.8 40.0 + - + +
486M HIS* 4.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 460 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371M THR* 5.6 1.9 - - - +
372M GLN* 5.6 0.3 - - - +
375M ILE* 3.4 19.5 - - - +
452M ARG* 2.6 35.9 + - - -
457M LEU* 4.6 4.3 - - - +
459M ASP* 1.3 74.7 - - - +
461M LEU* 1.3 63.6 + - - +
463M SER* 3.2 26.1 + - - +
473M TYR* 2.7 38.8 + - + -
474M LEU 4.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 461 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342M TRP* 3.9 44.2 - - + -
372M GLN* 2.9 36.6 + - - +
375M ILE* 3.7 34.8 - - + -
376M GLY* 4.9 1.3 - - - +
383M PHE* 5.0 2.0 - - + -
460M ASP* 1.3 75.0 - - - +
462M VAL* 1.3 62.4 + - - +
463M SER 4.2 0.7 - - - -
474M LEU* 2.8 13.4 + - + +
475M GLY* 3.8 8.0 - - - +
476M VAL* 4.5 6.7 - - + -
488M ARG* 3.5 43.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 462 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342M TRP* 4.7 4.0 - - + -
372M GLN* 3.4 16.8 - - - +
461M LEU* 1.3 79.6 - - - +
463M SER* 1.3 64.5 + - - +
464M GLN 3.8 23.3 - - - +
465M GLU* 4.2 14.4 - - + +
472M LYS 5.0 0.4 - - - +
473M TYR* 3.7 2.3 - - - -
474M LEU* 2.8 62.4 + - + +
9N C 4.5 18.2 - - - +
10N T 5.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 463 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ARG* 3.5 23.5 + - - +
441A ARG* 3.9 17.9 - - - -
444M PHE* 3.6 3.1 - - - -
448M LEU* 3.5 13.6 - - - +
452M ARG* 4.5 5.3 + - - -
460M ASP* 3.2 27.9 + - - +
461M LEU 4.2 1.2 - - - -
462M VAL* 1.3 72.0 - - - +
464M GLN* 1.3 61.7 + - - +
472M LYS 4.5 0.2 - - - -
473M TYR* 3.5 23.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 464 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A HIS* 5.6 0.3 + - - -
441A ARG* 3.3 52.8 + - - +
469A GLN* 5.5 3.5 - - - +
444M PHE* 3.6 22.0 - - + -
445M SER* 4.3 9.3 + - - -
462M VAL* 3.8 9.7 - - - +
463M SER* 1.3 83.9 - - - +
465M GLU* 1.3 66.0 + - - +
466M GLU* 3.7 32.4 + - + +
471M GLN* 3.6 26.5 - - + +
472M LYS 3.5 5.8 - - - -
9N C 3.9 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 465 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462M VAL* 4.2 10.4 - - + +
464M GLN* 1.3 76.9 - - - +
466M GLU* 1.3 61.0 + - - +
467M ASN* 3.9 19.4 + - - +
470M GLN 3.6 1.2 - - - +
471M GLN* 3.4 6.1 - - - -
472M LYS* 2.7 76.9 + - + +
474M LEU* 5.4 5.0 - - + +
8N A 3.3 42.8 + - - +
9N C 3.5 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 466 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A GLU* 3.0 33.3 - - - +
468A GLY* 3.9 22.4 - - - +
469A GLN* 3.9 17.6 - - + +
471A GLN* 4.9 7.2 + - - +
464M GLN* 3.7 34.3 + - + +
465M GLU* 1.3 76.2 - - - +
467M ASN* 1.3 58.8 + - - +
468M GLY 4.0 4.6 + - - +
469M GLN 5.8 0.5 - - - -
470M GLN 3.6 5.6 - - - +
471M GLN* 3.5 22.8 + - + +
8N A 3.4 23.9 + - - +
9N C 2.8 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 467 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465M GLU* 3.9 17.0 + - - +
466M GLU* 1.3 73.2 - - - +
468M GLY* 1.3 60.5 + - - +
470M GLN* 2.8 36.8 + - + +
529M GLU* 3.6 20.9 + - - +
530M HIS* 2.7 39.7 + - + +
6N G 5.9 0.8 - - - +
7N T 4.2 25.4 + - - +
8N A 3.9 22.2 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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