Contacts of the helix formed by residues 492 - 501 (chain M) in PDB entry 2DFS
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 ASN 492 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459M GLU* 2.9 50.4 + - - +
462M GLN* 4.7 2.6 - - - +
463M GLN* 3.3 30.6 - - - +
466M ASN* 3.7 13.5 + - - +
489M PHE* 6.0 1.0 - - - -
490M TYR 5.0 0.2 - - - +
491M ASP* 1.4 76.2 + - - +
493M GLN* 1.4 63.8 + - - +
494M PRO* 3.5 4.7 - - - -
495M CYS* 3.2 18.5 + - + +
496M ILE* 3.3 19.3 + - - +
553M PHE* 4.6 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 493 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460M LYS* 5.4 1.4 + - - -
463M GLN* 2.8 32.9 + - - +
491M ASP* 3.0 24.4 + - - +
492M ASN* 1.4 77.9 + - - +
494M PRO* 1.3 58.5 - - + +
496M ILE* 3.2 19.7 + - - +
497M ASN* 2.9 60.8 + - - +
500M GLU* 5.6 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 494 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491M ASP* 3.3 22.7 - - + +
492M ASN* 3.6 4.5 - - - -
493M GLN* 1.3 87.4 - - + +
495M CYS* 1.4 56.5 + - - +
497M ASN* 3.8 8.6 - - + +
498M LEU* 3.1 26.3 + - - +
535M CYS* 5.5 2.8 - - - -
537M LEU* 3.7 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 495 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459M GLU* 3.5 33.9 - - - +
492M ASN* 3.2 14.1 + - + +
494M PRO* 1.4 74.5 - - - +
496M ILE* 1.4 64.7 + - - +
498M LEU* 3.2 5.7 + - - +
499M ILE* 3.2 28.3 + - - +
537M LEU* 3.5 18.6 - - + +
550M ILE* 4.2 12.6 - - - -
551M LYS 3.9 18.8 - - - +
552M HIS* 3.9 13.5 - - - -
553M PHE 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 496 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456M TYR* 5.0 4.4 - - + +
459M GLU* 3.8 31.0 - - + +
460M LYS* 3.9 32.3 - - + +
463M GLN* 3.5 27.6 - - + +
492M ASN* 3.6 28.3 - - - +
493M GLN* 3.2 26.7 + - - +
495M CYS* 1.4 73.7 - - - +
497M ASN* 1.3 57.8 + - - +
499M ILE* 3.4 10.6 + - - +
500M GLU* 2.9 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 497 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493M GLN* 2.9 47.8 + - - +
494M PRO* 3.8 8.2 - - + +
496M ILE* 1.3 75.5 - - - +
498M LEU* 1.3 62.1 + - - +
500M GLU* 5.0 3.6 - - - +
501M ALA* 2.9 45.3 + - + +
504M GLY* 4.6 1.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 498 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494M PRO 3.1 15.9 + - - +
495M CYS* 3.2 10.1 + - - +
497M ASN* 1.3 73.8 - - - +
499M ILE* 1.3 58.1 + - + +
504M GLY* 3.2 7.6 - - - -
505M VAL* 2.9 32.8 + - + +
531M HIS* 4.1 33.0 - - + +
535M CYS* 4.3 17.5 - - + -
537M LEU* 3.8 38.4 - - + +
538M PHE* 4.1 5.4 - - + -
550M ILE* 3.9 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 499 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452M PHE* 3.8 33.0 - - + +
456M TYR* 3.6 46.4 - - + -
459M GLU* 4.8 4.0 - - + -
495M CYS* 3.2 22.3 + - - +
496M ILE* 3.7 7.2 - - - +
498M LEU* 1.3 81.9 - - + +
500M GLU* 1.4 57.9 + - - +
501M ALA 3.8 0.2 - - - -
504M GLY 4.2 1.0 - - - -
505M VAL* 3.7 7.0 + - + +
506M LEU* 3.3 34.6 + - + +
507M ASP 4.7 0.3 + - - -
550M ILE* 5.3 4.5 - - + -
552M HIS* 3.9 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 500 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456M TYR* 2.6 43.2 + - + +
460M LYS* 2.6 36.9 + - - -
493M GLN* 5.6 0.3 - - - +
496M ILE* 2.9 26.4 + - + +
497M ASN* 5.1 3.5 + - - +
499M ILE* 1.4 72.8 - - - +
501M ALA* 1.3 66.3 + - - +
506M LEU* 4.7 5.6 - - + -
507M ASP* 5.7 1.0 - - - +
641M ARG* 2.6 47.5 + - - +
645M HIS* 3.6 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 501 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497M ASN* 2.9 34.4 + - + +
499M ILE 4.7 0.2 - - - +
500M GLU* 1.3 84.2 - - - +
502M LYS* 1.4 66.3 + - - +
504M GLY* 3.0 20.4 + - - +
507M ASP* 3.7 8.5 - - - +
----------------------------------------------------------
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