Contacts of the helix formed by residues 453 - 460 (chain B) in PDB entry 1OFD
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 THR 453 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B GLY 4.4 2.7 - - - -
452B TYR* 1.3 73.4 + - - +
454B ALA* 1.3 64.6 + - - +
455B GLU* 3.4 26.7 - - + +
456B ASP* 2.8 42.3 + - - +
457B VAL* 3.3 10.2 + - - +
768B PHE* 5.4 3.1 - - - -
780B LEU* 4.0 5.4 - - - -
781B GLU 3.4 8.1 + - - +
783B PHE* 3.0 35.4 - - + +
785B PHE* 4.5 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B THR* 1.3 73.2 - - - +
455B GLU* 1.3 58.0 + - - +
457B VAL* 3.3 4.3 + - - +
458B GLU* 2.9 52.1 + - - +
780B LEU* 3.7 24.4 - - + +
781B GLU 3.0 20.4 + - - +
782B ASN* 3.7 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 455 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B THR* 3.3 7.7 - - + +
454B ALA* 1.3 73.8 - - - +
456B ASP* 1.3 60.3 + - - +
458B GLU* 4.7 1.8 - - - -
459B MET* 2.9 58.7 + - + +
460B VAL* 3.4 4.8 + - - +
782B ASN* 3.4 20.5 - - - +
783B PHE 2.8 26.7 + - - +
784B GLY 4.2 0.5 - - - -
785B PHE* 3.0 25.9 + - + +
786B VAL* 2.9 39.4 + - + +
787B ASN* 3.8 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 456 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B GLY 3.9 2.6 - - - +
452B TYR* 4.5 3.8 - - + -
453B THR* 2.8 48.1 + - - +
455B GLU* 1.3 77.3 - - - +
457B VAL* 1.3 58.1 + - + +
460B VAL* 3.3 17.0 + - - +
461B VAL* 2.9 28.0 + - - +
648B TRP* 3.2 42.0 + - + +
785B PHE* 5.8 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B GLN* 4.8 15.3 - - - +
452B TYR* 4.8 7.2 - - + -
453B THR 3.4 15.0 - - - +
454B ALA* 3.9 5.2 - - - +
456B ASP* 1.3 77.2 - - + +
458B GLU* 1.3 71.0 + - + +
461B VAL* 3.4 15.6 + - + -
462B VAL* 2.9 45.5 + - + +
672B SER* 5.6 3.6 - - - -
676B TRP* 6.0 3.1 - - + -
780B LEU* 3.6 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B ALA* 2.9 36.6 + - - +
455B GLU* 4.5 1.9 + - - -
457B VAL* 1.3 85.5 - - + +
459B MET* 1.3 64.2 + - + +
462B VAL* 3.9 10.3 - - + +
463B PRO* 3.4 15.9 - - - +
690B ARG* 5.9 0.5 + - - -
782B ASN* 4.3 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 459 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B GLU* 2.9 38.5 + - + +
458B GLU* 1.3 82.6 - - + +
460B VAL* 1.3 62.7 + - + +
463B PRO* 3.3 13.1 - - - +
471B PRO* 3.3 22.2 - - - +
473B PHE* 6.2 1.1 - - - -
782B ASN* 5.6 2.9 - - - +
786B VAL* 3.8 37.9 - - + -
787B ASN* 5.5 10.8 - - + +
1070B LEU* 4.5 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 460 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B GLU 4.1 8.3 - - - +
456B ASP* 3.3 19.6 + - - +
458B GLU 3.7 0.2 - - - -
459B MET* 1.3 85.1 - - + +
461B VAL* 1.3 63.1 + - - +
462B VAL 3.5 0.9 - - - -
463B PRO* 3.5 2.5 - - - +
464B MET* 2.8 61.8 + - + +
471B PRO* 4.2 11.3 - - + +
648B TRP* 4.4 7.4 - - + +
649B SER* 4.2 20.6 - - - -
786B VAL* 6.2 0.4 - - + -
1070B LEU* 4.1 20.2 - - + -
----------------------------------------------------------
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