Contacts of the helix formed by residues 439 - 450 (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 ASP 439 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B PHE* 4.3 1.8 - - - +
438B ASN* 1.3 81.8 - - - +
440B ALA* 1.3 64.7 + - - +
441B GLN* 4.1 7.4 - - + +
442B THR* 3.3 35.6 + - - +
443B VAL* 3.4 16.5 + - - +
675B GLN* 5.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B ASN 3.8 3.8 + - - -
439B ASP* 1.3 71.3 - - - +
441B GLN* 1.3 64.2 + - - +
443B VAL* 3.2 13.4 + - - +
444B LEU* 3.1 32.2 + - + +
675B GLN* 5.1 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B ASP* 4.6 6.7 - - + -
440B ALA* 1.3 78.7 - - - +
442B THR* 1.3 62.2 + - - +
444B LEU* 3.2 9.3 + - + +
445B GLN* 3.0 28.0 + - + +
778B LYS* 5.6 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B PHE* 4.1 17.3 - - + -
439B ASP* 3.3 32.2 + - - +
440B ALA 3.2 0.4 - - - -
441B GLN* 1.3 76.0 - - - +
443B VAL* 1.3 65.3 + - - +
445B GLN* 3.3 8.9 + - - +
446B GLN* 3.0 31.6 + - + +
608B ILE* 3.5 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B PHE* 4.3 19.7 - - + -
439B ASP 3.5 14.8 - - - +
440B ALA* 3.2 9.8 + - - +
442B THR* 1.3 77.3 - - - +
444B LEU* 1.3 63.3 + - + +
446B GLN* 3.4 3.8 + - - +
447B GLN* 3.0 52.2 + - + +
668B LEU* 4.9 8.1 - - + +
671B GLU* 4.9 2.2 - - + -
672B SER* 5.4 1.1 - - - -
675B GLN* 3.6 49.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B ALA* 3.1 25.6 + - + +
441B GLN* 3.2 10.5 + - - +
443B VAL* 1.3 84.1 - - + +
445B GLN* 1.3 57.6 + - - +
447B GLN* 3.4 14.1 + - - +
448B ALA* 2.9 30.0 + - - +
778B LYS 4.9 15.9 - - - +
779B LYS* 4.4 5.2 - - - -
780B LEU* 3.6 43.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B GLN* 3.0 21.1 + - + +
442B THR* 3.8 8.6 - - - +
444B LEU* 1.3 75.1 - - - +
446B GLN* 1.3 65.9 + - - +
448B ALA* 3.3 3.8 + - - +
449B ALA* 2.9 31.4 + - - +
772B ALA* 3.0 31.2 + - + +
773B PHE* 3.6 34.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B PHE* 4.6 6.7 - - + -
442B THR* 3.0 23.5 + - + +
443B VAL* 3.8 4.3 - - - +
445B GLN* 1.3 82.3 + - - +
447B GLN* 1.3 64.1 + - - +
449B ALA* 3.4 2.8 + - - +
450B PHE* 3.0 52.1 + - + +
608B ILE* 3.5 41.2 - - + +
609B LEU* 3.1 31.4 + - - +
667B TYR* 5.5 1.4 + - - -
668B LEU* 3.9 19.5 - - + -
773B PHE* 4.8 7.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B VAL* 3.0 37.0 + - + +
444B LEU* 3.5 26.8 - - - +
446B GLN* 1.3 77.5 - - - +
448B ALA* 1.3 63.3 + - - +
450B PHE 3.2 0.2 + - - -
451B GLY 3.2 5.0 + - - -
452B TYR* 2.9 55.3 + - + +
457B VAL* 4.8 9.9 - - - +
668B LEU* 3.8 12.5 - - + +
672B SER* 2.8 32.4 + - - +
675B GLN* 6.0 0.2 - - - +
780B LEU* 3.8 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B LEU 2.9 18.6 + - - +
445B GLN* 3.8 4.5 - - - +
447B GLN* 1.3 76.3 - - - +
449B ALA* 1.3 61.1 + - - +
451B GLY* 3.3 11.1 + - - -
452B TYR 4.1 5.7 - - - +
768B PHE* 3.7 19.5 - - - +
771B MET* 4.8 12.6 - - + +
772B ALA* 3.9 20.0 - - + +
780B LEU* 3.7 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B GLN 2.9 18.5 + - - +
446B GLN* 3.7 6.7 - - - +
447B GLN 3.2 0.2 - - - -
448B ALA* 1.3 78.6 - - - +
450B PHE* 1.3 59.4 + - + +
451B GLY 3.3 1.1 + - - -
609B LEU* 3.8 16.3 - - + +
615B PHE* 3.5 17.6 - - - -
765B VAL 4.9 0.5 - - - +
768B PHE* 3.8 18.3 - - - +
769B HIS* 4.7 3.3 + - - +
772B ALA* 3.6 16.8 - - + +
773B PHE* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B GLN* 3.0 48.0 + - + +
447B GLN 3.2 2.0 + - - +
449B ALA* 1.3 77.4 - - - +
451B GLY* 1.3 59.2 + - - +
452B TYR* 3.5 6.7 + - + -
602B ASP* 3.6 38.4 - - + -
609B LEU* 3.9 27.8 - - + -
615B PHE* 3.6 42.0 - + + -
645B ALA* 3.4 34.8 - - + +
646B GLN* 2.8 39.5 + - + +
648B TRP* 4.1 3.6 - - - -
667B TYR* 4.3 3.1 - - - -
768B PHE* 5.3 0.2 - - - -
----------------------------------------------------------
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