Contacts of the helix formed by residues 460 - 470 (chain B) in PDB entry 4FE1
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 PRO 460 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B ILE 3.5 1.5 - - - +
459B GLU* 1.3 85.8 - - + +
461B VAL* 1.3 51.6 + - - +
462B PHE* 3.4 3.1 - - - -
463B ALA* 3.1 16.0 + - + -
464B GLN* 2.7 37.1 + - - +
518B ILE* 4.0 13.7 - - + -
519B GLY* 3.0 47.8 - - - +
522B ASP* 4.7 0.9 - - + -
523B PHE* 4.1 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B ILE* 6.1 0.2 - - + -
459B GLU* 2.6 39.5 + - + +
460B PRO* 1.3 68.9 - - - +
462B PHE* 1.3 90.1 + - + +
464B GLN* 3.6 11.4 - - - +
465B PHE* 2.9 29.5 + - - +
477B PHE* 3.7 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 462 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B PRO 3.4 0.4 - - - -
461B VAL* 1.3 95.2 - - + +
463B ALA* 1.3 56.9 + - - +
465B PHE* 3.3 10.2 - - + +
466B ILE* 3.0 38.0 + - + +
523B PHE* 6.5 0.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 463 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B PRO* 3.2 16.1 - - + +
462B PHE* 1.3 77.7 - - - +
464B GLN* 1.3 66.5 + - - +
465B PHE 3.1 0.9 - - - -
466B ILE* 3.1 8.8 + - - +
467B GLN* 2.9 29.0 + - + +
518B ILE* 3.5 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 464 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B GLU* 2.7 30.1 + - - +
460B PRO* 2.7 29.0 + - - +
461B VAL* 3.6 18.2 + - - +
463B ALA* 1.3 73.2 - - - +
465B PHE* 1.3 58.0 + - - +
467B GLN* 3.3 2.8 + - - +
468B ALA* 2.9 29.6 + - - +
475B TYR* 3.3 44.7 - - + -
477B PHE* 3.6 17.6 - - + -
518B ILE* 3.2 30.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 465 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B VAL 2.9 19.5 + - - +
462B PHE* 3.3 11.9 - - - +
464B GLN* 1.3 76.5 - - - +
466B ILE* 1.3 72.4 + - + +
468B ALA* 3.3 2.1 + - - +
469B ALA* 2.9 36.0 + - + +
477B PHE* 3.4 32.9 - + + -
479B THR* 4.2 22.2 - - + -
480B LEU* 4.8 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 466 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B PHE* 3.0 18.8 + - + +
463B ALA* 3.1 8.3 + - - +
465B PHE* 1.3 89.1 - - + +
467B GLN* 1.3 66.0 + - + +
469B ALA* 3.0 10.4 + - + +
470B HIS* 2.9 49.0 + - + +
515B PHE* 5.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 467 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B ALA* 2.9 17.8 + - + +
464B GLN* 3.6 6.5 - - - +
466B ILE* 1.3 76.5 - - + +
468B ALA* 1.3 62.6 + - - +
470B HIS* 3.0 22.0 + - - +
472B LYS* 3.1 23.9 + - + +
475B TYR* 2.8 34.8 + - + -
507B ILE* 4.1 0.9 - - - +
515B PHE* 3.6 41.0 + - + +
516B LEU 3.3 22.6 + - - +
518B ILE* 3.8 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 468 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B GLN 2.9 12.9 + - - +
465B PHE 3.4 9.2 - - - +
467B GLN* 1.3 78.3 - - - +
469B ALA* 1.3 54.4 + - - +
471B GLY* 2.5 29.5 + - - -
472B LYS* 3.0 20.8 + - - +
475B TYR* 4.5 3.3 - - + -
477B PHE* 3.6 33.4 - - + +
479B THR 4.4 0.7 - - - +
482B SER* 3.2 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 469 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B PHE* 2.9 23.3 + - + +
466B ILE* 3.1 17.3 - - + +
468B ALA* 1.3 74.3 - - - +
470B HIS* 1.3 60.7 + - + +
471B GLY 3.1 0.2 - - - -
479B THR* 3.7 5.1 + - - +
480B LEU* 2.7 46.2 - - + +
481B LEU* 3.2 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 470 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B ILE* 2.9 39.6 + - + +
467B GLN* 3.4 8.9 - - - +
468B ALA 3.0 1.0 + - - -
469B ALA* 1.3 80.9 - - + +
471B GLY* 1.3 57.3 + - - +
472B LYS 3.7 0.9 - - - -
481B LEU* 3.7 14.4 - - + +
503B TRP* 2.9 40.5 + + + +
504B LEU* 3.9 0.7 - - - +
507B ILE* 3.8 16.5 - - + +
515B PHE* 3.2 37.4 - + - -
----------------------------------------------------------
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