Contacts of the helix formed by residues 484 - 496 (chain A) 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 484 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A LEU 3.5 1.3 - - - +
483A GLN* 1.3 83.3 - - - +
485A VAL* 1.3 52.2 + - - +
486A PHE 3.4 2.9 - - - -
487A ALA* 2.9 22.1 + - + -
488A GLN* 2.8 50.8 + - + +
531A LEU* 3.7 22.9 - - + +
532A GLY 3.3 24.5 - - - +
535A ASP* 4.7 1.1 - - + -
536A PHE* 4.6 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A GLN* 2.8 18.8 + - + +
484A PRO* 1.3 70.5 - - - +
486A PHE* 1.3 83.7 + - + +
488A GLN* 4.2 9.1 - - - +
489A TRP* 3.0 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A PRO 3.4 0.8 - - - -
485A VAL* 1.3 92.7 - - + +
487A ALA* 1.3 61.0 + - - +
489A TRP* 3.9 28.3 - + + -
490A VAL* 2.9 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A PRO* 2.9 18.3 + - + +
486A PHE* 1.3 77.6 - - - +
488A GLN* 1.3 65.6 + - - +
490A VAL* 3.9 3.2 - - - +
491A GLN* 3.0 31.6 + - + +
531A LEU* 3.6 25.1 - - + -
539A HIS* 6.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A GLN* 2.7 39.2 + - - +
484A PRO* 2.8 30.7 + - + +
485A VAL* 4.2 6.6 - - - +
487A ALA* 1.3 73.3 - - - +
489A TRP* 1.3 63.0 + - - +
491A GLN* 3.6 12.2 + - - +
492A ASN* 3.5 19.1 + - - +
531A LEU* 3.1 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A VAL* 3.0 24.7 + - + +
486A PHE* 3.6 30.7 - + + +
487A ALA 3.2 0.2 - - - -
488A GLN* 1.3 79.2 - - - +
490A VAL* 1.3 84.6 + - + +
492A ASN* 3.7 5.9 + - - +
493A LEU* 3.5 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A PHE* 2.9 25.6 + - + +
487A ALA* 4.1 3.6 - - - +
489A TRP* 1.3 91.9 - - + +
491A GLN* 1.3 66.1 + - + +
492A ASN 3.2 0.2 - - - -
493A LEU* 3.1 14.2 + - + +
494A HIS* 2.9 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A ALA* 3.0 23.9 + - + +
488A GLN* 3.8 12.8 - - - +
489A TRP 3.4 0.2 - - - -
490A VAL* 1.3 75.4 - - + +
492A ASN* 1.3 57.2 + - - +
494A HIS* 3.3 4.2 + - - +
495A THR* 2.8 30.3 + - - -
512A ALA 3.9 11.7 + - - -
513A PHE* 3.3 36.2 - - + +
529A ILE* 3.3 26.5 + - - +
530A VAL* 5.3 0.7 - - - -
531A LEU* 3.4 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A GLN 3.5 8.9 + - - +
489A TRP* 3.8 8.9 + - - +
490A VAL 3.2 0.2 - - - -
491A GLN* 1.3 79.6 - - - +
493A LEU* 1.3 58.5 + - - +
495A THR* 2.9 13.6 + - - +
496A LEU* 2.7 65.9 + - - +
513A PHE 4.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A TRP* 3.5 42.6 + - + +
490A VAL* 3.1 16.9 + - + +
492A ASN* 1.3 85.1 - - - +
494A HIS* 1.3 67.8 - - + +
496A LEU* 3.4 12.5 + - + +
497A ALA* 3.2 19.4 + - - +
501A THR* 4.7 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A VAL* 2.9 38.0 + - + +
491A GLN 3.6 6.5 - - - +
493A LEU* 1.3 81.7 - - + +
495A THR* 1.3 58.3 + - - +
497A ALA* 3.1 25.6 + - + +
498A PRO* 3.5 5.2 - - - +
508A THR* 3.9 9.3 - - - +
509A ALA* 5.2 0.9 + - + -
513A PHE* 3.3 50.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A GLN 2.8 10.3 + - - -
492A ASN* 2.9 21.8 + - - +
494A HIS* 1.3 76.7 - - - +
496A LEU* 1.3 59.9 + - + +
497A ALA 3.2 0.9 - - - -
498A PRO* 3.1 14.6 - - - +
508A THR* 3.6 13.6 + - - +
513A PHE* 2.6 36.2 + - - +
514A GLY* 3.3 20.7 + - - +
515A GLY* 4.2 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A ASN* 2.7 49.6 + - - +
493A LEU* 3.9 13.9 - - + +
494A HIS 3.2 0.2 - - - -
495A THR* 1.3 78.2 - - + +
497A ALA* 1.3 65.1 + - - +
498A PRO* 3.4 2.8 - - - -
499A GLY 3.6 1.6 + - - -
500A GLY* 3.4 20.3 + - - -
501A THR* 4.3 1.2 + - - -
----------------------------------------------------------
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