Contacts of the strand formed by residues 485 - 492 (chain D) in PDB entry 2FGJ
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 LEU 485 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473D ILE* 4.8 2.7 - - + +
474D ARG* 3.3 7.4 - - - -
475D PHE* 3.0 38.1 + - + +
483D VAL* 3.4 9.3 - - - +
484D ILE* 1.3 85.3 - - + +
486D ASP* 1.3 60.8 + - - +
488D ILE* 4.3 14.8 - - + -
507D GLY* 4.1 21.3 - - - +
510D THR* 4.2 13.5 - - + -
511D LEU* 3.8 31.0 - - + +
514D LEU* 3.4 34.1 - - + -
676D MET* 4.6 4.9 - - + -
679D GLY* 3.6 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 486 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474D ARG* 3.3 21.3 - - - +
483D VAL* 3.8 13.0 - - + -
484D ILE 4.1 0.6 + - - +
485D LEU* 1.3 76.0 - - - +
487D ASN* 1.3 81.6 + - - +
488D ILE* 3.0 13.0 + - - +
678D LYS 5.6 1.1 - - - +
679D GLY 3.1 7.4 + - - +
680D LYS* 3.3 47.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 487 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472D ASN* 3.7 14.7 - - - +
473D ILE 3.3 13.2 + - - +
474D ARG* 3.9 3.6 - - - +
486D ASP* 1.3 87.9 + - - +
488D ILE* 1.3 63.6 + - - +
489D ASN* 3.1 24.8 + - - -
680D LYS* 4.4 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 488 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470D PHE* 3.6 31.4 - - + +
472D ASN 3.2 17.5 + - - -
473D ILE* 3.2 24.4 + - + +
485D LEU* 4.3 15.7 - - + -
486D ASP 3.0 24.0 + - - +
487D ASN* 1.3 73.4 - - - +
489D ASN* 1.3 61.6 + - - +
490D LEU* 4.4 2.7 - - + -
511D LEU* 3.8 25.6 - - + -
676D MET* 5.1 2.9 - - - -
679D GLY 3.9 13.7 - - - +
680D LYS* 4.1 0.9 - - - -
681D ILE* 3.9 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 489 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470D PHE 3.3 3.8 - - - +
471D ARG* 3.7 6.4 - - + +
472D ASN* 2.8 44.0 + - - +
487D ASN* 3.1 24.6 + - - -
488D ILE* 1.3 71.3 - - - +
490D LEU* 1.3 62.6 + - - +
681D ILE* 3.9 13.1 - - - +
684D GLN* 4.9 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 490 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468D ILE 4.3 0.2 - - - -
469D THR* 3.3 3.9 - - - +
470D PHE* 2.5 70.2 + - + +
488D ILE* 4.4 4.9 - - + -
489D ASN* 1.3 75.4 - - - +
491D SER* 1.3 64.2 + - - +
492D ILE* 3.7 28.9 - - + -
500D ILE* 6.2 1.6 - - + -
511D LEU* 4.6 17.5 - - + -
672D ARG* 3.4 20.2 - - - +
674D ILE* 3.3 33.9 - - + -
681D ILE* 4.5 5.4 - - + -
684D GLN* 4.5 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 491 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467D ASP 4.7 7.1 + - - -
468D ILE 3.2 4.2 + - - -
469D THR* 4.0 18.5 + - - +
490D LEU* 1.3 79.6 - - - +
492D ILE* 1.3 55.9 + - - +
493D LYS* 4.0 2.0 + - - +
672D ARG* 2.5 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 492 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467D ASP 3.2 3.4 + - - -
468D ILE* 2.7 55.0 + - + +
470D PHE* 5.3 2.2 - - + -
490D LEU* 3.7 30.1 - - + -
491D SER* 1.3 76.5 + - - +
493D LYS* 1.3 66.2 + - - +
494D GLN 3.9 0.5 + - - -
496D GLU* 4.3 2.0 - - + -
498D ILE* 3.4 37.5 - - + -
515D ILE* 5.4 1.8 - - + -
656D THR* 3.4 30.5 - - + -
658D ILE* 4.3 21.3 - - + -
672D ARG* 3.7 5.2 - - - +
----------------------------------------------------------
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