Contacts of the strand formed by residues 468 - 475 (chain C) 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 ILE 468 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C ASP* 1.3 83.1 - - + +
469C THR* 1.3 64.4 + - - +
470C PHE* 4.3 10.0 - - + -
490C LEU 3.6 1.6 - - - +
491C SER* 3.3 4.3 - - - -
492C ILE* 2.8 52.7 + - + +
493C LYS 6.3 0.2 - - - -
494C GLN* 6.1 0.7 - - - +
515C ILE* 4.1 28.5 - - + -
526C VAL* 5.3 1.8 - - + -
527C LEU 3.3 6.7 - - - +
528C ILE* 4.3 17.7 - - + -
626C ILE* 3.6 33.9 - - + -
656C THR* 4.1 26.0 - - + +
658C ILE* 4.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 469 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C ASP* 4.6 6.6 + - - -
468C ILE* 1.3 79.5 + - - +
470C PHE* 1.3 68.0 + - - +
471C ARG* 3.6 41.2 + - + +
490C LEU 3.3 2.0 - - - +
491C SER* 3.8 20.0 + - - +
525C GLN 3.7 1.0 - - - +
526C VAL* 3.3 9.9 - - - +
527C LEU* 2.8 51.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 470 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C ILE* 4.3 9.4 - - + -
469C THR* 1.3 77.5 - - - +
471C ARG* 1.3 62.0 + - - +
473C ILE* 3.7 22.9 - - + -
488C ILE* 3.9 15.0 - - + +
489C ASN* 3.3 10.2 - - - +
490C LEU* 2.7 62.3 + - + +
492C ILE* 5.3 0.2 - - + -
511C LEU* 3.3 44.2 - - + -
514C LEU* 4.1 22.0 - - + -
515C ILE* 3.7 30.7 - - + -
525C GLN 3.7 3.1 - - - -
526C VAL* 4.2 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 471 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469C THR* 3.6 28.1 + - + +
470C PHE* 1.3 69.2 - - - +
472C ASN* 1.3 74.6 + - - +
473C ILE* 3.1 2.0 + - - +
489C ASN* 4.1 2.2 - - - -
524C GLY* 3.1 4.0 - - - -
525C GLN* 2.9 61.2 + - + +
527C LEU* 4.3 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 472 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C ARG* 1.3 77.4 - - - +
473C ILE* 1.3 63.1 + - - +
474C ARG* 3.4 3.1 + - - +
487C ASN* 3.0 32.7 + - - +
488C ILE 3.4 2.1 + - - -
489C ASN* 3.0 24.1 + - - +
523C ASN* 3.5 18.6 - - - +
524C GLY* 3.7 6.8 - - - -
525C GLN* 6.0 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 473 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C PHE* 3.7 24.0 - - + -
471C ARG 3.1 4.4 + - - +
472C ASN* 1.3 73.4 - - - +
474C ARG* 1.3 66.4 + - - +
475C PHE* 4.7 0.2 - - + -
485C LEU* 3.8 9.3 - - + +
486C ASP* 3.4 3.8 + - - -
487C ASN 2.8 22.5 + - - -
488C ILE* 3.0 27.7 + - + +
514C LEU* 3.8 24.7 - - + -
521C PRO* 3.7 16.4 - - + -
523C ASN 3.5 8.7 - - - +
524C GLY 3.6 1.6 - - - -
525C GLN 3.4 44.9 - - - +
526C VAL* 3.7 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 474 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C ASN 3.4 0.9 + - - +
473C ILE* 1.3 73.5 - - - +
475C PHE* 1.3 65.1 + - - +
476C ARG* 4.5 9.9 - - - +
483C VAL* 3.7 22.7 - - + +
485C LEU 3.2 2.9 - - - -
486C ASP* 3.3 32.6 + - - +
487C ASN* 4.6 0.7 - - - +
521C PRO* 3.7 2.1 - - - +
522C GLU* 3.2 55.8 + - + +
523C ASN* 2.9 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 475 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C ILE* 4.7 1.1 - - + -
474C ARG* 1.3 76.0 - - - +
476C ARG* 1.3 88.7 + - - +
477C TYR* 3.9 15.0 - + - -
483C VAL* 4.0 2.3 - - - -
484C ILE* 3.0 9.5 + - + -
485C LEU* 2.7 42.4 + - + +
510C THR* 3.6 33.4 - - + -
514C LEU* 3.6 35.7 - - + -
518C PHE* 3.5 29.2 - + - -
519C TYR* 4.4 5.6 - + + -
520C ILE 3.7 30.7 - - - -
521C PRO* 3.9 5.8 - - + -
522C GLU* 4.9 2.0 - - - +
----------------------------------------------------------
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