Contacts of the strand formed by residues 478 - 486 (chain C) in PDB entry 5D4C
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 VAL 478 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C VAL* 3.4 3.1 - - - +
475C VAL* 3.0 33.8 + - + +
476C GLY 3.2 6.8 - - - +
477C GLY* 1.3 83.6 - - - +
479C VAL* 1.3 67.8 + - - +
480C THR* 3.5 8.3 + - + +
506C ASN* 3.4 22.7 - - + +
507C ARG* 3.3 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 479 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C ARG* 3.5 46.5 + - + +
473C ARG 3.9 4.5 - - - +
474C VAL* 4.3 11.0 - - + +
478C VAL* 1.3 75.1 - - - +
480C THR* 1.3 67.3 + - - +
481C ASP* 4.6 1.0 - - - +
503C LEU* 3.7 25.8 - - + -
506C ASN* 2.6 46.7 + - - +
508C ILE* 4.2 11.0 - - + -
532C MET* 3.9 16.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 480 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C ARG* 3.3 23.6 - - - +
473C ARG* 2.7 47.8 + - + +
475C VAL* 4.8 10.8 - - + -
478C VAL* 4.3 11.2 - - + +
479C VAL* 1.3 78.7 - - - +
481C ASP* 1.3 61.4 + - - +
482C GLU* 3.3 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 481 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ARG* 3.7 26.2 + - - -
12C VAL* 3.8 26.2 - - + +
472C ARG* 4.1 3.4 + - - +
480C THR* 1.3 77.3 - - - +
482C GLU* 1.3 62.7 + - - +
483C VAL* 3.4 16.5 + - - +
506C ASN* 4.3 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 482 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C TYR 3.7 0.3 - - - +
472C ARG* 3.5 4.7 - - - -
473C ARG* 2.9 76.9 + - - +
480C THR* 3.2 14.0 + - - +
481C ASP* 1.3 76.2 - - - +
483C VAL* 1.3 62.0 + - - +
484C VAL* 3.8 12.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 483 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C VAL* 4.2 7.9 - - + -
13C ILE* 3.6 48.5 - - + -
470C PRO* 3.6 18.2 - - + -
471C TYR 3.2 12.6 - - - +
472C ARG* 4.4 8.3 - - + -
481C ASP 3.4 16.7 + - - +
482C GLU* 1.3 76.6 - - - +
484C VAL* 1.3 64.2 + - - +
485C TYR* 4.0 12.2 + - + -
534C VAL* 4.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 484 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469C THR 3.8 0.3 - - - +
470C PRO 3.7 0.2 - - - -
471C TYR* 2.9 33.2 + - - +
473C ARG* 3.9 13.7 - - - +
482C GLU* 3.8 27.6 - - + +
483C VAL* 1.3 75.2 - - - +
485C TYR* 1.3 73.2 + - - +
486C MET* 3.7 22.1 + - + +
490C GLU* 6.1 0.4 - - - +
531C PHE* 4.3 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 485 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ILE* 4.2 10.1 - - + +
16C PRO* 4.3 8.8 - - - +
458C TYR* 3.2 27.0 + - - -
460C ARG* 3.8 42.7 + - + -
468C ARG* 3.3 44.4 + - + +
469C THR 3.6 5.8 - - - -
470C PRO* 3.4 39.5 - - + +
483C VAL* 4.0 12.9 + - + -
484C VAL* 1.3 79.3 - - - +
486C MET* 1.3 59.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 486 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C ARG* 2.9 15.8 + - - -
468C ARG* 3.1 9.9 - - - +
469C THR 3.0 25.3 + - - +
471C TYR* 3.9 24.7 - - + -
484C VAL* 3.9 17.3 - - + +
485C TYR* 1.3 78.4 - - - +
487C THR* 1.3 66.4 + - - +
490C GLU* 4.2 9.0 - - + +
491C GLU* 3.9 19.3 - - + +
494C TYR* 3.9 22.4 - - + -
496C ILE* 5.0 1.6 - - + -
531C PHE* 3.5 54.7 - - + -
----------------------------------------------------------
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