Contacts of the helix formed by residues 470 - 483 (chain C) in PDB entry 4ICU
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 THR 470 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C SER 3.3 8.5 + - - +
469C MET* 1.3 74.1 - - - +
471C ILE* 1.3 65.1 + - - +
472C GLN* 3.8 8.0 + - - +
473C LYS* 3.2 30.7 + - - +
474C VAL* 3.0 24.0 + - - +
508C ASP 3.6 11.7 - - - -
509C LEU* 3.4 24.9 - - + +
510C LYS 3.4 9.0 - - - +
511C SER* 4.0 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 471 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C THR* 1.3 72.8 - - - +
472C GLN* 1.3 58.3 + - - +
474C VAL* 3.2 5.8 + - + +
475C LYS* 2.8 41.5 + - - +
491C LEU* 3.8 18.4 - - + -
505C LEU* 3.8 40.8 - - + +
507C ASN 3.7 18.8 - - - +
508C ASP* 3.4 7.1 + - - +
510C LYS 3.1 16.7 + - - +
512C LEU* 3.9 30.5 - - + +
515C TYR* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 472 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C THR* 3.8 8.4 + - - +
471C ILE* 1.3 78.3 - - - +
473C LYS* 1.3 83.6 + - + +
475C LYS* 3.5 8.3 + - - +
476C GLY* 2.9 22.5 + - - -
486C VAL* 5.1 8.2 - - + +
508C ASP* 3.0 42.6 + - + +
509C LEU* 3.9 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 473 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469C MET* 3.3 25.9 - - + +
470C THR* 3.2 23.1 + - - +
472C GLN* 1.3 98.7 - - + +
474C VAL* 1.3 60.1 + - - +
476C GLY* 3.3 3.1 + - - +
477C LEU* 3.0 23.0 + - - +
480C ARG* 4.8 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 474 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C LEU* 4.4 10.1 - - + -
469C MET* 3.7 26.2 - - + -
470C THR 3.0 19.2 + - - +
471C ILE* 3.2 11.2 + - + +
473C LYS* 1.3 74.0 - - - +
475C LYS* 1.3 65.0 + - - +
477C LEU* 3.3 5.1 + - + +
478C LEU* 3.0 28.6 + - + +
491C LEU* 3.8 19.3 - - + -
512C LEU* 4.2 22.4 - - + -
523C LEU* 3.9 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 475 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C ILE* 2.8 32.9 + - - +
472C GLN* 3.6 8.3 - - - +
474C VAL* 1.3 72.2 - - - +
476C GLY* 1.3 53.4 + - - +
478C LEU* 4.5 3.1 - - - -
479C SER* 2.7 38.3 + - - -
486C VAL* 4.1 29.0 + - + +
489C LEU* 3.4 44.0 + - + +
490C LEU* 5.4 0.4 - - - +
491C LEU* 4.3 22.4 - - + +
505C LEU 4.9 2.7 + - - -
506C GLU* 4.6 11.1 + - - -
508C ASP* 3.3 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 476 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C GLN 2.9 16.0 + - - -
473C LYS* 3.3 6.2 + - - -
474C VAL 3.2 0.4 - - - -
475C LYS* 1.3 74.8 - - - +
477C LEU* 1.3 61.3 + - - +
479C SER* 3.2 2.8 + - - -
480C ARG* 3.0 45.0 + - - +
486C VAL* 4.3 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 477 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463C LYS* 4.5 31.6 - - + +
465C LEU* 3.8 28.0 - - + -
469C MET* 4.3 9.4 - - + -
473C LYS 3.0 13.3 + - - +
474C VAL* 3.6 7.4 - - + +
476C GLY* 1.3 75.2 - - - +
478C LEU* 1.3 73.7 + - + +
480C ARG* 3.4 22.5 + - - +
481C LEU* 3.1 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 478 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450C ILE* 4.7 19.3 - - + -
452C TYR* 5.3 0.9 - - - +
461C LEU* 6.0 1.6 - - + -
463C LYS* 6.6 0.4 - - + -
474C VAL* 3.0 32.0 + - + +
475C LYS* 3.9 5.2 - - - +
477C LEU* 1.3 86.8 - - + +
479C SER* 1.3 54.2 + - - +
481C LEU* 3.3 14.3 + - + -
482C LEU* 2.8 51.3 + - + +
489C LEU* 4.2 9.2 - - + -
491C LEU* 3.9 19.1 - - + -
523C LEU* 4.5 3.1 - - + -
525C VAL* 3.6 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 479 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C LYS 2.7 22.9 + - - -
476C GLY 3.5 4.9 - - - -
478C LEU* 1.3 73.4 - - - +
480C ARG* 1.3 57.7 + - - +
482C LEU* 5.1 0.7 - - - -
483C LYS* 2.9 30.3 + - - -
484C VAL* 2.7 26.8 + - - +
485C PRO* 4.3 0.9 - - - +
486C VAL* 3.7 24.0 + - - +
489C LEU* 3.9 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 480 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469C MET* 6.2 0.4 - - - +
473C LYS 4.8 2.2 + - - -
476C GLY* 3.0 32.1 + - - +
477C LEU* 3.5 29.9 - - - +
479C SER* 1.3 77.2 - - - +
481C LEU* 1.3 60.6 + - - +
483C LYS* 4.0 21.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 481 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452C TYR* 4.2 18.2 - - - +
461C LEU* 4.3 20.0 - - + -
463C LYS* 6.2 1.8 - - - -
477C LEU* 3.1 27.4 + - + +
478C LEU* 3.7 18.4 - - + +
480C ARG* 1.3 79.6 - - - +
482C LEU* 1.3 63.8 + - + +
483C LYS* 3.8 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 482 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452C TYR* 3.4 37.5 - - + +
455C GLN* 5.8 0.2 - - - +
478C LEU* 2.8 29.0 + - + +
481C LEU* 1.3 78.8 - - + +
483C LYS* 1.3 71.0 + - - +
484C VAL* 3.7 18.1 - - + +
489C LEU* 4.2 8.1 - - + -
525C VAL* 4.1 15.9 - - + -
527C TRP* 3.7 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 483 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C SER 2.9 11.4 + - - +
480C ARG* 4.0 18.4 - - - +
481C LEU 3.4 5.2 - - - +
482C LEU* 1.3 82.2 - - - +
484C VAL* 1.3 61.3 + - - +
485C PRO* 4.7 2.2 - - - +
----------------------------------------------------------
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