Contacts of the helix formed by residues 472 - 483 (chain C) in PDB entry 2LVN
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 472 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C VAL* 1.3 90.7 - - + +
473C TYR* 1.3 66.6 + - - +
474C HIS* 4.6 2.0 - - + +
475C LEU* 3.1 24.8 + - + +
476C VAL* 3.1 23.5 + - - +
498C ILE* 4.6 1.8 - - + -
499C GLN 4.1 11.2 - - - +
500C VAL* 4.2 8.7 - - + -
501C PRO* 3.5 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 473 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C ASN* 2.7 27.6 + - + +
461C ALA 3.9 2.5 - - - -
462C HIS* 3.5 47.0 - + - +
465C GLN* 3.6 34.9 - - + +
471C VAL 3.5 4.4 + - - -
472C PRO* 1.3 70.9 - - - +
474C HIS* 1.3 57.7 + - - +
476C VAL* 3.1 8.5 + - - +
477C LEU* 3.0 59.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 474 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C PRO* 3.3 2.4 - - + +
473C TYR* 1.3 77.4 - - + +
475C LEU* 1.3 73.0 + - + +
477C LEU* 3.2 27.5 - - + +
478C GLN* 3.1 20.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 475 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C PRO* 3.1 26.9 + - + +
474C HIS* 1.3 84.4 - - + +
476C VAL* 1.3 63.1 + - - +
478C GLN* 3.4 26.2 + - - +
479C ASP* 3.4 14.4 + - - +
498C ILE* 3.8 23.4 - - + +
499C GLN* 3.3 28.5 - - + +
501C PRO* 4.0 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 476 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C ALA* 3.6 15.5 - - + +
464C ILE* 3.7 25.4 - - + -
465C GLN* 4.8 2.2 - - - +
471C VAL* 3.5 28.3 - - + -
472C PRO 3.1 17.2 + - - +
473C TYR* 3.3 10.3 - - - +
474C HIS 3.1 0.2 - - - -
475C LEU* 1.3 76.9 - - - +
477C LEU* 1.3 64.5 + - - +
478C GLN 3.1 0.4 - - - -
479C ASP* 2.9 13.2 + - - +
480C LEU* 3.0 35.4 + - + +
489C THR* 3.7 5.8 - - + -
498C ILE* 4.2 15.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
457C LEU* 3.9 5.2 - - + +
458C ASN* 3.3 47.1 - - - +
461C ALA* 3.5 16.8 - - + -
473C TYR* 3.0 34.0 + - + +
474C HIS* 3.2 36.3 - - + +
476C VAL* 1.3 75.9 - - - +
478C GLN* 1.3 61.0 + - - +
480C LEU* 3.3 15.5 + - - +
481C GLN* 3.3 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 478 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C HIS* 3.1 10.3 + - + +
475C LEU* 3.4 32.5 + - + +
476C VAL 3.1 0.4 - - - -
477C LEU* 1.3 81.1 - - - +
479C ASP* 1.3 56.1 + - - +
481C GLN* 2.9 25.8 + - + +
482C LEU* 3.0 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 479 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C LEU 3.4 2.2 + - - +
476C VAL 2.9 9.6 + - - +
478C GLN* 1.3 79.5 - - - +
480C LEU* 1.3 53.8 + - - +
482C LEU* 2.9 12.8 + - - +
483C THR* 2.7 50.3 + - - -
489C THR* 2.7 30.9 + - + -
492C ASN* 2.9 33.4 + - - +
497C ARG* 3.7 13.0 - - - +
498C ILE* 3.6 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 480 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C LEU* 3.6 35.3 - - + +
460C MET* 3.4 28.3 - - + -
461C ALA* 4.1 7.0 - - + -
464C ILE* 3.9 6.7 - - + -
476C VAL* 3.0 46.7 + - + +
477C LEU 3.5 10.1 - - - +
478C GLN 3.1 0.2 - - - -
479C ASP* 1.3 76.8 - - - +
481C GLN* 1.3 57.4 + - - +
484C ARG* 3.0 29.4 - - - +
485C SER 3.6 13.7 - - - +
486C VAL* 3.9 11.7 - - + +
489C THR* 3.5 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 481 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C ASN* 3.0 33.6 + - - +
457C LEU* 3.1 22.3 - - - +
477C LEU 3.3 12.7 + - - +
478C GLN* 2.9 17.6 + - + +
480C LEU* 1.3 77.3 - - - +
482C LEU* 1.3 69.2 + - + +
484C ARG* 4.1 21.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
478C GLN* 3.0 36.8 - - + +
479C ASP* 2.9 18.3 + - - +
481C GLN* 1.3 84.7 - - + +
483C THR* 1.3 68.0 + - + +
484C ARG* 5.2 0.3 - - - +
497C ARG* 6.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 483 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C ASP* 2.7 31.9 + - - +
482C LEU* 1.3 81.7 - - + +
484C ARG* 1.3 67.8 + - - +
485C SER* 3.0 12.5 + - - -
488C ILE* 3.6 27.8 - - + +
489C THR* 3.0 11.8 + - - -
492C ASN* 3.3 26.7 - - - +
----------------------------------------------------------
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