Contacts of the helix formed by residues 2537 - 2546 (chain C) in PDB entry 1G50
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 TYR2537 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2330C GLU* 5.2 1.9 + - - -
2344C GLY 3.7 5.2 + - - -
2347C THR* 3.5 32.1 - - - -
2348C ASN* 3.1 50.1 + - + +
2351C ASP* 2.8 26.0 - - + +
2535C PRO* 3.3 31.3 + - + +
2536C LEU* 1.3 73.7 - - - +
2538C ASP* 1.3 63.0 + - - +
2539C LEU 3.4 1.1 - - - -
2540C LEU* 3.3 7.3 + - + +
2541C LEU* 2.8 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP2538 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2351C ASP* 4.8 1.0 - - - +
2536C LEU 2.9 10.7 + - - +
2537C TYR* 1.3 67.2 - - - +
2539C LEU* 1.3 59.2 + - - +
2540C LEU 3.1 1.8 - - - -
2541C LEU* 3.6 9.3 - - + +
2542C GLU* 2.7 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2539 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2351C ASP* 3.4 23.9 + - - +
2354C LEU* 3.2 50.7 - - + +
2355C VAL* 3.9 16.2 - - + -
2358C ILE* 4.3 17.5 - - + -
2537C TYR 3.4 0.8 - - - -
2538C ASP* 1.3 81.6 + - - +
2540C LEU* 1.3 60.2 + - - +
2542C GLU* 3.5 26.9 - - - +
2543C MET* 3.5 15.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2540 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2347C THR* 3.6 44.6 - - + +
2350C ALA* 4.0 15.0 - - + -
2351C ASP* 3.3 14.4 + - + +
2354C LEU* 3.7 12.8 - - + -
2383C TRP* 3.4 37.0 - - + -
2525C LEU* 4.2 16.2 - - + -
2534C VAL* 4.8 7.0 - - + -
2537C TYR* 3.3 13.6 + - + +
2538C ASP 3.1 0.2 - - - -
2539C LEU* 1.3 78.1 - - - +
2541C LEU* 1.3 66.5 + - + +
2542C GLU 3.1 1.3 - - - -
2543C MET* 3.4 3.3 + - - +
2544C LEU* 3.1 22.1 + - - +
2600C EST 6.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2541 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2529C LYS* 3.8 29.6 - - + -
2534C VAL* 5.1 9.4 - - + -
2535C PRO 4.3 16.6 - - - +
2536C LEU* 4.8 6.1 - - - -
2537C TYR 2.8 20.1 + - - +
2538C ASP* 3.1 10.7 + - + +
2540C LEU* 1.3 78.7 - - + +
2542C GLU* 1.3 57.0 + - - +
2544C LEU* 3.4 9.0 + - + +
2545C ASP* 2.9 51.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2542 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2376C VAL* 5.4 6.2 - - - +
2380C GLU* 5.0 4.6 - - - +
2538C ASP 2.7 17.2 + - - +
2539C LEU* 3.5 19.9 - - - +
2541C LEU* 1.3 75.1 - - - +
2543C MET* 1.3 86.3 + - + +
2545C ASP* 3.3 5.8 + - - +
2546C ALA* 3.0 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET2543 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2354C LEU* 3.7 20.4 - - + -
2376C VAL* 5.8 2.9 - - + -
2379C LEU* 4.7 3.6 - - - -
2380C GLU* 3.5 42.6 - - + +
2383C TRP* 3.3 44.4 + - + +
2539C LEU* 3.5 16.8 + - + +
2540C LEU 3.4 6.6 + - - +
2542C GLU* 1.3 107.5 - - + +
2544C LEU* 1.3 58.5 + - - +
2546C ALA* 3.2 18.8 - - - +
2547C HIS* 3.4 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2544 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2383C TRP* 4.3 4.0 - - + -
2522C MET* 3.6 45.5 - - + +
2525C LEU* 3.6 37.2 - - + +
2526C TYR* 4.0 26.3 - - + +
2529C LYS* 4.3 18.6 - - + -
2534C VAL* 6.5 0.4 - - + -
2540C LEU 3.1 16.1 + - - +
2541C LEU* 3.7 11.9 - - + +
2542C GLU 3.1 0.6 - - - -
2543C MET* 1.3 73.6 - - - +
2545C ASP* 1.3 65.8 + - - +
2546C ALA 2.9 5.8 + - - -
2547C HIS* 3.1 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP2545 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2526C TYR* 5.4 5.5 - - - -
2529C LYS* 4.0 15.2 - - - +
2541C LEU* 2.9 38.6 + - - +
2542C GLU* 3.8 4.9 - - - +
2544C LEU* 1.3 80.1 - - - +
2546C ALA* 1.3 57.7 + - - +
2547C HIS* 3.0 10.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2546 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2380C GLU* 3.8 39.5 - - + +
2542C GLU 3.0 12.6 + - - +
2543C MET 3.2 16.2 - - - +
2544C LEU 2.9 0.6 - - - -
2545C ASP* 1.3 78.1 - - - +
2547C HIS* 1.3 62.8 + - - +
----------------------------------------------------------
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