Contacts of the helix formed by residues 56 - 65 (chain L) in PDB entry 5O9Z
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 TRP 56 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54L GLY 3.6 5.9 + - - +
55L HIS* 1.3 71.9 - - - +
57L ASP* 1.3 54.4 + - - +
58L THR 3.5 0.2 - - - -
59L VAL* 4.9 2.0 - - - -
60L LEU* 2.7 41.4 + - + +
80L VAL* 5.4 12.8 - - + -
212R LEU* 6.3 0.6 - - - +
216R VAL* 4.3 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 57 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55L HIS* 3.3 2.6 - - + +
56L TRP* 1.3 76.4 - - - +
58L THR* 1.3 60.9 + - - +
60L LEU* 3.4 3.5 + - - +
61L GLN* 2.9 31.9 + - - +
212R LEU 5.7 0.4 - - - +
215R ASN* 4.5 8.3 - - + +
216R VAL* 4.2 17.9 - - - +
219R MET* 4.2 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 58 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L ASP* 4.6 19.3 - - - -
55L HIS* 4.1 13.1 + - - +
57L ASP* 1.3 79.0 - - - +
59L VAL* 1.3 58.2 + - - +
61L GLN* 3.9 3.8 - - - +
62L ALA* 2.9 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L ASP* 5.3 3.9 - - + +
51L ILE* 5.0 20.2 - - + +
55L HIS 3.5 18.2 + - - +
56L TRP* 4.5 2.5 - - - +
57L ASP 3.4 0.2 - - - -
58L THR* 1.3 79.1 - - - +
60L LEU* 1.3 56.1 + - - +
62L ALA* 4.3 3.3 - - - +
63L ILE* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56L TRP* 2.7 24.2 + - + +
57L ASP* 3.8 4.0 - - - +
59L VAL* 1.3 76.9 - - - +
61L GLN* 1.3 59.9 + - - +
63L ILE* 3.8 3.8 - - - +
64L GLN* 2.9 30.0 + - - +
219R MET* 6.3 0.9 - - + -
220R LEU* 5.2 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 61 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57L ASP 2.9 18.1 + - - +
58L THR* 4.1 3.6 - - - +
60L LEU* 1.3 73.7 - - - +
62L ALA* 1.3 61.2 + - - +
64L GLN* 3.3 6.0 + - - +
65L SER* 2.9 30.2 + - - -
219R MET* 5.9 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47L PHE* 6.2 4.3 - - + -
58L THR 2.9 19.4 + - - +
59L VAL* 4.3 3.8 - - - +
61L GLN* 1.3 77.1 - - - +
63L ILE* 1.3 61.4 + - - +
65L SER* 3.5 13.4 + - - -
66L LEU* 3.6 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59L VAL 2.9 23.0 + - - +
60L LEU* 4.0 4.5 - - - +
62L ALA* 1.3 77.7 - - - +
64L GLN* 1.3 58.2 + - - +
66L LEU* 3.0 23.3 + - - +
68L LEU* 5.1 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 64 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60L LEU 2.9 19.5 + - - +
61L GLN* 3.3 6.5 + - - +
63L ILE* 1.3 75.9 - - - +
65L SER* 1.3 58.5 + - - +
66L LEU 3.3 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 65 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L THR 5.6 2.0 + - - -
61L GLN 2.9 17.1 + - - -
62L ALA* 3.5 8.0 + - - -
63L ILE 3.3 0.8 - - - -
64L GLN* 1.3 76.3 - - - +
66L LEU* 1.3 57.6 + - - +
----------------------------------------------------------
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