Contacts of the helix formed by residues 54 - 61 (chain C) in PDB entry 3P9I
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 54 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C SER 5.8 0.2 - - - +
53C LEU* 1.3 76.7 - - - +
55C PRO* 1.3 76.1 - - - +
56C THR* 3.6 8.6 + - - -
57C GLU* 3.0 45.6 + - - +
58C VAL* 3.0 12.3 + - - +
101C ARG 3.9 8.5 - - - +
102C SER* 4.6 7.6 - - - -
103C TYR* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C LEU 4.5 0.4 - - - +
54C THR* 1.3 86.9 - - - +
56C THR* 1.3 56.4 + - - +
58C VAL* 3.3 8.4 + - + +
59C ALA* 2.8 31.9 + - - +
71C PRO* 3.1 31.3 - - + +
74C VAL* 4.4 6.8 - - + +
75C ASP* 3.5 36.6 - - + +
101C ARG 3.1 20.0 - - - +
103C TYR* 4.1 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C THR* 3.1 8.2 + - - -
55C PRO* 1.3 81.2 - - - +
57C GLU* 1.3 60.4 + - + +
59C ALA* 3.3 2.1 + - - +
60C ALA* 3.0 29.8 + - + +
71C PRO* 4.0 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LYS* 4.7 7.7 + - - -
52C SER 4.3 2.9 - - - +
53C LEU* 3.7 29.1 - - + +
54C THR* 3.0 45.0 + - - +
56C THR* 1.3 77.1 - - + +
58C VAL* 1.3 65.6 - - - +
60C ALA* 3.4 14.9 + - - +
61C LYS* 3.5 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU* 3.8 23.6 - - + +
44C ILE* 3.7 19.4 - - + +
45C LEU* 4.4 12.8 - - + -
53C LEU* 3.7 27.1 - - + +
54C THR 3.0 17.5 + - - +
55C PRO* 3.6 7.0 - - + +
57C GLU* 1.3 75.6 - - - +
59C ALA* 1.3 63.0 + - - +
61C LYS* 3.2 18.2 + - - +
62C LEU* 3.6 8.0 - - - +
74C VAL* 3.7 21.1 - - + -
78C LEU* 4.6 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C PRO 2.8 17.9 + - - +
56C THR 3.7 4.0 - - - +
58C VAL* 1.3 75.1 - - - +
60C ALA* 1.3 58.7 + - - +
62C LEU* 3.0 28.6 + - - +
64C SER* 3.2 18.4 + - - +
70C ALA* 4.1 12.3 - - + +
71C PRO* 3.8 32.8 - - + -
74C VAL* 4.4 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C THR* 3.0 18.5 + - + +
57C GLU* 3.6 9.9 - - - +
58C VAL 3.3 0.6 - - - -
59C ALA* 1.3 76.6 - - - +
61C LYS* 1.3 63.3 + - + +
62C LEU 3.1 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ILE* 3.5 29.2 + - + +
53C LEU* 4.4 22.4 - - - +
57C GLU* 3.5 13.8 + - - +
58C VAL 3.2 12.5 + - - +
59C ALA 3.1 1.0 - - - -
60C ALA* 1.3 82.0 - - + +
62C LEU* 1.3 60.3 + - - +
63C PRO* 4.6 1.4 - - - +
----------------------------------------------------------
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