Contacts of the helix formed by residues 66 - 69 (chain I) in PDB entry 1S9C
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 GLN 66 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62I VAL 2.9 19.3 + - - +
63I ILE* 3.6 25.3 - - - +
64I ILE 3.3 1.0 - - - -
65I GLY* 1.3 74.6 - - - +
67I LYS* 1.3 52.9 + - - +
68I SER 2.4 21.2 + - - -
69I MET* 2.7 23.2 + - + +
70I MET* 3.6 13.7 - - - +
142I PHE* 3.5 15.9 - - + -
188I TYR* 4.9 5.1 + - - -
191I SER 4.0 10.2 - - - +
192I GLY* 4.5 1.9 - - - -
193I ASP* 4.1 32.9 + - - +
217I LEU* 3.3 29.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 67 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I PHE* 3.6 33.4 - - + +
19I SER 4.6 11.7 + - - +
20I TYR* 4.9 17.5 - - + -
63I ILE 4.0 4.4 + - - -
64I ILE 4.2 2.9 + - - +
65I GLY 3.4 2.4 - - - -
66I GLN* 1.3 74.0 - - - +
68I SER* 1.3 56.6 + - - +
69I MET 3.7 0.2 - - - -
70I MET* 4.7 12.1 + - - +
72I GLY* 5.9 0.2 - - - -
73I GLY* 4.7 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 68 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I LEU* 4.8 4.9 - - - -
18I PHE* 3.6 26.1 - - - -
65I GLY 3.3 14.9 + - - -
66I GLN 2.4 17.2 + - - -
67I LYS* 1.3 71.4 - - - +
69I MET* 1.3 50.7 + - - -
70I MET 3.0 12.5 + - - +
73I GLY* 4.0 9.3 - - - -
74I LEU* 3.6 10.4 + - - +
110I ALA* 3.9 20.0 - - - +
126I MET* 2.8 28.0 - - - +
128I VAL* 4.4 4.7 - - - +
142I PHE* 5.5 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 69 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I GLN* 2.7 28.4 + - + +
68I SER* 1.3 72.9 + - - +
70I MET* 1.3 65.2 + - + +
74I LEU* 4.0 11.7 - - - +
87I VAL* 5.8 2.7 - - + +
88I LEU 6.2 0.2 - - - -
89I HIS* 3.8 31.4 - - + +
126I MET* 3.9 9.4 - - - -
142I PHE* 3.3 49.8 - - + -
144I LEU* 3.7 23.9 - - + +
193I ASP* 3.9 21.3 - - - +
217I LEU* 5.4 0.4 - - + -
----------------------------------------------------------
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