Contacts of the helix formed by residues 82 - 91 (chain I) in PDB entry 3CII
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 82 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I THR* 1.3 72.9 - - - +
83I ASN* 1.3 76.0 + - + +
85I SER* 2.7 19.8 + - - -
86I ARG* 3.3 40.5 + - - +
96I LEU* 3.7 13.5 - - + +
116I TRP* 3.2 56.7 - + + +
117I ILE 3.2 19.3 + - - -
118I GLY* 4.2 6.5 - - - -
119I LEU 3.9 26.3 + - - +
120I SER* 4.7 6.7 - - - -
131I GLU* 3.9 18.4 - - + -
152I CYS* 3.3 33.4 - - + +
153I ILE 4.4 0.2 + - - -
166I CYS* 4.5 10.8 - - + -
168I ASP 3.8 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 83 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I THR* 3.3 13.0 - - + +
82I TRP* 1.3 93.6 - - + +
84I GLU* 1.3 64.9 + - + +
86I ARG* 3.2 36.1 + - - +
87I HIS* 3.5 21.2 + - - -
166I CYS 4.7 6.8 + - - +
167I GLU* 4.7 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I LYS* 4.4 18.7 + - + +
81I THR* 2.8 40.3 + - + +
82I TRP 3.3 0.4 - - - -
83I ASN* 1.3 79.6 - - + +
85I SER* 1.3 58.1 + - - +
87I HIS* 3.3 12.2 + - - +
88I LEU* 2.9 40.9 + - + +
169I LYS* 6.0 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I LYS* 4.9 1.3 - - - +
81I THR 3.0 15.5 + - - -
82I TRP* 2.7 24.1 + - - -
84I GLU* 1.3 73.8 - - - +
86I ARG* 1.3 66.0 + - - +
88I LEU* 3.0 13.2 + - - +
89I CYS* 2.9 27.4 + - - -
96I LEU* 3.7 16.7 - - - +
116I TRP* 4.2 3.8 - - - -
172I TYR* 3.8 36.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I TRP* 3.3 32.1 + - + +
83I ASN* 3.2 29.7 + - - +
85I SER* 1.3 84.2 + - - +
87I HIS* 1.3 84.1 + - + +
89I CYS* 3.0 10.9 + - - +
90I ALA* 3.0 12.7 + - + +
95I SER* 5.8 0.2 - - - -
96I LEU* 4.5 27.5 + - + +
131I GLU* 3.4 32.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 87 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I ASN* 3.5 35.3 + - - -
84I GLU* 3.3 11.1 + - - +
86I ARG* 1.3 97.0 + - + +
88I LEU* 1.3 58.0 + - + +
90I ALA* 3.0 11.5 + - + +
91I SER* 2.9 30.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I GLU* 5.9 0.2 - - - +
80I LYS* 3.8 33.4 - - + -
84I GLU* 2.9 31.9 + - + +
85I SER* 3.0 11.6 + - - +
87I HIS* 1.3 75.0 - - + +
89I CYS* 1.3 64.3 + - - +
91I SER* 3.3 19.3 + - - +
92I GLN* 3.7 19.4 + - - +
172I TYR* 4.5 17.0 - - + +
174I CYS* 4.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 89 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85I SER 2.9 16.3 + - - -
86I ARG 3.4 6.3 - - - +
88I LEU* 1.3 74.6 - - - +
90I ALA* 1.3 63.9 + - - +
92I GLN* 3.1 4.8 + - - -
93I LYS 3.0 5.7 + - - -
94I SER* 2.8 40.0 + - - +
95I SER* 3.8 10.1 - - - -
96I LEU* 3.8 22.0 - - - +
172I TYR* 4.3 2.2 - - - -
174I CYS* 2.0 54.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I ARG* 3.0 12.8 + - + +
87I HIS* 3.0 18.0 + - + +
89I CYS* 1.3 78.2 - - - +
91I SER* 1.3 56.5 + - - +
93I LYS* 3.0 22.2 + - - +
94I SER 3.2 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 91 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87I HIS 2.9 14.0 + - - -
88I LEU* 3.3 23.9 + - - +
90I ALA* 1.3 75.6 - - - +
92I GLN* 1.3 61.4 + - - +
93I LYS* 3.3 6.0 + - - +
----------------------------------------------------------
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