Contacts of the strand formed by residues 81 - 85 (chain C) in PDB entry 1II4
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 ARG 81 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ILE* 4.3 1.6 - - + +
44C HIS 3.7 4.9 - - - -
45C PRO 2.6 27.5 + - - -
46C ASP* 3.4 13.7 + - - +
47C GLY* 2.9 22.5 - - - +
75C LYS* 3.3 3.2 - - - -
76C GLY* 2.8 26.9 + - - -
79C ALA* 3.0 16.7 - - + +
80C ASN* 1.3 80.8 - - - +
82C TYR* 1.3 67.0 + - - +
93C ALA* 2.9 37.4 + - + +
94C SER* 3.3 12.4 - - - +
95C LYS* 4.0 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C SER* 4.3 24.7 - - - -
74C ILE 3.5 3.8 - - - +
75C LYS* 2.9 56.6 + - + +
80C ASN 4.9 0.9 - - - -
81C ARG* 1.3 75.4 - - - +
83C LEU* 1.3 66.5 + - - +
84C ALA* 3.4 0.7 + - - +
93C ALA* 3.1 4.0 - - - -
94C SER* 2.7 42.6 + - - +
95C LYS 4.0 14.6 - - - -
96C SER* 5.2 0.2 - - - -
97C VAL* 3.3 35.8 - - + +
101C CYS* 3.8 20.9 - - + -
317G VAL* 4.3 12.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU* 4.3 11.4 - - + -
43C ILE* 4.1 17.1 - - + +
49C VAL* 3.8 36.8 - - + -
74C ILE* 2.7 41.5 + - + +
81C ARG 4.1 0.6 + - - -
82C TYR* 1.3 74.0 - - - +
84C ALA* 1.3 62.9 + - - +
91C LEU* 4.4 10.8 - - + -
92C LEU 3.7 3.1 - - - +
93C ALA* 4.5 1.1 - - - +
101C CYS* 3.3 23.0 - - - +
103C PHE* 3.5 17.9 - - + -
125C VAL* 3.7 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C TYR 4.0 2.7 - - - +
83C LEU* 1.3 78.0 - - - +
85C MET* 1.3 61.3 + - - +
86C LYS 4.1 1.0 + - - +
90C ARG 3.9 0.3 - - - +
91C LEU* 3.4 8.7 - - - +
92C LEU* 2.7 52.3 + - + +
94C SER* 4.7 3.8 - - - +
98C THR* 5.1 0.9 - - - +
100C GLU* 3.1 23.1 - - + +
101C CYS* 3.7 15.5 - - - -
103C PHE* 4.0 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ALA* 1.3 75.1 - - - +
86C LYS* 1.3 64.5 - - - +
89C GLY 3.9 7.6 - - - +
90C ARG 3.4 7.9 - - - +
91C LEU* 3.6 22.2 - - + -
100C GLU* 3.1 21.8 + - - +
103C PHE* 4.1 11.8 - - + -
117C SER* 3.8 19.8 + - - +
120C TYR* 3.1 19.9 - - - -
123C TRP* 3.3 44.2 - - + +
124C TYR 3.3 35.7 - - - +
125C VAL* 4.0 5.6 - - + +
136C GLY* 3.9 7.9 - - - +
----------------------------------------------------------
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