Contacts of the strand formed by residues 88 - 97 (chain C) in PDB entry 2N0A
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 ILE 88 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B SER 3.2 3.1 + - - +
88B ILE* 3.4 33.7 - - + -
89B ALA* 3.0 20.3 + - - +
90B ALA 4.9 2.2 - - - +
91B ALA* 4.0 19.3 - - + -
94B PHE* 4.1 7.2 - - + -
82C VAL* 5.4 1.7 - - - +
86C GLY 3.9 9.6 - - - +
87C SER* 1.3 84.5 + - - +
89C ALA* 1.3 58.0 + - - +
91C ALA* 4.2 9.2 - - + -
94C PHE* 4.0 31.9 - - + -
86D GLY 6.0 0.2 - - - +
87D SER* 5.8 0.2 - - - -
88D ILE* 3.4 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ALA* 3.4 10.9 - - - +
90B ALA* 2.8 32.6 + - - +
79C GLN* 3.4 9.5 + - - +
82C VAL* 4.2 23.2 - - + +
88C ILE* 1.3 71.7 - - - +
90C ALA* 1.3 61.0 + - - +
79D GLN* 3.1 28.3 - - - +
82D VAL* 5.7 0.2 - - + -
87D SER* 5.3 0.4 + - - -
88D ILE 3.0 7.7 + - - +
89D ALA* 3.4 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ALA* 3.3 5.4 - - - -
77C VAL* 4.0 18.4 - - + -
89C ALA* 1.3 76.7 - - + +
91C ALA* 1.3 61.0 + - - +
92C THR* 5.7 1.8 - - + -
77D VAL* 3.8 30.3 - - + -
79D GLN* 4.7 1.6 - - - +
88D ILE* 4.9 1.3 - - - +
89D ALA 2.8 25.3 + - - +
90D ALA* 4.5 1.3 - - - -
91D ALA* 3.1 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ALA 3.1 7.9 + - - +
91B ALA* 3.3 4.3 - - - +
92B THR* 3.1 23.7 + - - +
88C ILE* 4.2 18.8 - - + -
90C ALA* 1.3 74.8 - - - +
92C THR* 1.3 63.6 + - - +
93C GLY 3.5 1.6 + - - -
94C PHE* 4.3 13.1 + - + -
88D ILE* 4.0 24.0 - - + -
91D ALA* 3.3 10.5 - - + +
94D PHE* 5.0 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B THR* 3.2 13.5 - - + +
69C ALA 5.9 0.2 - - - -
71C VAL* 3.5 15.7 - - + +
75C THR* 4.7 17.0 - - + +
90C ALA* 5.7 1.6 - - + -
91C ALA* 1.3 71.5 - - - +
93C GLY* 1.3 60.2 + - - +
71D VAL* 3.0 25.7 - - + +
75D THR* 4.1 31.9 - - + +
91D ALA 3.1 9.4 + - - +
92D THR* 3.2 6.1 - - + -
93D GLY* 2.7 28.1 + - - -
94D PHE 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ALA 5.2 0.4 - - - -
92B THR* 2.7 24.6 + - - -
93B GLY* 3.8 1.3 - - - -
69C ALA* 3.6 25.8 - - - +
71C VAL* 3.4 8.0 - - - +
91C ALA 3.5 2.2 + - - -
92C THR* 1.3 70.5 - - - +
94C PHE* 1.3 58.4 + - - +
93D GLY* 3.7 1.5 - - - -
94D PHE* 2.8 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ALA* 5.0 3.6 - - + -
92B THR 4.0 0.2 + - - -
93B GLY 2.8 23.1 + - - +
94B PHE* 3.3 44.4 - + + -
95B VAL* 3.1 18.9 + - - +
69C ALA* 4.2 0.9 - - - +
88C ILE* 4.0 25.1 - - + -
91C ALA* 4.3 7.2 - - + -
93C GLY* 1.3 73.1 - - - +
95C VAL* 1.3 64.5 + - - +
96C LYS* 4.2 27.1 - - + -
88D ILE* 4.1 15.5 - - + -
94D PHE* 3.3 49.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLY* 3.9 14.8 - - - -
95B VAL* 3.3 27.8 - - + +
97B LYS* 6.3 1.3 - - + -
68C GLY* 3.6 23.6 - - - +
69C ALA* 3.8 6.1 - - + +
94C PHE* 1.3 79.1 - - - +
96C LYS* 1.3 63.3 + - - +
97C LYS* 4.6 22.7 - - + -
94D PHE* 3.1 6.6 + - - +
95D VAL* 3.3 29.6 - - + +
96D LYS 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B VAL 3.1 7.5 + - - +
96B LYS* 3.4 27.1 - - + +
97B LYS* 3.0 24.1 + - - +
94C PHE* 4.2 22.1 - - + -
95C VAL* 1.3 74.5 - - - +
97C LYS* 1.3 64.6 + - - +
98C ASP 3.7 19.5 + - - +
99C GLN* 2.8 38.8 + - - +
96D LYS* 3.4 39.8 - - + +
98D ASP* 5.1 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLY* 5.5 4.2 - - - -
68B GLY* 5.5 3.4 - - - +
97B LYS* 3.9 33.9 - - + +
67C GLY* 4.6 16.2 + - - -
68C GLY* 6.2 0.4 - - - -
95C VAL* 4.6 18.8 - - + -
96C LYS* 1.3 72.8 - - - +
98C ASP* 1.3 79.0 + - - +
96D LYS 3.0 10.4 + - - +
97D LYS* 4.5 20.7 - - + +
98D ASP 3.1 17.8 + - - -
99D GLN* 3.2 25.6 + - - +
----------------------------------------------------------
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