Contacts of the helix formed by residues 80 - 90 (chain C) in PDB entry 1SMK
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 ASN 80 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ALA* 4.1 12.6 + - + +
58C GLN* 5.7 1.6 - - - +
79C VAL* 1.3 84.8 - - - +
81C ALA* 1.3 62.3 + - - +
82C PRO* 3.4 6.0 - - - +
83C GLY* 3.3 6.0 + - - +
84C VAL* 3.1 26.3 + - + +
101C LEU* 4.0 4.6 - - - +
261D LYS* 4.7 4.0 - - - +
264D ALA* 4.2 23.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ALA* 6.1 1.8 - - + -
53C ALA* 4.7 4.3 - - - +
75C LEU* 4.2 12.8 - - + +
76C TYR 4.6 0.4 - - - -
77C ASP* 4.1 15.7 - - + +
79C VAL 3.0 4.9 + - - -
80C ASN* 1.3 72.7 - - - +
82C PRO* 1.3 73.1 - - + +
84C VAL* 3.3 5.7 + - - +
85C THR* 2.5 33.7 + - - +
99C GLY* 5.1 0.4 - - - -
100C PHE 3.4 29.8 - - - +
101C LEU* 4.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ASN* 3.5 4.7 - - - -
81C ALA* 1.3 94.8 - - + +
83C GLY* 1.3 55.9 - - - +
85C THR* 3.2 7.0 + - - +
86C ALA* 2.8 30.8 + - - +
99C GLY* 5.4 5.4 - - - -
100C PHE 5.9 0.2 - - - -
101C LEU* 3.9 32.8 - - + +
260D ALA* 4.3 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ASN* 3.3 8.4 + - - +
81C ALA 3.2 0.8 - - - -
82C PRO* 1.3 79.3 - - - +
84C VAL* 1.3 63.4 + - - +
86C ALA* 3.0 5.2 + - - +
87C ASP* 3.0 22.3 + - - +
257D VAL* 5.0 0.2 - - - +
260D ALA* 3.7 22.9 + - - -
261D LYS* 3.8 26.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ALA* 3.8 17.9 - - + +
53C ALA* 4.0 10.3 - - + -
58C GLN* 3.5 34.5 - - + +
61C ALA* 4.9 0.9 - - + -
75C LEU* 4.1 16.4 - - + -
80C ASN* 3.1 19.1 + - + +
81C ALA* 3.8 5.6 - - - +
83C GLY* 1.3 75.4 - - - +
85C THR* 1.3 57.7 + - - +
87C ASP* 3.4 7.0 + - - +
88C ILE* 3.0 28.7 + - + +
261D LYS* 4.6 6.0 - - - +
269D LEU* 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C LEU* 3.9 16.0 - - - +
81C ALA 2.5 25.1 + - - -
82C PRO* 3.5 6.5 - - - -
83C GLY 3.1 0.2 - - - -
84C VAL* 1.3 75.6 - - - +
86C ALA* 1.3 65.9 + - - +
88C ILE* 3.7 1.1 - - - +
89C SER* 2.8 27.8 + - - -
97C VAL* 4.0 15.7 - - + +
98C ARG* 3.5 12.8 - - - +
99C GLY* 3.1 40.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C PRO 2.8 12.2 + - - +
83C GLY 3.5 3.8 - - - +
85C THR* 1.3 72.2 - - - +
87C ASP* 1.3 63.0 + - - +
89C SER* 2.4 26.4 + - - -
90C HIS* 3.5 10.9 - - - -
256D GLU* 4.8 9.0 - - + +
257D VAL* 4.1 12.8 - - + -
260D ALA* 3.4 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C GLY 3.0 11.6 + - - +
84C VAL* 3.4 11.0 - - - +
86C ALA* 1.3 75.7 - - - +
88C ILE* 1.3 62.8 + - - +
90C HIS* 3.2 12.0 + - - +
257D VAL* 3.9 11.8 - - + +
261D LYS* 3.3 18.8 + - - -
267D ALA* 4.0 5.6 - - - -
268D THR* 2.7 28.7 + - - -
269D LEU* 2.9 19.1 + - + +
270D SER* 2.7 52.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ALA* 4.0 1.1 - - + -
62C MET* 3.5 26.0 - - - +
65C LYS* 3.5 29.0 - - + -
73C LEU* 4.6 2.0 - - + -
75C LEU* 3.9 18.6 - - + -
84C VAL* 3.0 22.4 + - + +
85C THR 3.2 3.1 + - - +
87C ASP* 1.3 76.0 - - - +
89C SER* 1.3 63.4 + - - +
90C HIS 3.2 0.9 + - - -
91C MET* 3.2 45.4 + - + +
97C VAL* 4.0 13.0 - - + -
269D LEU* 3.6 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C LYS* 4.6 3.4 + - - +
85C THR* 2.8 15.7 + - - -
86C ALA* 2.4 28.5 + - - -
88C ILE* 1.3 77.7 - - - +
90C HIS* 1.3 69.0 + - - +
91C MET 3.5 3.2 + - - +
97C VAL* 3.6 19.9 - - - +
199D THR* 3.4 18.7 - - - +
200D PHE* 5.1 0.7 - - - -
249D ARG* 5.0 3.2 + - - -
256D GLU* 4.7 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ALA 3.5 6.9 + - - -
87C ASP 3.2 8.9 + - - +
88C ILE 3.2 1.4 - - - -
89C SER* 1.3 88.6 + - - +
91C MET* 1.3 61.2 + - - +
192D LEU* 5.0 0.9 - - + -
195D VAL* 3.1 16.8 - - - +
196D ARG* 2.9 36.0 + - + +
199D THR* 2.8 22.2 + - - -
200D PHE* 3.4 25.7 - + - -
253D GLY* 3.4 28.0 - - - -
256D GLU* 2.9 26.8 + - - -
257D VAL* 3.5 17.7 - - + +
270D SER* 4.3 9.5 + - - -
----------------------------------------------------------
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