Contacts of the helix formed by residues 80 - 91 (chain C) in PDB entry 3AP3
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 GLY 80 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C A3P 2.6 39.3 + - - -
78C ARG 3.4 1.2 + - - -
79C SER* 1.3 71.4 - - - +
81C THR* 1.3 57.6 + - - +
82C THR 3.2 2.9 - - - -
83C LEU* 3.1 8.0 + - - +
84C MET 2.9 24.6 + - - -
181C MET* 3.7 8.9 - - - +
183C ARG* 4.8 0.2 - - - +
238C TYR* 4.0 15.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C A3P 2.6 29.4 + - - +
73C VAL* 4.3 2.1 - - - +
74C GLY* 4.0 19.7 - - - +
75C GLY 4.3 7.9 - - - +
76C VAL 4.5 0.7 - - - +
79C SER* 4.2 6.5 - - - +
80C GLY* 1.3 75.5 - - - +
82C THR* 1.3 63.1 + - - -
84C MET* 3.5 2.3 + - - +
85C ARG* 3.3 24.1 + - - +
158C LYS* 3.8 31.6 + - - +
160C PRO* 4.5 9.1 - - + +
181C MET* 3.6 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C A3P 2.6 24.2 + - - -
81C THR* 1.3 74.0 + - - +
83C LEU* 1.3 56.8 + - - +
85C ARG* 3.2 31.9 - - - +
86C ALA* 3.0 30.7 + - - +
158C LYS* 3.6 15.1 + - - +
279C LEU* 4.6 4.0 - - + -
283C GLU* 4.4 10.7 + - - +
285C SER* 3.0 28.9 + - - +
286C THR* 5.9 0.2 - - - -
289C VAL* 3.7 19.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
1C A3P 3.8 55.4 + - + +
80C GLY 3.1 11.9 + - - +
82C THR* 1.3 75.8 - - - +
84C MET* 1.3 69.7 + - - +
86C ALA* 3.1 12.6 + - + +
87C MET* 3.2 28.0 + - + +
238C TYR* 3.9 10.3 - - + -
241C LEU* 4.5 9.2 - - + -
242C VAL* 3.8 24.9 - - + -
267C HIS* 4.2 20.0 - - + +
289C VAL* 3.9 7.6 - - + +
293C VAL* 4.9 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C VAL* 3.8 16.8 - - + -
80C GLY 2.9 7.3 + - - +
81C THR 3.6 8.5 - - - +
83C LEU* 1.3 79.9 - - - +
85C ARG* 1.3 63.8 + - - +
87C MET* 3.1 17.8 + - + +
88C LEU* 3.3 35.8 + - + +
179C LEU* 4.6 8.1 - - + -
181C MET* 3.5 35.4 - - + +
236C VAL* 4.1 11.4 - - - -
241C LEU* 4.0 14.3 - - - +
249C LEU* 4.1 17.5 - - + -
252C ILE* 4.4 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C VAL* 4.7 3.8 - - + -
81C THR 3.3 11.8 + - - +
82C THR* 3.2 23.7 - - - +
84C MET* 1.3 76.2 - - - +
86C ALA* 1.3 59.5 + - - +
88C LEU* 2.8 15.2 + - - +
89C ASP* 2.7 56.2 + - - +
96C CYS* 3.9 19.2 - - + -
97C GLY 2.9 27.8 + - - -
98C GLU* 3.7 3.4 - - - +
158C LYS* 4.2 21.5 - - + +
277C VAL* 3.7 13.5 - - - +
278C SER 2.7 30.7 + - - -
279C LEU* 3.4 22.3 - - - +
283C GLU* 3.7 19.0 + - - -
----------------------------------------------------------
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 THR 3.0 20.1 + - - +
83C LEU* 3.1 6.0 + - - +
85C ARG* 1.3 80.9 - - - +
87C MET* 1.3 61.2 + - - +
89C ASP* 3.3 1.0 + - - -
90C ALA* 3.3 7.1 + - - +
267C HIS* 3.9 12.9 - - + +
277C VAL* 3.1 46.1 - - + +
279C LEU* 5.3 0.4 - - + -
289C VAL* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C LEU* 3.2 22.2 + - + +
84C MET* 3.1 12.2 + - + +
85C ARG 3.1 0.4 - - - -
86C ALA* 1.3 77.9 - - - +
88C LEU* 1.3 63.9 + - - +
90C ALA* 3.4 15.2 - - - +
91C HIS 3.8 0.7 + - - -
241C LEU* 3.3 40.6 - - + -
245C PRO* 5.6 0.7 - - - -
249C LEU* 3.7 28.0 - - + -
264C VAL* 3.4 39.7 - - - +
265C LEU* 5.3 3.1 - - - -
267C HIS* 3.7 23.3 - - + +
293C VAL* 4.2 20.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ILE* 5.0 8.5 - - + -
73C VAL* 4.1 12.8 - - + -
84C MET* 3.4 36.1 - - + +
85C ARG* 2.8 14.8 + - - +
87C MET* 1.3 75.9 - - - +
89C ASP* 1.3 64.1 + - - +
91C HIS* 3.3 22.6 - - - +
94C VAL* 3.3 22.5 - - + +
96C CYS* 4.3 12.8 - - - -
179C LEU* 4.0 19.1 - - + -
249C LEU* 4.2 14.6 - - + -
252C ILE* 4.7 10.5 - - + -
253C LEU* 4.7 13.5 - - + -
256C LEU* 5.0 5.4 - - + -
264C VAL* 5.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ARG* 2.7 27.8 + - - +
86C ALA 3.5 9.9 - - - +
87C MET 3.3 0.2 - - - -
88C LEU* 1.3 71.0 - - - +
90C ALA* 1.3 64.2 + - - +
91C HIS 3.0 4.9 - - - +
94C VAL 3.2 9.1 - - - +
95C ARG* 3.2 26.0 - - - +
96C CYS* 3.4 11.8 + - - +
97C GLY* 2.9 25.2 + - - -
275C GLY 2.9 18.5 - - - +
276C GLY* 2.9 27.2 - - - +
277C VAL* 3.8 14.8 - - + -
278C SER* 4.5 2.8 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
86C ALA 3.3 9.5 + - - +
87C MET* 3.4 12.8 - - - +
89C ASP* 1.3 79.9 - - - +
91C HIS* 1.3 62.5 + - - +
92C PRO* 3.3 5.2 - - - +
263C ALA* 3.8 20.7 - - - +
267C HIS* 4.1 14.6 - - + -
270C LEU* 3.5 34.8 - - + +
275C GLY 3.5 6.2 - - - +
276C GLY* 4.0 6.0 - - - -
277C VAL* 3.7 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C MET 3.8 4.2 + - - +
88C LEU* 3.3 17.8 + - - +
89C ASP 3.0 13.9 - - - +
90C ALA* 1.3 76.3 - - - +
92C PRO* 1.3 74.5 - - + +
93C GLU* 3.2 54.6 + - + +
94C VAL* 3.0 24.1 + - + +
253C LEU* 4.3 18.4 - - + -
258C ILE* 4.0 6.1 - - + +
259C ALA 3.0 24.0 + - - -
260C TRP 5.2 0.4 - - - -
261C SER* 3.5 26.9 - - - -
263C ALA* 4.8 3.7 - - - +
264C VAL* 4.7 10.7 - - + +
275C GLY 3.0 5.0 - - - +
----------------------------------------------------------
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