Contacts of the helix formed by residues 64 - 76 (chain C) in PDB entry 2PS2
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 HIS 64 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLY* 5.2 1.6 - - - -
70B ALA* 3.6 20.9 + - + -
71B GLY* 3.7 4.9 + - - -
74B THR* 2.8 33.2 - - + +
98B LEU* 3.8 12.4 - - + +
101B HIS* 3.3 35.1 - + - -
55C PRO* 3.9 6.1 - - - -
58C SER* 3.8 15.7 - - - +
63C SER* 1.3 78.5 + - - +
65C PRO* 1.3 67.9 - - + +
66C ARG* 3.7 7.6 - - + -
67C GLY* 2.7 56.6 + - - -
68C VAL* 3.0 10.9 + - - +
103C ASP* 4.1 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ASP* 3.4 56.3 - - + +
37C THR* 5.1 0.9 - - - +
55C PRO* 3.8 25.0 - - + +
57C GLY* 4.5 9.0 - - - +
64C HIS* 1.3 87.3 - - + +
66C ARG* 1.3 66.8 + - + +
68C VAL* 3.1 16.2 + - + +
69C ARG* 3.2 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ALA* 3.8 11.5 - - + +
73B ALA* 3.7 37.5 + - - +
74B THR* 3.3 24.0 + - - +
35C ASP* 5.7 0.4 - - - +
64C HIS* 3.3 13.5 - - + +
65C PRO* 1.3 81.0 - - + +
67C GLY* 1.3 57.4 + - - +
69C ARG* 3.6 17.0 + - - +
70C ALA* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B HIS* 5.1 1.4 + - - -
67B GLY* 5.9 2.2 - - - -
70B ALA* 4.5 2.0 - - - -
101B HIS* 5.5 1.3 - - - -
64C HIS* 2.7 41.8 + - - -
66C ARG* 1.3 72.6 - - - +
68C VAL* 1.3 63.2 + - - +
70C ALA* 3.8 6.0 - - - +
71C GLY* 2.9 22.0 + - - -
101C HIS* 4.9 8.5 + - - -
103C ASP* 5.0 5.3 - - - +
104C ALA* 4.5 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C THR* 4.0 24.2 - - + +
53C SER* 3.9 22.9 - - - +
55C PRO* 3.7 26.7 - - + -
64C HIS 3.0 12.9 + - - +
65C PRO* 3.1 7.2 + - + +
67C GLY* 1.3 77.1 - - - +
69C ARG* 1.3 62.4 + - - +
71C GLY 3.3 0.3 + - - -
72C ILE* 3.1 31.1 + - + +
103C ASP* 3.7 31.4 - - - +
104C ALA* 3.5 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C VAL* 4.2 18.8 - - + +
13C GLN* 3.6 18.9 - - - +
35C ASP* 2.9 41.5 + - - -
36C ALA 4.0 0.2 + - - -
37C THR* 2.8 46.1 + - + +
65C PRO* 3.2 22.7 + - - +
66C ARG* 4.1 15.5 - - - +
68C VAL* 1.3 73.9 - - - +
70C ALA* 1.3 64.3 + - - +
72C ILE* 3.3 8.9 + - - +
73C ALA* 3.0 23.6 + - - +
367C VAL* 4.3 14.8 - - - +
370C TYR* 4.7 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B HIS* 3.5 5.6 + - - +
66B ARG* 3.8 35.4 - - + +
67B GLY* 4.3 0.9 - - - +
70B ALA* 4.0 8.3 - - + -
66C ARG 3.0 19.0 + - - +
67C GLY* 3.8 4.5 - - - +
69C ARG* 1.3 75.4 - - - +
71C GLY* 1.3 62.3 + - - +
73C ALA* 3.3 9.0 + - - +
74C THR* 3.1 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B HIS* 3.8 12.8 + - - -
67C GLY 2.9 17.2 + - - -
68C VAL 3.7 1.8 - - - -
70C ALA* 1.3 75.7 - - - +
72C ILE* 1.3 64.3 + - - +
74C THR* 3.2 2.9 + - - -
75C MET* 3.0 34.2 + - - +
98C LEU* 4.0 9.6 - - - -
101C HIS* 5.0 0.7 - - - -
104C ALA* 3.7 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ILE* 4.7 5.4 - - + -
11C VAL* 3.8 24.0 - - + -
37C THR* 4.0 19.7 - - + -
39C VAL* 3.6 26.0 - - + -
68C VAL* 3.1 20.0 + - + +
69C ARG* 3.3 8.7 + - - +
71C GLY* 1.3 74.8 - - - +
73C ALA* 1.3 58.9 + - - +
75C MET* 4.4 6.1 - - - -
76C ALA* 2.8 39.6 + - + +
104C ALA* 3.5 21.0 - - - +
107C ALA* 4.8 3.4 - - + -
108C ILE* 4.3 16.4 - - + -
370C TYR* 4.1 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ARG* 3.6 28.2 + - - +
69C ARG 3.0 12.7 + - - +
70C ALA* 3.4 11.0 - - - +
71C GLY 3.2 0.2 - - - -
72C ILE* 1.3 78.2 - - - +
74C THR* 1.3 61.3 + - - +
77C PRO* 3.2 22.5 - - - +
370C TYR* 3.2 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B SER* 4.2 18.4 - - - +
64B HIS* 2.8 39.7 - - + +
65B PRO* 5.7 0.6 - - + +
66B ARG* 3.5 23.9 + - - +
70C ALA 3.1 4.3 + - - -
71C GLY 3.2 6.0 + - - -
73C ALA* 1.3 80.4 - - - +
75C MET* 1.3 59.6 + - - +
77C PRO* 4.0 6.4 - - - +
78C SER* 5.2 1.6 + - - -
97C ALA* 4.3 12.0 - - - +
98C LEU* 4.7 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C GLY 3.0 22.9 + - - +
72C ILE 4.2 1.8 - - - +
74C THR* 1.3 77.8 - - - +
76C ALA* 1.3 64.3 + - - +
77C PRO* 3.4 1.3 - - - -
78C SER* 2.8 24.6 + - - -
79C LEU* 3.5 16.0 - - + +
94C MET* 3.8 21.8 - - + +
97C ALA* 4.2 14.6 - - + -
98C LEU* 3.7 25.8 - - + -
104C ALA* 3.7 29.2 - - + +
105C LYS* 3.6 40.6 - - + -
108C ILE* 4.4 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ILE* 4.0 18.5 - - + +
72C ILE* 2.8 27.4 + - + +
75C MET* 1.3 71.8 - - - +
77C PRO* 1.3 68.3 - - + +
79C LEU* 2.9 22.4 + - - +
80C ILE* 3.5 9.0 + - - +
108C ILE* 5.1 1.5 - - + +
370C TYR* 3.4 35.7 - - + -
----------------------------------------------------------
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