Contacts of the helix formed by residues 52 - 72 (chain C) in PDB entry 1SHR
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 SER 52 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ASP* 2.7 48.0 + - - +
50C HIS* 2.8 25.2 + - - -
51C GLY* 1.3 76.5 - - - +
53C ALA* 1.3 60.4 + - - +
54C GLN* 3.5 8.4 + - - +
55C VAL* 3.1 17.5 + - - +
56C LYS* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C SER* 1.3 75.2 - - - +
54C GLN* 1.3 53.3 + - - +
56C LYS* 3.7 11.4 - - - +
57C GLY* 2.8 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C HIS* 3.3 19.0 + - - +
46C PHE* 3.5 34.2 - - + +
47C ASP* 2.8 35.1 - - + +
52C SER* 3.6 7.4 - - - +
53C ALA* 1.3 81.4 - - - +
55C VAL* 1.3 57.4 + - - +
57C GLY* 3.9 0.6 - - - -
58C HIS* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ALA* 3.8 25.5 - - + +
29C LEU* 4.0 14.8 - - + +
30C GLU* 4.7 6.7 - - + +
33C PHE* 4.5 6.5 - - + -
46C PHE* 4.9 4.3 - - + -
47C ASP 3.8 2.9 - - - +
48C LEU* 3.6 31.0 - - + -
50C HIS 4.0 7.9 - - - +
51C GLY* 4.6 10.3 - - - -
52C SER* 3.1 24.0 + - - +
54C GLN* 1.3 75.0 - - - +
56C LYS* 1.3 61.0 + - + +
58C HIS* 3.8 4.7 - - - +
59C GLY* 2.8 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLY 4.6 2.4 - - - +
26C ALA* 3.8 19.1 - - + +
51C GLY* 3.6 20.0 - - - +
52C SER 2.9 16.8 + - - +
53C ALA* 3.7 11.4 - - - +
55C VAL* 1.3 75.5 - - + +
57C GLY* 1.3 64.6 + - - +
59C GLY* 3.3 2.3 + - - -
60C LYS* 3.1 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ALA 2.8 20.1 + - - -
54C GLN* 3.9 1.1 - - - -
56C LYS* 1.3 73.1 - - - +
58C HIS* 1.3 61.9 + - - +
60C LYS* 3.3 19.9 + - - +
61C LYS* 3.3 17.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU* 3.8 11.2 - - + -
33C PHE* 6.3 0.2 - + - -
43C PHE* 3.7 14.4 - + - -
46C PHE* 3.7 20.3 - + + -
54C GLN 2.9 19.0 + - - +
55C VAL* 3.8 5.2 - - - +
57C GLY* 1.3 73.4 - - - +
59C GLY* 1.3 66.4 + - - +
60C LYS 3.0 0.2 - - - -
61C LYS* 3.0 18.9 + - + +
62C VAL* 3.0 26.5 + - + +
542C HEM 3.3 51.4 + + + +
543C CYN 2.9 37.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLY 3.7 8.9 - - - +
25C GLY* 3.8 4.5 - - - -
26C ALA 3.6 19.7 - - - -
29C LEU* 3.7 11.6 - - - +
55C VAL 2.8 18.0 + - - -
56C LYS 3.3 2.8 + - - -
58C HIS* 1.3 75.8 - - - +
60C LYS* 1.3 56.1 + - - +
62C VAL* 3.5 3.9 + - - +
63C ALA* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ALA* 5.7 4.0 + - - +
21C ALA* 5.5 3.8 - - - +
22C GLY* 3.9 24.6 + - - +
56C LYS 3.1 12.2 + - - +
57C GLY* 3.3 14.1 - - - +
59C GLY* 1.3 74.9 - - - +
61C LYS* 1.3 62.5 + - + +
63C ALA* 3.3 1.7 + - - +
64C ASP* 2.9 56.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLY 3.3 15.9 + - - +
58C HIS* 3.0 19.0 + - - +
60C LYS* 1.3 77.6 - - + +
62C VAL* 1.3 62.8 + - - +
64C ASP* 3.3 9.6 + - - +
65C ALA 3.0 17.5 + - - -
542C HEM 3.6 59.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLY* 5.3 8.1 - - - +
29C LEU* 4.5 7.2 - - + -
58C HIS* 3.0 20.3 + - + +
59C GLY* 3.6 7.9 - - - +
61C LYS* 1.3 76.9 - - - +
63C ALA* 1.3 63.9 + - - +
65C ALA* 3.1 5.2 + - - +
66C LEU* 3.0 33.4 + - + +
101C LEU* 4.9 8.3 - - + -
542C HEM 4.0 36.1 - - + -
543C CYN 3.5 34.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C TRP* 4.0 10.6 - - + -
21C ALA* 3.3 44.4 - - + +
22C GLY* 3.6 4.3 - - - +
25C GLY* 5.0 2.4 - - - -
59C GLY 2.9 16.9 + - - +
60C LYS* 3.6 6.5 - - + +
62C VAL* 1.3 78.2 - - - +
64C ASP* 1.3 58.4 + - - +
66C LEU* 3.1 7.7 + - - +
67C THR* 2.8 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ALA* 6.0 0.2 - - - +
60C LYS* 2.9 57.9 + - - +
61C LYS* 3.3 7.7 + - - +
63C ALA* 1.3 75.5 - - - +
65C ALA* 1.3 62.3 + - - +
67C THR* 3.3 10.5 + - - -
68C ASN* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LYS 3.0 13.6 + - - +
62C VAL 3.1 8.3 + - - +
64C ASP* 1.3 76.5 - - - +
66C LEU* 1.3 57.3 + - - +
68C ASN* 3.2 9.2 + - - +
69C ALA* 2.9 27.8 + - - +
80C LEU* 4.1 5.8 - - + +
83C LEU* 3.6 32.5 - - + -
542C HEM 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C TRP* 3.8 23.1 - - + -
25C GLY* 6.3 2.2 - - - -
62C VAL* 3.0 29.2 + - + +
63C ALA* 3.5 7.9 - - - +
65C ALA* 1.3 74.9 - - - +
67C THR* 1.3 59.4 + - - +
69C ALA* 3.1 4.1 + - + +
70C VAL* 2.8 34.5 + - - +
105C LEU* 3.6 31.0 - - + -
128C PHE* 4.0 13.1 - - + -
129C LEU* 4.1 14.4 - - + -
132C VAL* 4.4 10.5 - - + -
542C HEM 4.0 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C TRP* 2.8 31.7 + - + +
21C ALA* 4.6 5.7 - - - +
63C ALA 2.8 15.7 + - - -
64C ASP* 3.5 14.1 + - - -
66C LEU* 1.3 76.5 - - - +
68C ASN* 1.3 58.9 + - - +
70C VAL* 3.4 2.8 + - - +
71C ALA* 3.0 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ASP 3.0 13.1 + - - +
65C ALA* 3.4 11.2 - - - +
67C THR* 1.3 76.4 - - - +
69C ALA* 1.3 58.5 + - - +
71C ALA* 3.4 3.5 + - - -
72C HIS* 2.9 56.2 + - - +
79C ALA* 3.7 32.6 + - - +
80C LEU* 4.1 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ALA 2.9 13.6 + - - +
66C LEU* 3.6 10.5 - - + +
68C ASN* 1.3 74.3 - - - +
70C VAL* 1.3 61.0 + - - +
72C HIS* 3.3 1.7 - - - +
73C VAL* 2.9 32.4 + - - +
76C MET* 4.0 19.1 - - - +
79C ALA* 5.7 0.9 - - - -
80C LEU* 4.1 19.7 - - + -
128C PHE* 3.7 18.5 - - + -
132C VAL* 4.2 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C VAL* 3.7 17.9 - - + +
11C LYS* 2.9 57.6 + - + +
14C TRP* 3.9 29.4 - - + -
66C LEU 2.8 21.4 + - - +
67C THR 3.6 4.9 - - - +
69C ALA* 1.3 79.6 - - - +
71C ALA* 1.3 59.6 + - - +
72C HIS 3.4 0.3 + - - -
73C VAL* 3.6 8.5 + - - +
128C PHE* 3.5 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LYS* 3.5 14.6 + - - +
67C THR* 3.0 18.8 + - + +
68C ASN* 3.7 7.0 - - - +
69C ALA 3.3 0.2 - - - -
70C VAL* 1.3 81.2 - - - +
72C HIS* 1.3 79.4 + - + +
73C VAL 3.5 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ASN* 2.9 36.9 + - - +
69C ALA 3.3 4.3 - - - -
71C ALA* 1.3 93.8 + - + +
73C VAL* 1.3 57.9 + - - +
74C ASP 3.1 3.8 - - - +
75C ASP* 2.9 30.6 + - + +
76C MET* 3.3 12.8 + - - +
79C ALA* 4.2 17.9 - - + +
----------------------------------------------------------
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