Contacts of the helix formed by residues 58 - 73 (chain X) in PDB entry 1SHT
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 58 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55X VAL 2.9 11.2 + - - +
57X ASN* 1.4 89.4 - - - +
59X TRP* 1.3 64.5 + - - +
60X ILE 3.2 2.5 - - - +
61X GLU* 2.8 43.8 + - - +
62X ILE* 3.1 23.2 + - - +
178X VAL* 3.8 13.9 - - + -
179X LEU* 3.3 42.3 - - + +
200X LYS* 4.7 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 59 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49X LEU* 4.2 22.4 - - + -
50X ASP 3.4 29.8 - - - -
51X LYS* 4.2 4.3 - - + -
55X VAL* 3.4 3.9 + - + +
56X ALA 3.4 15.1 + - - +
57X ASN 3.6 0.6 - - - -
58X ASN* 1.3 78.8 - - - +
60X ILE* 1.3 66.1 + - + +
62X ILE* 3.1 24.7 + - + +
63X TYR* 2.9 36.2 + - + +
84X VAL* 4.3 9.6 - - + -
109X LEU* 3.0 39.7 + - + -
110X LYS* 4.7 6.2 - - - +
112X VAL* 3.5 35.5 + - + -
114X PRO* 3.8 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 60 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57X ASN 5.2 2.6 + - - +
58X ASN* 3.2 1.2 - - - -
59X TRP* 1.3 85.3 - - + +
61X GLU* 1.3 57.4 + - - +
63X TYR* 3.4 8.6 + - + +
64X ASN* 2.9 48.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 61 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58X ASN* 2.8 41.4 + - + +
60X ILE* 1.3 77.7 - - - +
62X ILE* 1.3 64.3 + - + +
64X ASN* 3.4 7.5 + - - +
65X PHE* 3.1 24.3 + - - +
178X VAL* 4.5 2.3 - - - +
179X LEU 4.9 1.4 + - - -
199X VAL* 3.3 32.8 - - + +
200X LYS* 2.9 41.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49X LEU* 4.2 13.5 - - + -
50X ASP 3.8 20.2 - - - +
55X VAL* 4.1 17.3 - - + -
58X ASN 3.1 14.6 + - - +
59X TRP* 3.1 32.7 + - + +
61X GLU* 1.3 73.1 - - + +
63X TYR* 1.3 66.3 + - - +
65X PHE* 3.3 4.2 + - - +
66X VAL* 3.1 28.3 + - + +
146X LEU* 4.0 33.4 - - + +
178X VAL* 3.9 30.5 - - + -
199X VAL* 5.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 63 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59X TRP* 2.9 27.6 + - + +
60X ILE* 3.6 9.6 - - + +
62X ILE* 1.3 79.7 - - - +
64X ASN* 1.3 80.2 + - - +
66X VAL* 3.3 8.6 + - - +
67X GLN* 3.0 47.6 + - + +
106X LEU* 3.1 52.1 + - + +
107X GLU* 5.6 0.3 + - - -
109X LEU* 4.0 22.7 - - + -
110X LYS* 3.6 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 64 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60X ILE* 2.9 39.8 + - - +
61X GLU* 3.9 7.1 - - - +
62X ILE 3.3 0.4 - - - -
63X TYR* 1.3 96.7 - - - +
65X PHE* 1.3 59.2 + - - +
67X GLN* 3.3 5.9 + - - +
68X GLN* 2.9 48.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 65 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47X PHE* 5.0 1.3 - + - -
61X GLU 3.1 17.0 + - - +
62X ILE 3.6 4.3 - - - +
64X ASN* 1.3 74.5 - - - +
66X VAL* 1.3 68.7 + - + +
68X GLN* 3.2 12.6 + - - +
69X LEU* 3.0 40.1 + - + +
144X ILE* 4.6 2.7 - - + -
146X LEU* 4.2 18.4 - - + -
176X VAL* 4.0 32.1 - - + -
197X PHE* 6.2 1.1 - - + -
199X VAL* 3.8 27.8 - - + -
205X ALA* 5.2 8.1 - - + -
206X LEU* 4.1 29.2 - - + -
209X ILE* 4.3 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47X PHE* 4.0 24.4 - - + -
49X LEU* 3.8 33.7 - - + -
62X ILE* 3.1 16.6 + - + +
63X TYR* 3.5 8.7 - - - +
65X PHE* 1.3 74.6 - - + +
67X GLN* 1.3 63.7 + - - +
69X LEU* 3.3 1.4 + - - +
70X ALA* 3.0 23.9 + - - +
82X PHE* 3.5 37.5 - - + -
106X LEU* 4.2 3.1 - - + -
109X LEU* 4.1 11.0 - - + -
146X LEU* 4.7 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 67 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63X TYR* 3.0 44.0 + - + +
64X ASN* 3.8 7.6 + - - +
66X VAL* 1.3 77.8 - - - +
68X GLN* 1.3 65.2 + - + +
70X ALA* 3.8 2.3 - - - +
71X GLU* 2.7 59.6 + - + +
106X LEU* 4.1 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 68 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64X ASN* 2.9 34.3 + - - +
65X PHE* 3.6 14.3 - - - +
67X GLN* 1.3 78.6 - - + +
69X LEU* 1.3 57.4 + - - +
71X GLU* 3.9 3.8 - - - +
72X ARG* 2.9 35.6 + - - +
206X LEU* 4.1 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45X LEU* 4.3 6.5 - - + -
47X PHE* 3.9 13.7 - - + -
65X PHE* 3.0 37.5 + - + +
66X VAL 4.0 2.2 - - - +
68X GLN* 1.3 77.7 - - - +
70X ALA* 1.3 58.1 + - - +
72X ARG* 4.9 0.2 - - - -
73X PHE* 2.9 60.1 + - + +
74X VAL* 3.4 3.4 + - - +
144X ILE* 3.5 32.1 - - + -
206X LEU* 4.0 14.8 - - + +
209X ILE* 4.4 11.2 - - + -
210X ILE* 3.7 19.3 - - + +
213X ILE* 5.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47X PHE* 4.6 2.8 - - + -
66X VAL 3.0 18.1 + - - +
67X GLN* 3.8 7.0 - - - +
69X LEU* 1.3 76.8 - - - +
71X GLU* 1.3 61.7 + - + +
74X VAL* 3.4 26.6 + - - +
80X LEU* 3.6 24.9 - - + -
82X PHE* 5.1 3.4 - - + -
99X ARG* 3.3 20.8 + - - +
102X ILE* 4.7 11.4 - - + -
106X LEU* 5.0 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67X GLN* 2.7 55.0 + - + +
68X GLN* 4.1 3.8 - - - +
70X ALA* 1.3 81.3 - - + +
72X ARG* 1.3 60.4 + - + +
74X VAL 5.3 1.2 - - - +
99X ARG* 4.8 6.5 + - - +
106X LEU* 4.8 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 72 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68X GLN 2.9 18.8 + - - +
69X LEU 4.5 0.2 - - - +
71X GLU* 1.3 78.0 - - + +
73X PHE* 1.3 58.7 - - - +
206X LEU* 3.7 26.3 - - + +
207X LYS* 3.9 35.4 - - - +
210X ILE* 3.5 30.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 73 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43X PHE* 4.0 7.2 - + - -
45X LEU* 4.1 27.8 - - + -
69X LEU* 2.9 29.9 + - + +
71X GLU 3.5 0.2 - - - -
72X ARG* 1.3 80.9 - - - +
74X VAL* 1.3 60.7 + - + +
75X SER* 2.9 12.2 + - - -
78X MET* 3.3 44.1 - - + +
210X ILE* 3.5 31.9 - - + -
213X ILE* 3.5 36.3 - - + -
214X LEU* 3.7 29.2 - - + -
----------------------------------------------------------
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