Contacts of the helix formed by residues 67 - 80 (chain O) in PDB entry 5XS0
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 GLU 67 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51O TYR 4.6 1.8 + - - -
53O SER* 3.7 20.4 + - - +
65O TYR* 3.6 28.2 + - + +
66O ILE* 1.3 77.7 - - - +
68O GLY* 1.3 67.0 + - - +
69O HIS* 2.8 33.4 + - + +
70O ARG* 3.0 29.3 + - + +
71O VAL* 3.1 11.1 + - - +
152O LYS* 5.3 0.4 - - - +
167P LEU 4.6 1.4 - - - +
169P LYS* 3.3 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66O ILE 3.7 1.0 + - - -
67O GLU* 1.3 73.1 - - - +
69O HIS* 1.3 59.6 + - - +
71O VAL* 3.0 6.5 + - - +
72O ILE* 2.9 36.0 + - - +
148O THR* 4.5 15.9 - - - +
152O LYS* 4.5 17.1 - - - +
167P LEU* 5.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 69 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67O GLU* 2.8 36.5 + - + +
68O GLY* 1.3 74.6 - - - +
70O ARG* 1.3 83.6 + - + +
72O ILE* 3.4 2.2 + - - -
73O ASN* 2.9 35.1 + - - -
164P ASN* 3.0 38.1 + - - +
165P CYS* 6.1 0.2 - - - -
167P LEU* 3.6 41.2 + - + +
168P ASP* 3.9 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195N ASP* 5.1 0.4 - - - +
50O GLU 3.8 16.3 + - - -
51O TYR* 3.6 46.0 + - + +
53O SER* 3.7 15.4 + - - -
66O ILE* 3.7 12.6 - - + -
67O GLU* 3.0 28.4 + - + +
69O HIS* 1.3 98.7 - - + +
71O VAL* 1.3 56.6 + - - +
73O ASN* 3.4 5.4 + - - +
74O LEU* 2.9 36.1 + - - +
168P ASP* 4.4 10.3 + - - -
170P ASP* 4.4 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66O ILE* 3.7 32.1 - - + +
67O GLU 3.1 14.1 + - - +
68O GLY 3.0 6.6 + - - +
70O ARG* 1.3 76.5 - - - +
72O ILE* 1.3 64.9 + - + +
74O LEU* 3.3 8.2 + - + +
75O ALA* 2.9 23.4 + - - +
151O LEU* 5.8 1.3 - - + -
152O LYS* 4.1 26.5 - - + -
155O LEU* 3.6 32.1 - - + -
162O LEU* 4.3 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68O GLY* 2.9 19.9 + - - +
69O HIS* 3.6 2.9 - - - +
71O VAL* 1.3 77.2 - - + +
73O ASN* 1.3 56.1 + - - +
75O ALA* 3.3 3.5 + - - +
76O ASN* 2.9 47.4 + - - +
84O TRP* 4.1 11.1 - - + -
151O LEU* 4.7 19.3 - - + -
155O LEU* 5.6 1.1 - - + -
156P ARG* 4.1 5.8 - - + +
157P SER* 3.5 39.3 - - - +
164P ASN* 3.2 33.2 - - - +
167P LEU* 5.5 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 73 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195N ASP* 4.0 20.1 + - + +
69O HIS* 2.9 27.9 + - - +
70O ARG* 3.9 5.5 - - - +
72O ILE* 1.3 72.8 - - - +
74O LEU* 1.3 66.1 + - - +
76O ASN* 3.7 5.7 + - - +
77O GLU* 2.9 30.8 + - + +
46P ARG* 5.8 3.4 - - - +
159P GLY* 4.3 5.4 - - - -
160P ASN* 3.2 42.0 + - - +
164P ASN* 3.1 17.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192N LYS* 3.6 30.1 - - + -
195N ASP* 3.8 4.4 + - - +
47O LEU* 4.4 4.5 - - + -
51O TYR* 3.5 39.7 - - + +
66O ILE* 4.5 14.6 - - + -
70O ARG 2.9 27.6 + - - +
71O VAL* 3.6 10.1 - - + +
73O ASN* 1.3 76.1 - - - +
75O ALA* 1.3 57.7 + - - +
77O GLU* 3.3 5.5 + - + +
78O MET* 2.9 34.3 + - + +
161O ALA* 3.5 22.7 - - + +
162O LEU* 3.8 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71O VAL 2.9 17.3 + - - +
72O ILE 3.8 1.6 - - - +
74O LEU* 1.3 75.5 - - - +
76O ASN* 1.3 57.8 - - - +
78O MET 4.4 0.2 - - - +
79O PHE* 2.9 41.9 + - + -
84O TRP* 3.7 33.9 - - + -
155O LEU* 4.2 11.9 - - + -
162O LEU* 3.7 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 76 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72O ILE* 2.9 33.1 + - - +
73O ASN* 3.3 9.1 + - - +
75O ALA* 1.3 75.6 - - - +
77O GLU* 1.3 61.8 + - + +
80O GLY* 2.9 28.6 + - - -
81O TYR* 3.6 17.2 - - - +
84O TRP* 2.8 23.6 + - - +
40P GLN* 3.2 14.8 - - - +
157P SER 3.3 20.8 + - - +
158P PHE* 3.5 21.2 + - - +
159P GLY* 3.6 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192N LYS* 6.2 0.2 - - - -
195N ASP* 3.5 39.4 - - + +
196N LEU* 3.5 19.8 - - - +
197N GLU* 4.4 14.7 + - + +
200N VAL* 4.5 0.7 - - - +
201N GLU* 5.4 2.8 + - - +
204N ARG* 3.5 13.7 + - - -
73O ASN* 2.9 21.4 + - + +
74O LEU* 3.8 4.3 - - - +
76O ASN* 1.3 80.4 - - + +
78O MET* 1.3 63.4 + - + +
40P GLN* 4.5 6.6 + - - +
44P ARG* 3.0 52.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 78 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192N LYS* 5.6 5.4 - - - -
197N GLU* 4.1 15.0 - - + +
200N VAL* 3.5 12.5 - - + +
204N ARG* 2.6 18.8 + - - -
39O ILE* 3.5 52.9 - - + +
42O ALA* 3.9 22.2 - - + -
43O LEU* 3.6 29.6 - - + -
74O LEU* 2.9 24.0 + - + +
75O ALA* 3.3 3.1 + - - +
77O GLU* 1.3 78.8 - - + +
79O PHE* 1.3 68.8 + - + +
161O ALA* 4.6 8.5 - - + -
162O LEU* 4.7 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81N TYR* 4.2 13.7 - + - -
204N ARG* 3.3 21.2 + - - +
31O TYR* 3.6 18.9 + - - +
35O GLU* 4.9 1.0 - - - +
39O ILE* 4.4 13.7 - - + -
43O LEU* 4.8 3.6 - - + -
75O ALA* 2.9 27.6 + - + +
78O MET* 1.3 87.9 - - + +
80O GLY* 1.3 60.6 + - - +
82O ASN* 4.8 0.7 - - - +
83O GLY* 3.3 33.9 - - - +
84O TRP* 3.8 15.0 - - + +
115O LEU* 3.7 30.5 - - + -
116O LYS* 5.7 1.6 - - - -
155O LEU* 4.8 4.7 - - + -
158O PHE* 4.3 13.7 - + + -
162O LEU* 3.5 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 80 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204N ARG* 3.6 11.6 - - - +
76O ASN 2.9 21.1 + - - -
79O PHE* 1.3 80.8 - - - +
81O TYR* 1.3 66.8 + - - -
82O ASN* 3.0 5.5 + - - -
83O GLY 3.1 8.7 + - - -
84O TRP* 3.2 14.9 - - - -
36P TYR* 4.3 7.4 - - - -
40P GLN* 3.2 11.7 - - - -
----------------------------------------------------------
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