Contacts of the helix formed by residues 65 - 74 (chain B) in PDB entry 1XR2
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 ASP 65 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LYS* 5.3 0.2 - - - +
62B SER* 2.9 14.2 + - - -
64B TYR* 1.3 81.1 - - + +
66B PHE* 1.3 62.2 + - - +
67B VAL* 3.0 13.5 + - - +
68B LEU* 2.7 31.7 + - + +
69B ASP* 3.0 24.8 + - - -
90B TYR* 3.2 4.0 + - - -
110B TYR* 2.7 25.3 + - - +
111B HIS 5.2 1.1 - - - +
112B TYR* 3.2 17.3 - - - +
113B LEU* 3.2 33.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LYS* 6.3 0.7 - - - -
59B ASN 5.8 2.0 - - - +
60B GLU 5.6 3.6 - - - +
62B SER* 3.3 10.0 + - - -
65B ASP* 1.3 71.9 + - - +
67B VAL* 1.3 75.8 + - + +
69B ASP* 3.4 16.2 - - + +
70B THR* 2.9 26.7 + - - -
105B PHE* 3.7 38.4 - + - -
110B TYR* 3.4 36.6 - + - -
146B TRP* 3.9 26.2 - + + -
148B ILE* 3.9 20.8 - - + +
312B PHE* 3.7 33.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ASP* 3.0 11.2 + - - +
66B PHE* 1.3 98.8 - - + +
68B LEU* 1.3 65.7 + - - +
70B THR* 3.2 8.0 + - - -
71B ALA* 3.1 19.8 + - - +
105B PHE* 4.3 0.7 - - + -
112B TYR* 3.7 36.8 - - + -
113B LEU 3.7 8.1 - - - +
115B PRO* 3.7 16.8 - - + +
148B ILE* 4.8 7.2 - - + -
153B PHE* 4.1 11.0 - - + -
156B LEU* 4.1 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TYR* 4.9 0.9 - - + -
65B ASP* 2.7 20.3 + - + +
67B VAL* 1.3 77.6 - - - +
69B ASP* 1.3 62.4 + - - +
71B ALA* 3.0 9.4 + - + +
72B VAL* 2.9 22.8 + - + +
90B TYR* 3.6 50.9 - - + +
93B MET* 3.6 33.4 - - + -
94B ALA* 4.2 4.9 - - + +
100B LEU* 3.8 15.7 - - + -
113B LEU* 3.6 31.8 + - + -
115B PRO* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B SER* 2.7 33.9 + - - -
63B TYR 4.8 0.5 + - - -
65B ASP 3.0 12.7 + - - +
66B PHE* 3.4 11.8 - - - +
67B VAL 3.2 0.2 - - - -
68B LEU* 1.3 76.9 - - - +
70B THR* 1.3 56.7 + - - +
72B VAL* 3.1 7.5 + - - +
73B MET* 2.9 29.0 + - - +
90B TYR* 2.5 35.6 + - - -
128B LYS* 4.2 28.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B PHE 2.9 14.6 + - - -
67B VAL* 3.2 9.8 + - - -
69B ASP* 1.3 79.5 - - - +
71B ALA* 1.3 61.2 + - - +
73B MET* 3.3 18.8 + - + +
74B VAL* 3.2 22.7 + - + +
148B ILE* 3.8 23.7 + - + +
153B PHE* 3.4 27.4 - - + -
181B TYR* 3.5 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL 3.1 10.9 + - - +
68B LEU* 3.0 17.4 + - + +
70B THR* 1.3 74.1 - - - +
72B VAL* 1.3 63.7 + - + +
74B VAL* 3.3 2.8 + - - +
75B GLY 3.1 4.2 + - - -
76B ALA* 2.8 49.1 + - + +
93B MET* 5.4 0.4 - - + -
100B LEU* 5.7 1.3 - - + -
115B PRO* 4.1 13.9 - - + -
153B PHE* 3.7 19.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 2.9 22.7 + - + +
69B ASP* 3.5 9.9 - - - +
71B ALA* 1.3 77.2 - - - +
73B MET* 1.3 66.9 + - - +
75B GLY 3.0 10.6 + - - -
76B ALA 4.8 0.2 + - - -
77B VAL* 4.9 4.7 - - + -
84B TYR* 3.8 49.1 - - + +
90B TYR* 4.1 14.6 - - + -
93B MET* 4.5 7.4 - - + -
125B LEU* 3.2 20.3 - - + +
126B GLU* 4.2 18.6 + - + +
128B LYS* 5.2 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ASP 2.9 13.1 + - - +
70B THR* 3.4 22.4 - - + +
71B ALA 3.2 0.2 - - - -
72B VAL* 1.3 78.2 - - - +
74B VAL* 1.3 74.7 + - + +
123B TYR 3.5 0.5 - - - +
124B LEU* 3.7 4.8 - - + -
125B LEU 3.0 25.3 + - - -
126B GLU 3.3 24.7 + - - +
128B LYS* 5.6 3.1 - - + +
129B PRO* 3.9 31.6 - - + -
147B VAL* 5.7 7.2 - - + -
180B VAL* 4.5 1.1 - - + +
181B TYR* 4.1 31.0 - - + -
184B VAL* 4.0 26.5 - - + -
185B PHE* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B THR* 3.2 18.1 + - + +
71B ALA* 3.6 6.1 - - - +
73B MET* 1.3 93.1 - - + +
75B GLY* 1.3 58.7 + - - +
76B ALA 3.3 1.9 + - - +
122B PHE* 3.5 30.8 - - + -
123B TYR 3.1 25.7 + - - +
153B PHE* 4.1 15.5 - - + -
177B LEU* 3.8 26.5 - - + -
180B VAL* 3.9 19.5 - - + -
181B TYR* 4.3 5.6 - - + -
----------------------------------------------------------
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