Contacts of the helix formed by residues 123 - 135 (chain D) in PDB entry 2XB2
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 THR 123 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D TRP* 3.4 6.8 - - - -
121D TYR* 4.1 1.4 - - - +
122D GLU* 1.3 92.5 - - + +
124D TYR* 1.3 64.3 + - - +
125D LYS* 3.9 6.8 + - - +
126D GLU* 2.6 43.7 + - - +
127D ALA* 3.2 20.6 + - - +
39X THR* 4.6 9.2 - - + -
41X ASP* 3.6 16.4 - - - +
54X TYR* 3.8 15.9 - - + +
59X GLU 5.4 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D PRO* 3.9 27.2 - - + +
73D TRP* 3.3 47.1 - + + +
123D THR* 1.3 73.0 - - - +
125D LYS* 1.3 58.6 + - - +
127D ALA* 3.3 2.4 + - - +
128D GLN* 2.8 64.4 + - + -
148D TRP* 3.7 16.1 + + - -
41X ASP* 3.5 4.1 + - - +
47X GLU* 5.1 7.4 - - + -
50X LEU* 4.7 7.9 - - + -
51X ARG* 3.6 42.8 + - + -
54X TYR* 3.9 24.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D THR* 3.2 7.9 + - - +
124D TYR* 1.3 83.1 - - - +
126D GLU* 1.3 59.3 + - + +
128D GLN* 3.7 5.6 - - - +
129D ALA* 2.8 32.5 + - + +
54X TYR* 3.5 49.6 + - + +
57X GLY* 4.3 6.1 + - - -
58X PHE 3.7 12.9 + - - -
59X GLU* 3.8 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D TYR 3.4 19.8 - - - +
97D GLY* 3.0 6.6 - - - -
98D GLU* 2.9 34.5 + - - +
121D TYR* 3.7 18.9 - - + -
122D GLU* 3.5 9.6 + - - +
123D THR* 2.6 46.4 + - - +
125D LYS* 1.3 77.9 - - + +
127D ALA* 1.3 63.8 + - - +
129D ALA* 3.1 4.5 + - - +
130D ALA* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D TRP* 3.7 22.2 - - + +
75D LEU* 3.4 19.5 - - + +
121D TYR* 3.4 19.4 - - + -
123D THR 3.2 5.3 + - - +
124D TYR 3.7 4.5 - - - +
126D GLU* 1.3 79.7 - - - +
128D GLN* 1.3 62.6 + - - +
131D MET* 3.1 19.1 + - - +
148D TRP* 3.5 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D TYR* 2.8 53.7 + - + +
125D LYS* 3.9 6.6 + - - +
127D ALA* 1.3 71.1 - - - +
129D ALA* 1.3 66.2 + - - +
131D MET* 3.3 16.3 + - + +
132D GLU* 3.1 49.0 + - - +
148D TRP* 3.8 12.2 - - + -
51X ARG* 4.5 17.6 + - - +
54X TYR* 5.8 3.4 - - - +
55X ALA* 6.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D TYR* 3.3 23.7 - - + +
125D LYS* 2.8 20.9 + - + +
126D GLU* 3.3 9.2 - - - +
128D GLN* 1.3 77.2 - - - +
130D ALA* 1.3 52.0 + - - +
131D MET 3.1 0.5 + - - -
132D GLU* 3.4 6.7 + - - +
133D GLY* 2.8 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 130 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D LEU* 4.0 3.6 - - + -
93D PHE* 4.0 11.2 - - + -
96D TYR* 3.2 22.1 - - + -
121D TYR* 3.3 43.5 - - + +
126D GLU 2.9 6.0 + - - +
127D ALA 4.0 2.0 - - - +
129D ALA* 1.3 75.1 - - - +
131D MET* 1.3 57.9 + - - +
134D LEU* 2.9 31.6 + - - +
146D VAL* 4.2 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 131 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D LEU* 4.2 2.4 - - + +
127D ALA 3.1 13.8 + - - +
128D GLN* 3.3 22.9 - - + +
129D ALA 3.1 0.6 - - - -
130D ALA* 1.3 73.5 - - - +
132D GLU* 1.3 66.1 + - + +
135D ASN* 2.8 39.6 + - + +
146D VAL* 3.2 31.8 - - + +
147D ASP* 4.1 15.0 - - - +
148D TRP* 3.5 50.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D GLN* 3.1 45.2 + - + +
129D ALA* 4.0 4.4 - - - +
131D MET* 1.3 83.4 - - + +
133D GLY* 1.3 62.2 + - - +
134D LEU 3.4 0.5 + - - -
135D ASN* 3.9 12.5 + - - +
137D GLN* 5.6 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D TYR* 3.1 30.6 + - - -
129D ALA 2.8 18.3 + - - -
132D GLU* 1.3 79.2 - - - +
134D LEU* 1.3 56.4 + - - +
135D ASN 5.2 0.2 - - - -
137D GLN* 3.5 17.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D LYS* 3.1 52.0 - - + +
93D PHE* 3.5 45.8 - - + -
96D TYR* 3.9 14.6 - - + +
130D ALA 2.9 14.6 + - - +
133D GLY* 1.3 81.9 - - - +
135D ASN* 1.3 68.0 + - - +
136D GLY 3.3 0.7 + - - -
137D GLN* 3.1 31.7 + - + +
144D ILE* 3.7 15.0 - - + +
146D VAL* 4.4 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D MET* 2.8 25.9 + - + +
132D GLU* 3.9 9.4 + - - +
133D GLY 3.8 0.6 - - - -
134D LEU* 1.3 71.6 - - - +
136D GLY* 1.3 61.4 + - - +
137D GLN* 3.1 13.2 + - - -
144D ILE 4.1 0.2 - - - -
145D SER* 3.2 16.0 + - - +
146D VAL* 2.7 46.0 + - - +
147D ASP* 4.5 6.7 + - - +
----------------------------------------------------------
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