Contacts of the strand formed by residues 147 - 152 (chain A) in PDB entry 2XOA
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 TRP 147 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN* 3.4 33.4 - - + -
73A LEU* 3.8 18.4 - - + -
78A LEU* 3.6 27.6 - - + +
81A MET* 4.4 16.7 - - + -
82A LEU* 4.8 4.0 - - + +
106A ALA* 3.6 33.9 - - + -
107A ILE 3.6 12.6 - - - -
108A LEU* 3.8 27.4 - - + -
141A ALA 4.6 6.7 + - - -
143A GLY 3.3 26.0 + - - -
144A GLU* 3.1 13.7 + - - +
145A ALA 3.3 1.8 - - - +
146A CYS* 1.3 90.4 - - - +
148A TRP* 1.3 69.6 + - - +
173A SER* 3.9 1.0 - - - -
174A VAL* 3.0 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A HIS 3.8 0.2 - - - +
106A ALA* 3.1 3.3 - - - -
107A ILE* 2.6 52.5 + - + +
109A LEU* 4.8 10.1 - - + -
118A LEU* 3.0 43.6 + - + +
119A SER* 3.7 24.7 - - - +
120A CYS* 3.8 14.4 - - + -
135A VAL* 4.2 14.1 - - + -
145A ALA 4.6 1.1 - - - -
146A CYS 3.7 12.0 + - - -
147A TRP* 1.3 82.2 - - - +
149A THR* 1.3 64.1 + - - +
171A LEU* 4.4 15.3 - - + -
172A VAL 3.3 11.7 - - - +
173A SER* 3.5 32.3 - - - -
174A VAL* 4.4 0.2 - - - -
178A ARG 4.8 0.2 - - - -
179A TYR 5.0 0.4 - - - -
180A LEU* 3.9 39.0 - - + -
193A ALA* 5.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 5.6 10.3 - - + -
104A GLY 4.0 12.1 - - - +
105A HIS 3.3 11.0 - - - +
106A ALA* 3.9 16.2 - - + -
148A TRP* 1.3 72.5 - - - +
150A MET* 1.3 62.0 + - - +
151A HIS* 3.2 27.7 + - - +
170A ILE 3.6 0.9 - - - +
171A LEU* 3.4 6.8 - - - +
172A VAL* 2.8 44.2 + - - +
174A VAL* 4.2 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 3.8 31.9 - - + -
102A LEU 3.5 22.9 - - - +
103A TYR* 3.8 11.5 - - + -
104A GLY 2.9 29.6 + - - +
105A HIS* 3.0 23.1 + - + +
107A ILE* 3.4 36.1 - - + -
149A THR* 1.3 74.7 - - - +
151A HIS* 1.3 66.3 + - - +
163A VAL* 4.1 12.1 - - + -
169A LEU* 4.8 12.3 - - + -
170A ILE 3.6 4.0 - - - +
171A LEU* 3.5 22.9 - - + -
202A MET* 4.9 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 3.7 4.0 - - - -
104A GLY* 4.9 2.2 + - - -
149A THR* 3.2 38.7 + - - +
150A MET* 1.3 76.8 + - - +
152A PRO* 1.3 73.7 - - + +
159A GLU* 3.0 29.3 + - - -
169A LEU* 3.5 5.5 - - - +
170A ILE* 2.9 45.3 + - + +
172A VAL* 3.7 25.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 3.4 28.7 - - + -
150A MET 4.4 0.7 - - - +
151A HIS* 1.3 96.3 - - + +
153A ALA* 1.3 60.0 + - - +
154A SER 3.3 8.5 + - - +
157A ARG* 3.5 42.8 - - + +
158A SER* 4.5 8.3 - - - -
159A GLU* 4.7 8.5 - - + +
170A ILE* 4.7 3.6 - - - +
----------------------------------------------------------
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