Contacts of the strand formed by residues 146 - 152 (chain U) in PDB entry 5A0Q
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 ALA 146 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40U ARG* 3.5 30.8 + - + +
41U CYS 3.7 9.9 - - - +
43U ASP* 4.4 0.9 - - - +
44U GLY 3.4 34.3 - - - +
45U VAL* 4.0 0.7 - - + -
139U SER 3.7 6.5 - - - -
140U TYR* 3.4 11.9 - - + +
144U ASP 4.0 0.7 - - - +
145U GLY* 1.3 71.8 - - - -
147U GLN* 1.3 72.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 147 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40U ARG* 4.1 18.3 + - - +
45U VAL* 3.4 5.3 - - - +
108U LEU* 3.6 25.4 - - + -
109U LYS* 5.5 5.4 - - + +
138U GLY* 3.1 3.5 - - - -
139U SER 2.9 33.3 + - - +
144U ASP* 3.1 47.3 + - + +
145U GLY 4.1 0.4 - - - +
146U ALA* 1.3 78.7 + - - +
148U LEU* 1.3 59.4 + - - +
149U TYR* 3.7 25.5 + - + -
159U GLY* 5.6 0.3 - - - -
160U TYR 5.5 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38U GLY* 3.7 10.5 - - - -
39U ILE 3.8 0.9 - - - +
40U ARG* 3.3 37.5 - - + +
45U VAL* 3.8 23.3 - - + -
47U PHE* 5.4 0.4 - - + -
136U MET* 3.6 35.0 - - + -
137U LEU 3.8 7.6 - - - +
138U GLY* 4.2 0.4 - - - -
147U GLN* 1.3 74.9 + - - +
149U TYR* 1.3 60.7 + - - +
159U GLY* 3.6 0.9 - - - -
160U TYR* 2.9 35.9 + - + +
162U GLY* 3.8 6.5 - - - +
163U CYS* 3.7 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 149 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108U LEU* 3.8 21.5 - - + +
109U LYS* 4.4 25.4 - - + +
112U ALA* 3.6 33.4 - - + -
113U ASP* 4.9 4.5 - - - -
135U PHE 4.1 0.2 - - - +
136U MET* 3.4 3.7 - - - -
137U LEU* 2.8 33.0 + - + +
147U GLN* 3.7 28.5 + - + -
148U LEU* 1.3 78.9 - - - +
150U MET* 1.4 60.2 + - - +
151U ILE* 4.2 2.2 + - + +
157U SER* 4.7 3.4 - - - -
158U TYR* 3.3 19.1 - - - +
159U GLY* 3.6 24.7 + - - -
160U TYR* 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 150 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134U SER* 3.3 24.5 - - - +
135U PHE 3.5 15.3 - - - +
136U MET* 3.9 4.0 - - + +
149U TYR* 1.4 72.1 - - - +
151U ILE* 1.4 60.8 + - - +
152U ASP* 3.3 34.1 - - - +
157U SER* 3.3 20.4 - - - -
158U TYR 3.2 10.8 + - - -
160U TYR* 3.4 29.6 - - + +
163U CYS* 3.6 21.5 - - - -
165U ILE* 3.4 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 151 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112U ALA* 3.4 36.1 - - + +
115U VAL* 4.0 7.2 - - + -
116U ALA* 3.8 30.1 - - + +
119U VAL* 4.3 5.2 - - + -
134U SER* 3.0 18.8 + - - -
135U PHE* 2.9 60.8 + - + +
137U LEU* 5.1 7.0 - - + +
149U TYR 4.9 3.4 - - - +
150U MET* 1.4 74.2 - - - +
152U ASP* 1.4 71.3 + - - +
155U GLY* 4.6 1.8 - - - -
156U VAL 3.9 3.1 - - - +
157U SER* 4.1 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 152 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27U MET* 3.9 10.9 - - + +
119U VAL* 3.4 9.4 - - - +
133U CYS 4.2 1.1 - - - -
134U SER* 3.7 6.5 + - - -
135U PHE* 5.9 0.2 - - - -
150U MET* 3.3 24.0 - - - +
151U ILE* 1.4 77.1 - - - +
153U PRO* 1.3 69.4 - - + +
154U SER* 3.0 21.1 - - - +
155U GLY 3.1 14.2 + - - -
156U VAL* 3.2 27.5 + - - +
158U TYR* 5.7 2.3 - - - -
160U TYR* 5.1 1.6 + - - -
165U ILE* 5.8 0.9 - - - +
----------------------------------------------------------
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