Contacts of the strand formed by residues 47 - 54 (chain Q) in PDB entry 2A3W
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 TYR 47 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Q ALA* 6.0 0.9 - - - +
41Q SER* 4.0 18.3 + - - -
43Q LEU* 3.7 36.2 + - + -
45Q ARG* 3.3 24.0 - - - +
46Q ALA* 1.3 74.7 - - - +
48Q SER* 1.3 60.0 - - - +
49Q LEU* 3.5 28.8 - - + +
64Q TYR* 3.7 8.2 - - - -
65Q LYS* 2.8 79.1 + - + +
148Q GLN* 3.5 6.1 - - - +
149Q SER 3.5 23.6 - - - +
150Q PHE* 3.6 19.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 48 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47Q TYR* 1.3 74.5 - - - +
49Q LEU* 1.3 62.2 + - - +
50Q PHE 3.6 5.9 + - - -
51Q SER* 3.7 12.1 + - - -
62Q LEU* 3.3 19.4 - - - +
63Q VAL 3.9 3.6 - - - -
64Q TYR* 3.9 5.4 - - - -
134Q GLY 5.0 3.9 + - - -
135Q GLN 3.8 4.1 + - - -
136Q GLU* 3.7 36.8 - - - -
148Q GLN 3.0 11.5 + - - -
150Q PHE* 3.5 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Q PHE* 3.5 31.7 - - + -
39Q ALA* 4.4 8.3 - - + -
47Q TYR* 3.5 26.3 + - + -
48Q SER* 1.3 74.4 - - - +
50Q PHE* 1.3 61.8 + - - +
63Q VAL* 2.8 25.9 + - + +
65Q LYS* 4.0 31.2 - - + +
71Q TYR* 4.5 2.7 - - + -
94Q ILE* 4.1 18.4 - - + -
132Q VAL 5.2 1.3 - - - -
133Q LEU* 3.7 18.4 - - - +
134Q GLY 5.1 0.4 + - - -
150Q PHE* 3.8 20.6 - - + -
154Q ILE* 4.1 15.6 - - + +
157Q LEU* 5.6 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 50 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22Q LEU* 4.1 6.7 - - + -
35Q LEU* 3.5 42.8 - - + -
37Q PHE* 4.8 2.5 - - + -
48Q SER* 3.6 2.6 + - - -
49Q LEU* 1.3 80.5 - - + +
51Q SER* 1.3 59.0 + - - +
52Q TYR* 4.1 22.9 - + + -
61Q LEU* 4.6 11.9 - - + -
62Q LEU* 3.3 8.0 - - - +
63Q VAL* 3.1 32.8 + - + -
131Q ILE* 3.4 31.4 - - + -
132Q VAL 4.1 3.8 - - - -
133Q LEU* 3.8 15.5 - - + -
157Q LEU* 4.1 7.0 - - + -
159Q MET* 3.9 16.4 - - + -
183Q LEU* 3.8 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 51 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Q SER* 3.7 8.3 - - - -
50Q PHE* 1.3 73.3 - - - +
52Q TYR* 1.3 61.9 + - - +
53Q ASN* 4.4 2.3 + - - -
62Q LEU* 4.1 7.1 - - - +
131Q ILE* 3.2 5.2 - - - +
132Q VAL* 2.8 42.1 + - - -
135Q GLN 3.5 23.6 - - - -
136Q GLU* 4.0 5.3 + - - -
137Q GLN* 3.0 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 52 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26Q LEU* 3.5 25.6 - - + +
30Q LEU* 4.1 3.8 - - + +
50Q PHE* 4.1 11.7 - + + -
51Q SER* 1.3 75.4 + - - +
53Q ASN* 1.3 68.3 + - - +
54Q THR* 3.8 8.3 - - + -
59Q ASN* 4.5 0.2 - - - -
60Q GLU* 3.4 5.2 + - + -
61Q LEU* 2.9 70.5 + - + +
62Q LEU* 5.1 0.4 - - - +
125Q VAL* 3.8 20.0 + - + +
126Q GLU 2.8 28.8 + - - -
127Q ALA* 4.2 0.2 - - - -
129Q PRO* 3.4 30.5 - - + +
130Q LYS 3.6 4.5 - - - -
131Q ILE* 3.8 22.2 - - + -
159Q MET* 4.9 4.5 - - + -
182Q ILE* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 53 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51Q SER* 4.4 3.1 + - - -
52Q TYR* 1.3 80.0 + - - +
54Q THR* 1.3 66.2 + - - +
57Q ARG 3.6 6.6 + - - +
58Q ASP* 2.8 32.0 + - - +
59Q ASN* 2.9 23.7 + - - +
60Q GLU* 4.4 1.3 - - - -
62Q LEU* 6.0 0.2 - - - +
129Q PRO* 3.3 5.2 - - - +
130Q LYS 3.0 30.7 + - - -
136Q GLU* 4.9 0.2 - - - +
137Q GLN* 3.5 25.2 + - - +
138Q ASP 4.0 0.2 - - - -
139Q SER* 3.3 32.1 + - - +
140Q TYR* 3.8 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 54 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52Q TYR* 3.8 13.2 - - + -
53Q ASN* 1.3 79.2 - - - +
55Q GLN* 1.3 57.5 + - - +
56Q GLY 3.0 1.2 + - - -
57Q ARG* 2.8 55.0 + - - +
60Q GLU* 4.0 6.8 - - + +
126Q GLU* 3.5 31.0 - - + +
127Q ALA 3.4 26.0 - - - +
128Q GLN 4.5 0.7 - - - -
129Q PRO* 4.2 3.1 - - + -
139Q SER 5.7 0.3 - - - -
140Q TYR* 3.5 15.5 - - - +
----------------------------------------------------------
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