Contacts of the strand formed by residues 69 - 74 (chain R) 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 VAL 69 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64R ALA* 4.0 0.2 - - - -
65R LEU* 3.2 11.2 + - + -
66R ASP* 3.0 47.7 + - - +
68R ASN* 1.3 99.0 + - - +
70R CYS* 1.3 62.9 + - - +
102R VAL 3.9 4.9 - - - +
104R VAL* 3.9 22.9 - - + -
107R ILE* 4.0 24.0 - - + -
133R ILE* 3.8 21.1 - - + -
134R VAL 3.6 12.6 - - - +
135R GLY* 4.2 1.1 - - - -
211R MET* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 70 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41R VAL* 4.8 1.1 - - - -
43R LEU* 4.1 2.0 - - - -
63R CYS 3.4 15.5 - - - +
64R ALA* 4.0 4.9 - - + +
65R LEU* 3.8 7.4 - - - -
69R VAL* 1.3 72.7 - - - +
71R MET* 1.4 62.7 + - - +
133R ILE* 3.7 6.2 - - - +
134R VAL* 2.8 59.9 + - - +
135R GLY 4.3 0.2 - - - -
211R MET* 3.6 23.6 - - + -
217R LEU* 3.4 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 71 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43R LEU* 4.7 5.5 - - - +
63R CYS* 2.9 33.6 + - + +
65R LEU* 3.5 13.5 - - + -
70R CYS* 1.4 75.0 - - - +
72R ALA* 1.4 64.1 + - - +
73R PHE* 3.8 26.1 + - + +
80R ALA 4.0 5.6 - - - +
83R VAL* 4.4 7.0 - - + -
84R ILE* 3.8 35.0 - - + -
111R ILE* 4.2 11.4 - - + -
129R ILE* 4.0 20.0 - - + -
131R ALA* 3.8 29.2 - - + -
132R LEU 3.8 4.7 - - - -
133R ILE* 4.0 14.8 - - + +
217R LEU* 5.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32R ALA* 3.8 4.8 - - + +
33R VAL 5.2 0.9 - - - +
43R LEU* 4.0 29.2 - - + -
44R GLY 5.1 1.6 - - - +
45R VAL* 4.4 18.8 - - + -
71R MET* 1.4 73.0 - - - +
73R PHE* 1.3 66.5 + - - +
132R LEU* 3.0 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 73 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32R ALA* 4.3 4.7 - - - +
45R VAL* 4.6 6.8 - - - +
63R CYS* 3.7 30.1 - - - -
71R MET* 3.8 28.6 - - + +
72R ALA* 1.3 79.1 - - - +
74R ALA* 1.3 66.8 - - - +
75R GLY 5.3 0.4 - - - -
77R THR* 3.3 34.5 - - - -
80R ALA* 3.3 36.3 - - + -
81R ARG* 4.7 5.4 - - + -
129R ILE* 4.4 2.9 - - + -
131R ALA* 3.9 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26R VAL* 4.1 8.5 - - + -
30R SER 3.6 16.6 - - - +
32R ALA* 3.9 6.5 - - + -
73R PHE* 1.3 76.4 - - - +
75R GLY* 1.3 60.5 + - - +
129R ILE* 3.4 6.2 - - - +
130R SER 3.0 35.3 + - - +
161R ILE* 3.4 31.9 - - + +
162R GLY* 4.5 1.6 - - - +
----------------------------------------------------------
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