Contacts of the strand formed by residues 84 - 99 (chain R) in PDB entry 5XS0
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 84 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26R PHE* 3.9 2.2 - - - -
72R ILE* 4.4 11.4 - - + -
75R ALA* 3.5 31.2 - - + -
76R ASN* 3.0 25.2 + - - +
79R PHE* 3.8 16.2 - - + -
80R GLY 3.4 16.4 - - - -
81R TYR 4.2 2.2 - - - +
83R GLY* 1.3 81.0 - - - +
85R ALA* 1.3 73.7 + - - +
86R HIS* 4.1 8.5 - - + -
113R VAL* 3.9 16.2 - - + -
114R GLN 3.2 8.7 - - - +
115R LEU* 4.0 7.0 - - + +
151R LEU* 3.7 38.6 - - + -
155R LEU* 4.1 11.7 - - + -
119S SER* 3.7 12.1 + - - -
121S HIS* 3.3 36.3 + + - -
157S SER* 3.7 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26R PHE* 3.5 20.0 - - + -
84R TRP* 1.3 79.5 - - - +
86R HIS* 1.3 57.5 + - - +
113R VAL* 3.1 6.2 - - - +
114R GLN 2.5 38.8 + - - +
120S TYR* 3.1 50.7 - - + +
121S HIS* 4.1 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 86 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84R TRP* 4.1 2.7 - - + -
85R ALA* 1.3 77.3 - - - +
87R SER* 1.3 62.1 + - - +
88R ILE* 5.6 0.4 - - + -
111R VAL* 3.8 15.0 - - + -
112R ARG 3.1 12.3 - - - +
113R VAL* 3.8 6.7 - - + -
147R VAL* 5.4 3.9 - - + +
151R LEU* 3.7 42.4 - - + +
120S TYR* 3.3 14.2 + - - -
121S HIS* 2.9 37.5 + + + -
122S GLU* 2.8 51.5 + - - +
123S ASP* 4.4 6.4 + - + -
157S SER* 3.7 15.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R HIS* 1.3 77.1 - - - +
88R ILE* 1.3 64.7 - - - +
89R THR* 3.5 3.5 + - - -
111R VAL* 3.4 6.5 - - - +
112R ARG* 2.9 48.1 + - - +
112S ARG* 5.1 6.5 - - - -
120S TYR* 3.8 19.2 + - - -
122S GLU* 3.6 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R HIS* 5.6 0.7 - - + -
87R SER* 1.3 72.9 - - - +
89R THR* 1.3 66.0 + - - +
90R GLN* 4.0 24.2 - - - +
91R GLN* 4.2 4.0 - - + +
109R ALA* 5.0 3.1 - - + -
110R PHE 3.6 5.6 - - - +
111R VAL* 4.7 5.8 - - + +
147R VAL* 3.7 32.5 - - + -
89S THR* 5.8 2.3 - - - +
110S PHE* 3.8 30.2 - - + -
122S GLU* 3.0 32.7 + - + +
123S ASP* 3.8 31.0 - - - -
124S VAL* 3.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88Q ILE 5.8 1.8 - - - +
87R SER* 3.5 4.6 + - - -
88R ILE* 1.3 73.9 - - - +
90R GLN* 1.3 60.8 + - + +
110R PHE* 2.7 17.0 + - + -
112R ARG* 3.9 15.8 - - - +
122R GLU* 2.9 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 90 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88R ILE* 3.4 6.6 - - - +
89R THR* 1.3 85.0 - - + +
91R GLN* 1.3 70.4 + - - +
92R ASN* 4.0 19.0 + - + +
109R ALA* 3.4 0.2 - - - -
110R PHE* 2.7 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 91 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88R ILE* 4.2 5.8 - - + +
90R GLN* 1.3 79.0 - - - +
92R ASN* 1.3 63.9 + - - +
93R VAL 4.4 0.2 + - - -
107R VAL* 3.8 14.4 - - + +
108R CYS 3.4 8.1 - - - +
109R ALA* 3.8 9.4 - - + +
143R ARG* 2.5 71.8 + - - +
146R ALA* 4.2 0.2 - - - +
147R VAL* 3.4 18.6 - - - +
110S PHE* 3.6 32.3 - - + -
124S VAL* 4.0 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143Q ARG* 4.1 13.1 - - - +
90R GLN* 4.0 19.6 + - + +
91R GLN* 1.3 73.9 - - - +
93R VAL* 1.3 74.2 + - - +
94R ASP* 3.3 18.3 + - - +
107R VAL* 3.7 2.2 - - - -
108R CYS* 2.9 47.1 + - - -
110R PHE* 5.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91R GLN 4.4 0.2 + - - -
92R ASN* 1.3 80.4 + - - +
94R ASP* 1.3 66.1 + - - +
95R PHE* 3.9 10.5 - - - +
96R VAL* 3.9 27.4 - - + -
106R GLY 4.0 2.5 - - - -
107R VAL* 3.8 21.8 - - + -
139R LEU* 4.5 5.6 - - + -
143R ARG* 3.3 40.8 - - - +
94S ASP* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 94 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93Q VAL* 5.1 0.5 - - - +
139Q LEU* 3.6 20.6 - - + +
143Q ARG* 2.7 34.9 + - - -
92R ASN* 3.3 21.2 + - - +
93R VAL* 1.3 74.4 - - - +
95R PHE* 1.3 62.2 + - + +
106R GLY 2.8 17.4 + - - +
108R CYS* 4.0 0.4 - - - -
126R TYR* 2.4 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 95 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135Q LYS* 3.5 36.3 - - + +
136Q ALA* 3.6 28.9 - - + -
139Q LEU* 3.7 23.1 - - + -
93R VAL* 3.4 4.1 - - - +
94R ASP* 1.3 84.7 - - + +
96R VAL* 1.3 69.3 + - - +
97R ASP* 3.3 26.5 - - - +
104R TYR* 3.2 33.7 - - + -
105R VAL* 3.5 4.4 - - - +
106R GLY* 3.4 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93R VAL* 3.9 17.7 - - + -
95R PHE* 1.3 80.5 - - - +
97R ASP* 1.3 66.4 + - - +
98R LEU 4.4 0.2 + - - -
103R PHE* 4.2 12.6 - - + -
104R TYR 3.8 3.6 - - - -
105R VAL* 4.0 13.9 - - + -
135R LYS* 4.1 26.2 - - + +
139R LEU* 4.0 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135Q LYS* 2.8 37.4 + - - -
95R PHE* 3.3 10.2 - - + +
96R VAL* 1.3 81.0 + - - +
98R LEU* 1.3 61.4 + - - +
99R ASN* 4.1 1.6 - - + -
102R LYS 3.7 0.7 - - - +
103R PHE* 3.5 8.9 - - - -
104R TYR* 3.1 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97R ASP* 1.3 75.6 - - - +
99R ASN* 1.3 57.9 + - - +
100R ASN 4.1 1.5 + - - +
101R GLY* 3.7 16.2 - - - +
102R LYS 3.3 29.2 - - - +
103R PHE* 3.8 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 99 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97R ASP* 4.1 2.6 - - + -
98R LEU* 1.3 71.0 - - - +
100R ASN* 1.3 104.3 + - - +
101R GLY 3.2 0.7 - - - -
102R LYS* 2.9 24.1 + - - +
104R TYR* 3.8 23.3 - - + +
----------------------------------------------------------
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