Contacts of the strand formed by residues 102 - 115 (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 LYS 102 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98R LEU* 3.3 6.9 - - - +
99R ASN 2.9 28.0 + - - +
100R ASN* 3.8 12.6 - - - +
101R GLY* 1.3 83.0 - - - +
103R PHE* 1.3 59.9 + - - +
104R TYR* 3.4 25.8 - - + +
131R GLY* 3.1 30.9 - - - +
132R LEU 3.7 4.0 - - - -
133R LYS* 5.1 5.2 - - + +
4W C 3.1 22.4 + - - -
5W C 3.1 43.4 + - - +
6W C 3.1 32.9 + - - +
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Residues in contact with PHE 103 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96R VAL* 4.2 11.2 - - + -
97R ASP 3.5 11.9 - - - -
98R LEU* 3.8 34.1 - - + -
101R GLY 4.9 1.8 - - - -
102R LYS* 1.3 72.3 - - - +
104R TYR* 1.3 62.6 + - - +
105R VAL* 4.2 3.8 - - + -
129R SER 3.4 7.1 - - - +
131R GLY 3.1 21.1 + - - -
132R LEU 2.7 15.9 + - - +
133R LYS* 3.3 30.1 - - - -
135R LYS* 3.5 55.4 - - + -
138R SER* 3.8 17.1 + - - +
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Residues in contact with TYR 104 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95R PHE* 3.2 23.2 - - + -
97R ASP* 3.1 33.4 + - + +
99R ASN* 3.8 23.4 + - + +
100R ASN* 5.0 1.0 + - - -
102R LYS* 3.4 42.8 - - + +
103R PHE* 1.3 76.3 - - - +
105R VAL* 1.3 60.4 + - - +
129R SER 3.4 4.5 - - - -
130R GLU* 3.5 30.1 - - + +
131R GLY 3.9 3.8 - - - -
3W C 3.3 25.8 - - + -
4W C 3.1 33.1 + - - -
5W C 4.2 0.3 + - - -
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Residues in contact with VAL 105 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136Q ALA* 4.3 0.7 - - - +
93R VAL* 4.7 0.2 - - + -
95R PHE* 3.5 14.1 - - - +
96R VAL* 4.0 23.8 - - + -
103R PHE* 4.7 2.2 - - + -
104R TYR* 1.3 81.9 - - - +
106R GLY* 1.3 61.3 + - - +
107R VAL* 3.7 14.1 - - + -
127R GLY 3.8 0.2 - - - +
128R VAL* 3.6 9.0 - - - +
129R SER 2.9 30.1 + - - +
130R GLU* 5.2 0.8 - - - +
135R LYS* 5.5 0.4 - - + +
138R SER* 4.0 25.1 - - - +
139R LEU* 3.9 21.1 - - + +
142R ALA* 3.7 23.8 - - + -
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Residues in contact with GLY 106 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136Q ALA* 4.5 1.6 - - - -
94R ASP* 2.8 26.9 + - - +
95R PHE* 3.4 25.5 + - - +
105R VAL* 1.3 74.0 - - - +
107R VAL* 1.3 64.2 + - - +
126R TYR* 3.6 24.2 - - - -
127R GLY 3.5 4.3 - - - -
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Residues in contact with VAL 107 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91R GLN* 3.8 24.7 - - + +
92R ASN 3.7 9.0 - - - +
93R VAL* 3.8 22.4 - - + -
105R VAL* 3.7 11.0 - - + -
106R GLY* 1.3 79.5 - - - +
108R CYS* 1.3 70.6 + - - +
126R TYR* 3.3 7.3 - - - -
127R GLY 2.6 37.7 + - - -
139R LEU* 4.9 0.4 - - + -
142R ALA* 3.7 27.6 - - + +
143R ARG* 4.0 11.4 - - + -
146R ALA* 3.4 10.6 - - + +
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Residues in contact with CYS 108 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143Q ARG* 3.4 42.0 - - - +
91R GLN* 3.4 5.2 - - - +
92R ASN* 2.9 55.6 + - - +
94R ASP* 4.0 1.1 + - - -
107R VAL* 1.3 74.7 - - - +
109R ALA* 1.3 60.6 + - - +
110R PHE* 3.7 12.3 - - - -
124R VAL* 4.3 4.5 - - + -
125R GLY 3.2 7.6 - - - +
126R TYR* 3.5 21.4 - - + -
146R ALA* 4.1 1.3 - - - -
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Residues in contact with ALA 109 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88R ILE* 5.0 2.0 - - + -
90R GLN 3.4 8.1 - - - +
91R GLN* 3.8 18.2 - - + +
108R CYS* 1.3 75.6 - - - +
110R PHE* 1.3 64.6 + - - +
111R VAL* 4.0 5.3 + - + -
124R VAL* 3.3 4.2 - - - +
125R GLY 2.6 37.5 + - - -
146R ALA 3.7 27.1 - - - +
147R VAL* 3.9 10.8 - - + +
150R GLY* 4.7 0.2 - - - -
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Residues in contact with PHE 110 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88Q ILE* 3.8 31.9 - - + -
91Q GLN* 3.4 47.3 - - + -
143Q ARG* 4.3 5.6 - - - -
88R ILE* 3.6 2.9 - - - -
89R THR* 2.7 40.9 + - + -
90R GLN* 2.7 38.4 + - + +
92R ASN* 5.4 0.2 - - + -
108R CYS* 3.7 24.2 - - - -
109R ALA* 1.3 74.9 - - - +
111R VAL* 1.3 59.2 + - - +
122R GLU* 3.9 13.9 - - - +
123R ASP 3.5 4.9 - - - +
124R VAL* 3.8 19.7 - - + -
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Residues in contact with VAL 111 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86R HIS* 3.8 26.7 - - + -
87R SER 3.4 11.2 - - - +
88R ILE* 4.9 7.2 - - + -
109R ALA* 4.0 2.7 + - + -
110R PHE* 1.3 79.1 - - - +
112R ARG* 1.3 64.8 + - - +
113R VAL* 4.1 2.0 - - + -
122R GLU* 3.3 3.4 - - - +
123R ASP 3.1 30.5 + - - +
147R VAL* 3.5 35.7 - - + +
150R GLY* 3.6 16.8 - - - +
151R LEU* 3.6 22.4 - - + +
154R ALA* 3.7 4.7 - - - +
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Residues in contact with ARG 112 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87Q SER* 5.0 3.6 - - - -
86R HIS* 3.1 2.5 - - - -
87R SER* 2.9 43.0 + - - +
89R THR* 3.9 17.3 - - - +
110R PHE 4.2 0.4 + - - -
111R VAL* 1.3 73.3 - - - +
113R VAL* 1.3 69.7 + - - +
114R GLN* 3.6 31.4 + - - +
118R GLY 4.7 0.2 + - - -
120R TYR* 3.2 48.9 - - + +
121R HIS 3.6 4.5 - - - +
122R GLU* 4.0 20.4 - - + -
120S TYR* 4.7 11.2 + - - -
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Residues in contact with VAL 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84R TRP* 3.9 12.1 - - + -
85R ALA 3.1 9.9 - - - +
86R HIS* 3.8 5.8 - - + -
111R VAL* 4.6 0.7 - - + -
112R ARG* 1.3 72.0 - - - +
114R GLN* 1.3 67.1 + - - +
120R TYR* 3.1 6.2 - - - +
121R HIS 2.8 37.3 + - - +
151R LEU* 3.7 27.6 - - + -
154R ALA* 3.6 22.4 - - + -
155R LEU* 3.6 27.8 - - + +
158R PHE* 3.7 18.7 - - + -
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Residues in contact with GLN 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26R PHE* 3.5 22.7 - - + -
27R GLY* 4.5 6.9 - - - -
84R TRP* 3.2 2.9 - - - +
85R ALA 2.5 41.0 + - - +
112R ARG* 3.6 26.1 + - - +
113R VAL* 1.3 76.0 - - - +
115R LEU* 1.3 72.0 - - - +
118R GLY* 3.4 25.2 + - - +
119R SER 3.2 11.9 - - - +
120R TYR* 4.4 3.1 - - + -
120S TYR* 2.9 29.4 + - - +
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Residues in contact with LEU 115 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81Q TYR* 3.6 33.0 - - + -
82Q ASN* 4.6 0.2 - - + -
26R PHE* 3.5 7.3 - - - -
31R TYR* 4.0 6.3 - - - +
79R PHE* 3.6 37.2 - - + -
83R GLY 3.3 9.4 - - - +
84R TRP* 4.0 7.6 - - + -
113R VAL* 5.1 0.2 - - + -
114R GLN* 1.3 82.5 - - - +
116R LYS* 1.3 59.8 + - - +
117R ASP* 2.9 23.4 + - - +
118R GLY 3.0 12.0 + - - -
119R SER* 2.7 22.1 + - - +
158R PHE* 3.6 36.3 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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