Contacts of the strand formed by residues 120 - 132 (chain J) 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 TYR 120 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26I PHE* 4.2 4.7 - + - -
84I TRP 4.5 0.4 + - - +
85I ALA* 3.1 34.2 - - + +
86I HIS 3.1 40.1 + - - -
87I SER* 3.5 21.1 + - - -
112I ARG* 4.6 7.8 + - - -
114I GLN* 3.6 35.9 + - - +
112J ARG* 4.0 39.3 - - + +
113J VAL 3.1 13.0 - - - +
114J GLN* 4.4 2.0 - - - -
118J GLY 3.3 16.6 - - - +
119J SER* 1.3 76.0 - - - +
121J HIS* 1.3 79.6 + - - +
158J PHE* 4.8 1.1 - - - -
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Residues in contact with HIS 121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76I ASN* 5.0 0.2 + - - -
81I TYR 4.3 3.2 + - - -
84I TRP* 3.5 54.3 + + - -
85I ALA* 4.0 0.7 - - - -
86I HIS* 2.8 30.0 + - + -
112J ARG* 3.5 1.7 - - - -
113J VAL* 2.8 36.8 + - - +
119J SER* 6.3 0.2 - - - -
120J TYR* 1.3 83.2 + - - +
122J GLU* 1.3 58.1 + - - +
154J ALA* 3.6 24.5 - - - +
157J SER* 3.6 23.7 + - - -
158J PHE* 3.3 42.7 - + + -
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Residues in contact with GLU 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I HIS* 3.0 30.3 + - - +
87I SER* 3.5 20.3 - - - -
88I ILE* 3.0 48.9 + - + +
147I VAL* 4.8 0.2 - - - +
89J THR* 3.0 35.5 + - - +
110J PHE* 3.9 8.5 - - + +
111J VAL 3.3 15.5 - - - +
112J ARG* 3.9 17.7 - - + +
121J HIS* 1.3 73.9 - - - +
123J ASP* 1.3 67.0 + - - +
154J ALA* 5.1 0.2 - - - -
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Residues in contact with ASP 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86I HIS* 4.3 7.7 + - + +
88I ILE* 3.7 12.1 - - - +
147I VAL* 3.3 23.7 - - - +
148I THR* 5.2 1.6 + - - -
151I LEU* 5.6 2.6 - - - +
110J PHE* 3.6 4.3 - - - -
111J VAL* 3.1 31.0 + - - +
122J GLU* 1.3 75.5 - - - +
124J VAL* 1.3 72.4 + - - +
125J GLY 4.2 0.3 + - - -
150J GLY 4.6 2.6 - - - +
153J ARG* 3.4 41.7 + - + +
154J ALA* 3.9 25.0 - - + +
157J SER* 4.6 4.5 + - - -
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Residues in contact with VAL 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88I ILE* 4.1 0.6 - - + +
91I GLN* 3.9 4.3 - - - +
143I ARG* 4.1 23.3 - - + +
144I LYS* 4.2 12.5 - - + +
147I VAL* 3.8 25.4 - - + -
108J CYS* 4.9 6.3 - - + -
109J ALA 3.4 3.4 - - - +
110J PHE* 3.5 43.1 - - + -
123J ASP* 1.3 82.8 + - - +
125J GLY* 1.3 73.6 + - - +
126J TYR* 5.3 1.6 - - + -
150J GLY* 4.0 3.1 - - - -
153J ARG* 2.9 28.1 + - - +
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Residues in contact with GLY 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144I LYS* 4.7 0.2 - - - -
108J CYS* 3.4 4.3 - - - +
109J ALA 2.9 31.6 + - - +
124J VAL* 1.3 81.4 - - - +
126J TYR* 1.3 60.5 + - - -
146J ALA* 3.5 8.7 - - - -
149J ASP* 3.4 6.5 - - - -
150J GLY* 3.3 27.8 - - - -
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Residues in contact with TYR 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136I ALA 3.4 17.9 - - - -
139I LEU* 3.2 21.6 - - + +
140I GLU* 3.5 44.8 - - + +
143I ARG* 3.9 12.6 - - + -
144I LYS* 4.1 3.5 - - + +
94J ASP* 2.3 39.6 + - - +
95J PHE* 4.2 0.2 - - - -
106J GLY* 3.7 20.5 - - - -
107J VAL 3.4 14.4 - - - -
108J CYS* 3.5 22.2 - - + -
124J VAL* 5.3 1.3 - - + -
125J GLY* 1.3 72.8 - - - -
127J GLY* 1.3 64.5 + - - +
128J VAL* 3.7 15.3 - - + -
145J GLU* 3.5 9.0 - - - +
146J ALA* 3.4 12.7 - - - +
149J ASP* 3.3 14.9 + - - +
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Residues in contact with GLY 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106J GLY* 3.5 3.3 - - - -
107J VAL 2.8 35.8 + - - -
126J TYR* 1.3 75.4 - - - +
128J VAL* 1.3 63.7 + - - +
142J ALA* 3.1 31.7 - - - +
145J GLU* 3.8 8.1 - - - -
146J ALA* 3.5 3.8 - - - +
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Residues in contact with VAL 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136I ALA* 3.6 19.7 - - + +
137I LEU* 5.1 1.6 - - + +
140I GLU* 4.4 13.9 - - - +
105J VAL 3.4 3.4 - - - +
126J TYR* 3.7 20.4 - - + -
127J GLY* 1.3 79.6 - - - +
129J SER* 1.3 66.3 + - - +
130J GLU* 3.4 34.5 - - + +
141J LYS* 3.4 21.2 + - - +
142J ALA* 4.0 2.9 - - - +
145J GLU* 3.5 14.6 + - - +
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Residues in contact with SER 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103J PHE 3.1 8.5 - - - +
105J VAL* 3.0 33.4 + - - +
128J VAL* 1.3 75.8 - - - +
130J GLU* 1.3 61.0 + - - +
132J LEU* 3.3 17.8 - - - +
138J SER* 3.2 46.8 + - - -
141J LYS* 3.7 17.4 + - - +
142J ALA* 4.6 0.2 - - - +
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Residues in contact with GLU 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134I SER* 2.8 30.3 + - - -
136I ALA* 3.7 8.7 - - + +
137I LEU* 4.7 1.7 + - - +
103J PHE 3.3 4.5 - - - -
104J TYR* 3.0 38.2 - - + +
105J VAL 4.9 0.2 - - - +
128J VAL* 3.4 26.5 - - + +
129J SER* 1.3 77.4 + - - +
131J GLY* 1.3 59.8 + - - +
132J LEU* 3.5 4.9 + - - +
141J LYS* 5.3 1.2 - - - +
5Z C 5.8 0.3 - - - +
6Z C 4.0 19.2 + - - +
7Z C 4.1 10.4 + - - +
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Residues in contact with GLY 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102J LYS* 3.2 44.6 - - - +
103J PHE 3.1 8.5 + - - -
104J TYR* 4.6 3.9 - - - -
130J GLU* 1.3 73.3 - - - +
132J LEU* 1.3 65.6 + - - +
133J LYS* 3.7 3.3 + - - +
7Z C 4.1 10.2 + - - -
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Residues in contact with LEU 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102J LYS* 3.5 0.5 - - - -
103J PHE* 2.9 29.9 + - - +
129J SER* 3.3 21.1 - - - +
130J GLU 3.5 3.9 - - - +
131J GLY* 1.3 78.3 - - - +
133J LYS* 1.3 63.1 + - - +
134J SER* 3.5 5.8 - - - +
137J LEU* 4.5 18.6 - - + +
138J SER* 3.4 25.1 - - - +
141J LYS* 4.6 13.7 - - + +
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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