Contacts of the strand formed by residues 120 - 132 (chain N) in PDB entry 1H2I
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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26M PHE* 3.9 14.6 - + - -
84M TRP 4.9 0.6 + - - -
85M ALA* 2.9 47.6 - - + +
86M HIS* 3.1 27.4 + - - -
87M SER* 3.9 13.2 + - - -
112M ARG* 5.0 5.4 + - - -
114M GLN* 3.2 30.5 + - - +
112N ARG* 3.5 44.0 - - - +
113N VAL 3.2 13.2 - - - +
114N GLN* 4.2 1.6 - - - +
118N GLY 3.2 16.6 - - - -
119N SER* 1.3 78.0 - - - +
121N HIS* 1.3 69.0 + - - +
158N PHE* 4.8 3.9 - - - -
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Residues in contact with HIS 121 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76M ASN* 4.9 0.2 - - - -
81M TYR 4.5 3.6 - - - -
84M TRP* 3.3 49.0 + + - -
86M HIS* 2.8 41.5 - + + -
112N ARG* 3.6 2.1 - - - -
113N VAL* 2.9 39.7 + - + +
120N TYR* 1.3 84.7 + - - +
122N GLU* 1.3 61.9 + - - +
154N ALA* 3.6 10.9 - - - +
157N SER* 3.3 30.2 - - - +
158N PHE* 3.7 36.5 - + - -
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Residues in contact with GLU 122 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86M HIS* 3.0 31.3 + - - +
87M SER* 3.5 21.2 - - - -
88M ILE* 3.1 45.5 + - + +
147M VAL* 4.6 0.5 - - - +
89N THR* 2.6 38.0 + - - +
110N PHE* 3.8 6.1 - - - +
111N VAL 3.3 17.0 - - - +
112N ARG* 3.9 14.2 - - + +
121N HIS* 1.3 77.8 - - - +
123N ASP* 1.3 66.8 + - - +
154N ALA* 4.5 0.9 - - - -
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Residues in contact with ASP 123 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86M HIS* 4.9 4.8 + - + +
88M ILE* 3.7 11.9 - - - -
147M VAL* 3.5 17.5 - - - +
148M THR* 5.2 2.9 + - - -
110N PHE* 3.4 3.6 - - - +
111N VAL* 3.1 32.5 + - - +
122N GLU* 1.3 77.0 - - - +
124N VAL* 1.3 71.0 + - - +
150N GLY* 4.5 1.7 - - - +
153N ARG* 2.5 53.4 + - + +
154N ALA* 3.8 22.8 - - + +
157N SER* 5.1 2.1 + - - -
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Residues in contact with VAL 124 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88M ILE* 4.2 0.2 - - - +
91M GLN* 3.9 6.1 - - - +
143M ARG* 3.9 17.3 - - + +
144M LYS* 4.2 8.2 - - + -
147M VAL* 3.3 29.6 - - + -
108N CYS* 4.4 7.6 - - + -
109N ALA 3.2 9.4 - - - +
110N PHE* 3.1 38.1 - - + -
123N ASP* 1.3 86.9 + - - +
125N GLY* 1.3 59.4 + - - +
126N TYR* 6.1 0.4 - - + -
150N GLY* 4.0 2.2 - - - -
153N ARG* 2.8 39.8 + - - +
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Residues in contact with GLY 125 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144M LYS* 4.6 1.1 - - - -
108N CYS* 3.3 7.4 - - - +
109N ALA 2.8 29.1 + - - -
124N VAL* 1.3 77.7 - - - +
126N TYR* 1.3 62.4 + - - +
146N ALA* 3.5 7.4 - - - -
149N ASP* 3.3 11.4 - - - -
150N GLY* 3.3 23.6 - - - -
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Residues in contact with TYR 126 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136M ALA* 3.8 15.0 - - - -
139M LEU* 3.5 17.1 - - + +
140M GLU* 3.6 43.6 - - + +
143M ARG* 3.8 14.6 - - + -
144M LYS* 4.1 4.4 - - - +
94N ASP* 2.6 39.9 + - - +
95N PHE* 4.0 2.9 - - - -
106N GLY* 3.4 22.9 - - - -
107N VAL 3.3 16.6 - - - -
108N CYS* 3.6 17.5 - - + -
124N VAL* 6.1 0.4 - - + -
125N GLY* 1.3 73.3 - - - -
127N GLY* 1.3 70.8 + - - +
128N VAL* 3.7 12.3 - - + -
145N GLU* 3.8 2.4 - - - +
146N ALA* 3.5 10.5 + - - -
149N ASP* 2.8 21.2 + - - +
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Residues in contact with GLY 127 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106N GLY* 3.6 1.4 - - - -
107N VAL 2.7 36.0 + - - -
126N TYR* 1.3 75.9 - - - +
128N VAL* 1.3 67.0 + - - +
142N ALA* 3.3 28.3 - - - +
145N GLU* 4.0 7.2 - - - -
146N ALA* 3.6 5.7 - - - +
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Residues in contact with VAL 128 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136M ALA* 3.7 32.1 - - + -
137M LEU* 5.0 6.7 - - + -
140M GLU* 5.0 9.9 - - - +
105N VAL 3.4 2.7 - - - +
126N TYR* 3.7 19.3 - - + -
127N GLY* 1.3 82.2 - - - +
129N SER* 1.3 62.4 + - - +
130N GLU* 3.8 24.0 - - + +
141N LYS* 2.7 34.7 + - - +
142N ALA* 4.1 3.5 - - - +
145N GLU* 3.7 7.5 + - - +
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Residues in contact with SER 129 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103N PHE 3.3 5.6 - - - +
105N VAL* 2.8 37.8 + - - +
128N VAL* 1.3 78.4 - - - +
130N GLU* 1.3 61.2 + - - +
132N LEU* 3.7 15.8 - - - +
138N SER* 3.4 47.2 + - - -
141N LYS* 4.0 13.5 - - - +
142N ALA* 4.5 0.7 - - - -
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Residues in contact with GLU 130 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134M SER* 3.0 28.4 + - - -
135M LYS 5.0 0.7 + - - -
136M ALA* 3.9 9.3 + - + +
137M LEU* 4.1 7.8 - - - +
95N PHE* 5.7 0.3 - - - -
103N PHE 3.5 2.2 - - - -
104N TYR* 3.5 31.6 - - + +
105N VAL 4.9 0.4 - - - +
128N VAL* 3.8 22.7 - - + +
129N SER* 1.3 80.2 + - - +
131N GLY* 1.3 61.9 + - - +
132N LEU* 3.6 5.6 + - - +
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Residues in contact with GLY 131 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102N LYS* 3.2 39.3 - - - +
103N PHE 3.0 11.9 + - - -
104N TYR* 3.7 10.0 - - - -
130N GLU* 1.3 73.6 - - - +
132N LEU* 1.3 66.8 + - - -
133N LYS* 4.6 1.7 - - - +
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Residues in contact with LEU 132 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102N LYS* 3.3 1.6 - - - -
103N PHE* 2.8 29.5 + - - -
129N SER* 3.7 20.9 - - - +
130N GLU 3.6 4.4 - - - +
131N GLY* 1.3 78.9 - - - +
133N LYS* 1.3 62.2 + - - +
134N SER* 4.0 6.7 - - - +
137N LEU* 4.1 25.4 - - + +
138N SER* 3.5 17.0 + - - +
141N LYS* 5.1 8.1 - - + -
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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