Contacts of the strand formed by residues 120 - 130 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26D PHE* 3.9 13.2 - + - -
84D TRP 4.9 0.2 + - - -
85D ALA* 2.9 48.1 - - + +
86D HIS 3.2 27.2 + - - -
87D SER* 3.9 12.9 + - - -
112D ARG* 4.9 5.7 + - - -
114D GLN* 3.2 30.7 + - - +
112E ARG* 3.5 46.0 - - + +
113E VAL 3.2 14.8 - - - +
114E GLN* 4.2 2.0 - - - +
118E GLY 3.2 15.7 - - - -
119E SER* 1.3 77.1 - - - +
121E HIS* 1.3 69.7 + - - +
158E PHE* 4.8 3.3 - - - -
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Residues in contact with HIS 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D TYR 4.4 4.5 - - - -
84D TRP* 3.4 44.3 + + - -
86D HIS* 2.8 41.7 - + + -
112E ARG* 4.5 1.6 - - - -
113E VAL* 3.0 41.7 + - + +
119E SER* 6.2 0.2 - - - -
120E TYR* 1.3 84.5 + - - +
122E GLU* 1.3 61.4 + - - +
154E ALA* 3.7 10.9 - - - +
157E SER* 3.4 34.3 - - - -
158E PHE* 3.6 33.9 - + - -
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Residues in contact with GLU 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D HIS* 3.0 29.9 + - - -
87D SER* 3.5 21.5 - - - -
88D ILE* 3.0 46.6 + - + +
147D VAL* 4.7 0.7 - - - +
89E THR* 2.7 37.0 + - - +
110E PHE* 3.8 7.1 - - - +
111E VAL 3.2 18.4 - - - +
112E ARG* 3.9 13.8 - - + +
121E HIS* 1.3 76.5 - - - +
123E ASP* 1.3 68.4 + - - +
154E ALA* 4.5 1.1 - - - -
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Residues in contact with ASP 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D HIS* 5.0 4.9 + - + +
88D ILE* 3.7 11.3 - - - +
147D VAL* 3.5 16.3 - - - +
148D THR* 5.1 2.8 + - - -
151D LEU* 6.1 0.7 - - - +
109E ALA 3.7 0.2 - - - +
110E PHE* 3.4 4.2 - - - +
111E VAL* 3.0 31.7 + - - +
122E GLU* 1.3 77.3 - - - +
124E VAL* 1.3 71.4 + - - +
150E GLY 4.4 2.2 - - - +
153E ARG* 2.4 53.7 + - + +
154E ALA* 3.7 23.7 - - + +
157E SER* 5.1 2.9 + - - -
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Residues in contact with VAL 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D GLN* 3.9 5.6 - - - +
143D ARG* 3.7 21.1 - - + +
144D LYS* 4.2 4.8 - - + +
147D VAL* 3.2 32.3 - - + -
108E CYS* 4.4 7.6 - - + -
109E ALA 3.2 10.5 - - - +
110E PHE* 3.1 37.0 - - + -
123E ASP* 1.3 86.8 + - - +
125E GLY* 1.3 65.0 + - - +
126E TYR* 6.4 0.2 - - + -
150E GLY* 4.0 2.9 - - - -
153E ARG* 2.9 33.8 + - - +
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Residues in contact with GLY 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D LYS* 4.5 1.1 - - - -
108E CYS* 3.2 6.9 - - - +
109E ALA 2.7 30.4 + - - -
124E VAL* 1.3 77.1 - - - +
126E TYR* 1.3 60.6 + - - +
146E ALA 3.5 7.4 - - - -
149E ASP* 3.4 6.7 - - - -
150E GLY* 3.3 27.2 - - - -
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Residues in contact with TYR 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D ALA 3.6 16.8 - - - -
139D LEU* 3.4 18.9 - - + +
140D GLU* 3.4 45.6 - - + +
143D ARG* 3.8 13.7 - - + -
144D LYS* 4.0 5.3 - - + +
94E ASP* 2.5 36.1 + - - +
95E PHE* 4.0 1.4 - - - -
106E GLY* 3.4 26.1 - - - -
107E VAL 3.2 16.6 - - - -
108E CYS* 3.6 17.7 - - + -
124E VAL* 6.4 0.2 - - + -
125E GLY* 1.3 73.5 - - - -
127E GLY* 1.3 65.7 + - - +
128E VAL* 3.7 15.6 + - + +
145E GLU* 4.0 2.8 - - - +
146E ALA* 3.5 9.2 + - - -
149E ASP* 2.9 21.8 + - - +
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Residues in contact with GLY 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E GLY* 3.6 1.0 - - - -
107E VAL 2.6 37.3 + - - -
126E TYR* 1.3 75.0 - - - +
128E VAL* 1.3 66.3 + - - +
142E ALA* 3.2 29.9 - - - +
145E GLU* 4.1 6.3 - - - -
146E ALA* 3.4 7.2 - - - +
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Residues in contact with VAL 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D ALA* 3.5 33.4 - - + +
137D LEU* 4.7 7.4 - - + -
140D GLU* 4.9 10.8 - - - +
105E VAL 3.4 3.4 - - - +
126E TYR* 3.7 20.4 + - + -
127E GLY* 1.3 79.6 - - - +
129E SER* 1.3 61.9 + - - +
130E GLU* 3.7 24.0 - - + +
141E LYS* 2.8 33.7 + - - +
142E ALA* 4.1 3.3 - - - +
145E GLU* 3.7 8.0 + - - +
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Residues in contact with SER 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E PHE 3.4 5.4 - - - +
104E TYR* 3.4 0.2 - - - -
105E VAL* 2.8 38.8 + - - +
128E VAL* 1.3 77.7 - - - +
130E GLU* 1.3 62.0 + - - +
132E LEU* 3.7 16.1 - - - +
138E SER* 3.3 47.0 + - - -
141E LYS* 3.9 14.2 - - - +
142E ALA* 4.5 0.4 - - - -
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Residues in contact with GLU 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D SER* 2.8 31.3 + - - -
135D LYS 4.8 0.7 + - - -
136D ALA* 3.9 8.6 + - + +
137D LEU* 3.9 10.9 - - - +
95E PHE* 5.8 0.2 - - - -
103E PHE 3.5 2.7 - - - -
104E TYR* 3.6 30.9 - - + +
105E VAL 4.9 0.7 - - - +
128E VAL* 3.7 18.9 - - + +
129E SER* 1.3 80.2 + - - +
131E GLY* 1.3 60.4 + - - +
132E LEU* 3.6 6.4 + - - +
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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