Contacts of the helix formed by residues 123 - 137 (chain A) in PDB entry 3H8E
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 HIS 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ASP* 4.1 15.0 + - - -
121A ASP* 3.0 4.5 + - + -
122A ALA* 1.4 96.0 + - + +
124A TYR* 1.3 66.4 + - - +
127A TYR* 3.2 27.2 - - - +
161A ALA* 4.3 4.2 - - + +
162A ASP* 3.2 28.8 + - - -
164A ALA* 5.0 1.8 - - - +
165A GLY* 3.5 29.9 + - - +
168A GLU* 3.6 22.0 - - + -
169A VAL* 3.7 20.6 - - + +
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Residues in contact with TYR 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ASP* 2.9 19.7 + - - +
123A HIS* 1.3 78.1 - - - +
125A GLY* 1.3 64.1 + - - +
127A TYR 3.2 1.6 + - - -
128A ARG* 2.8 64.7 + - + +
168A GLU* 3.7 17.0 - - + +
171A ARG* 3.4 43.7 + - - +
172A ALA* 3.4 38.3 - - - +
175A HIS* 2.6 30.4 + - - -
489A GLN* 5.0 2.0 + - - -
492A LEU* 4.5 1.9 - - - +
497A ALA 5.2 0.9 + - - -
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Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ARG* 3.8 26.6 - - - -
121A ASP* 2.7 18.5 + - - -
124A TYR* 1.3 84.4 - - - +
126A LYS* 1.3 61.5 + - - +
127A TYR 3.3 0.3 + - - -
128A ARG* 3.4 13.4 + - - +
129A LEU* 3.4 17.5 + - - +
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Residues in contact with LYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A TRP* 2.9 63.8 + - + +
112A LEU 2.9 21.5 + - - -
113A ASP* 3.1 18.0 + - - +
115A VAL 2.7 28.5 + - - +
117A VAL* 4.2 13.7 - - + +
120A ARG* 4.0 9.7 - - + +
121A ASP 3.2 20.1 + - - +
122A ALA* 3.6 24.5 + - - +
125A GLY* 1.3 77.2 - - - +
127A TYR* 1.4 73.4 + - + +
129A LEU* 3.5 1.0 + - - +
130A LEU* 3.2 10.6 + - - +
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Residues in contact with TYR 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A TRP* 5.2 0.4 - + - -
110A LEU* 5.6 1.9 + - + -
112A LEU* 3.9 10.1 + - + +
113A ASP* 3.9 26.8 + - - -
122A ALA 3.3 21.1 - - - -
123A HIS* 3.2 26.0 + - - +
124A TYR 3.2 2.2 + - - -
125A GLY 3.2 0.4 - - - -
126A LYS* 1.4 92.5 + - + +
128A ARG* 1.3 59.2 + - - +
129A LEU 3.2 1.1 - - - -
130A LEU* 3.8 30.7 - - + +
131A ALA* 2.8 33.4 + - - +
159A LEU* 3.8 34.3 - - + +
160A LEU 4.0 11.9 + - - -
161A ALA* 5.2 2.0 - - + -
169A VAL* 3.7 25.8 - - + -
172A ALA* 3.8 11.5 - - + +
173A VAL* 5.5 1.3 - - + -
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Residues in contact with ARG 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A TYR* 2.8 72.6 + - + +
125A GLY* 3.5 11.4 - - - +
127A TYR* 1.3 77.7 - - - +
129A LEU* 1.3 65.8 + - + +
132A GLU* 3.1 38.5 + - - +
172A ALA* 3.5 25.0 - - + +
175A HIS* 3.8 8.3 - - - -
176A ALA* 3.8 7.1 - - - +
179A ILE* 3.5 32.0 - - - +
409A ARG 5.2 3.5 + - - +
410A ALA* 4.0 21.2 + - - +
489A GLN* 2.8 36.9 + - - +
492A LEU* 4.3 5.4 - - - +
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Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ASP* 3.4 41.5 - - + +
89A TRP* 4.0 14.8 - - + -
90A ARG* 3.7 30.1 + - + +
120A ARG* 3.5 28.3 - - - +
125A GLY 3.4 12.4 + - - +
126A LYS 3.8 6.5 - - - +
127A TYR 3.2 0.6 - - - -
128A ARG* 1.3 86.8 - - + +
130A LEU* 1.4 68.1 + - - +
132A GLU* 4.7 2.2 - - - +
133A THR* 3.1 29.5 + - - -
409A ARG 4.3 4.3 - - - +
410A ALA* 4.6 5.6 - - - +
411A ASP* 4.1 10.8 - - + -
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Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 5.1 0.2 - - + -
89A TRP* 3.6 39.1 - - + +
90A ARG* 5.9 0.2 - - - -
93A VAL* 3.7 29.9 - - + +
110A LEU* 4.5 13.2 - - + -
112A LEU* 4.1 13.5 - - + -
126A LYS 3.2 9.9 + - - +
127A TYR* 3.4 19.9 + - + +
129A LEU* 1.4 78.5 - - - +
131A ALA* 1.4 65.2 + - - +
134A LEU* 2.9 36.8 + - + +
159A LEU* 3.8 31.4 - - + -
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Residues in contact with ALA 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 3.8 24.2 - - + -
127A TYR 2.8 22.9 + - - +
130A LEU* 1.4 81.2 - - + +
132A GLU* 1.3 57.5 - - - +
134A LEU* 3.4 1.9 + - - +
135A LEU* 3.0 36.1 + - + +
159A LEU* 5.4 0.4 - - + -
173A VAL* 4.4 13.0 - - + -
176A ALA* 3.4 20.0 - - + -
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Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ARG* 3.6 23.4 + - - +
128A ARG* 3.1 26.0 + - - +
129A LEU* 4.0 2.1 - - - +
131A ALA* 1.3 77.2 - - - +
133A THR* 1.3 56.9 + - - +
135A LEU* 4.9 1.3 - - - -
136A ASP* 2.8 38.3 + - + +
176A ALA* 3.6 16.3 - - + +
179A ILE* 3.9 20.8 - - + +
180A ALA* 5.0 2.5 - - + -
183A MET* 3.3 21.5 - - + +
410A ALA 4.3 11.8 - - - +
485A PRO* 3.1 30.5 - - - +
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Residues in contact with THR 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ARG* 2.8 60.0 + - + +
93A VAL* 3.9 15.3 - - + -
94A ALA* 4.0 16.8 - - + +
129A LEU 3.1 11.8 + - - -
130A LEU* 3.7 3.4 - - - -
132A GLU* 1.3 75.5 - - - +
134A LEU* 1.3 57.8 + - - +
136A ASP* 4.4 2.6 - - - +
137A GLY* 2.9 28.1 + - - -
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 2.6 40.7 - - + +
3A LEU* 4.5 12.1 - - + -
93A VAL* 4.3 9.2 - - + +
96A VAL* 6.4 0.7 - - + -
97A ALA* 3.9 28.9 - - + +
100A LEU* 5.6 2.9 - - + -
110A LEU* 4.4 13.9 - - + -
130A LEU* 2.9 22.4 + - + +
131A ALA* 3.7 4.9 - - - +
133A THR* 1.3 78.9 - - - +
135A LEU* 1.3 60.1 + - + +
137A GLY* 3.8 1.2 + - - -
138A GLU* 3.6 23.8 + - - +
154A LEU* 5.3 4.3 - - + -
157A VAL* 3.8 30.3 - - + -
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.7 46.7 - - + +
3A LEU* 4.6 18.8 - - + -
131A ALA* 3.0 23.5 + - + +
134A LEU* 1.3 73.3 - - - +
136A ASP* 1.3 66.7 + - - +
137A GLY 3.1 1.8 - - - -
138A GLU* 3.1 22.0 + - + +
139A TYR* 4.2 1.6 + - - +
176A ALA 4.3 2.2 - - - +
177A SER* 3.4 42.0 - - - +
180A ALA* 3.6 15.2 - - + +
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Residues in contact with ASP 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLU* 2.8 26.3 + - + +
133A THR* 4.4 2.5 - - - +
135A LEU* 1.3 73.3 - - - +
137A GLY* 1.3 60.1 + - - +
138A GLU 3.1 0.4 - - - -
139A TYR* 3.1 25.6 + - - +
180A ALA* 4.0 13.6 - - + +
183A MET* 3.6 39.1 - - + +
184A ALA* 5.0 0.9 + - - +
187A ARG* 2.8 37.4 + - - -
480A THR 4.6 1.9 - - - +
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Residues in contact with GLY 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LYS* 3.4 28.0 + - - +
133A THR 2.9 20.0 + - - -
134A LEU 4.2 3.6 - - - -
135A LEU 3.1 0.6 - - - -
136A ASP* 1.3 76.4 - - - +
138A GLU* 1.4 58.9 + - - +
139A TYR 3.2 5.6 + - - +
152A ARG* 5.0 1.2 + - - -
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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