Contacts of the helix formed by residues 102 - 117 (chain A) in PDB entry 3H1S
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 SER 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A LEU 4.2 6.0 - - - +
97A ILE* 4.0 10.5 + - - +
100A PHE* 3.2 6.7 + - - +
101A GLY* 1.3 78.2 - - - +
103A VAL* 1.3 61.2 + - - +
104A GLU* 3.8 6.1 + - - +
105A ASN* 3.1 31.6 + - - +
106A PHE* 2.9 27.2 + - - +
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Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A ALA* 6.1 0.7 - - + -
93A LYS* 3.7 31.9 - - + -
96A LEU* 4.3 25.8 - - + -
97A ILE* 4.5 8.8 - - + +
102A SER* 1.3 72.5 - - - +
104A GLU* 1.3 68.0 + - + +
106A PHE* 3.0 10.3 + - - +
107A LYS* 3.0 38.6 + - + +
183A TRP* 5.3 7.2 - - + -
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Residues in contact with GLU 104 (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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102A SER* 3.3 7.2 + - - +
103A VAL* 1.3 81.4 - - + +
105A ASN* 1.3 59.9 + - - +
107A LYS* 3.0 34.2 + - - +
108A GLU* 2.9 38.9 + - - +
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Residues in contact with ASN 105 (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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100A PHE 3.2 26.8 + - - +
101A GLY* 4.4 4.2 - - - -
102A SER* 3.1 26.0 + - - +
104A GLU* 1.3 75.1 - - - +
106A PHE* 1.3 59.4 + - - +
108A GLU* 3.7 16.8 - - - +
109A GLN* 3.0 44.1 + - - +
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Residues in contact with PHE 106 (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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96A LEU* 3.5 32.1 - - + -
100A PHE* 3.8 27.2 - + + +
102A SER 2.9 13.4 + - - +
103A VAL* 3.3 9.6 - - + +
105A ASN* 1.3 77.7 - - - +
107A LYS* 1.3 66.9 + - + +
109A GLN 3.4 0.3 + - - -
110A PHE* 2.8 59.0 + + + +
125A LEU* 3.6 35.7 - - + -
135A ILE* 4.1 6.3 - - + -
153A LEU* 4.3 5.2 - - + -
178A TRP* 3.7 18.6 - + - -
183A TRP* 3.9 21.5 - + - -
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Residues in contact with LYS 107 (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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103A VAL* 3.0 22.6 + - + +
104A GLU* 3.0 40.2 + - - +
106A PHE* 1.3 77.2 - - + +
108A GLU* 1.3 64.4 + - - +
111A SER* 2.8 31.7 + - - -
178A TRP* 3.0 71.4 - - + +
183A TRP* 4.5 13.2 - - + +
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Residues in contact with GLU 108 (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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104A GLU* 2.9 23.2 + - - +
105A ASN* 3.7 20.1 - - - +
107A LYS* 1.3 74.9 - - - +
109A GLN* 1.3 60.3 + - + +
111A SER* 3.0 8.0 + - - -
112A LYS* 2.8 29.4 + - - +
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Residues in contact with GLN 109 (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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100A PHE* 3.6 42.6 + - - +
105A ASN* 3.0 25.1 + - - +
106A PHE* 4.0 1.6 - - - +
108A GLU* 1.3 78.8 - - + +
110A PHE* 1.3 57.6 + - - +
112A LYS* 3.4 8.9 + - - +
113A ALA* 2.9 29.1 + - - +
135A ILE* 3.8 14.9 - - + +
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Residues in contact with PHE 110 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A PHE* 2.8 42.1 + + + +
107A LYS 3.9 2.9 - - - +
109A GLN* 1.3 76.2 - - - +
111A SER* 1.3 59.3 + - - +
113A ALA* 3.3 3.3 + - - +
114A ALA* 2.9 28.1 + - - +
123A ALA* 3.5 27.8 - - + +
124A TRP 3.3 31.4 - - - -
125A LEU* 3.4 8.1 - - + -
135A ILE* 3.6 17.6 - - + +
153A LEU* 4.0 15.7 - - + -
155A PHE* 3.6 36.1 - + - -
178A TRP* 3.6 21.5 - + + -
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Residues in contact with SER 111 (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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107A LYS 2.8 22.6 + - - -
108A GLU* 3.5 5.4 - - - -
110A PHE* 1.3 74.2 - - - +
112A LYS* 1.3 67.1 + - - +
114A ALA* 3.3 1.6 + - - +
115A ILE* 2.9 37.1 + - - +
174A VAL* 3.6 20.7 - - - +
175A GLU* 5.3 1.0 + - - -
178A TRP* 3.0 25.7 + - - -
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Residues in contact with LYS 112 (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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108A GLU 2.8 13.5 + - - +
109A GLN* 3.7 11.9 - - - +
111A SER* 1.3 74.6 - - - +
113A ALA* 1.3 57.5 + - - +
115A ILE* 3.2 8.5 + - - +
116A ALA* 2.9 36.2 + - + +
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A GLN 2.9 18.1 + - - +
110A PHE 3.6 4.7 - - - +
111A SER 3.2 0.2 - - - -
112A LYS* 1.3 75.4 - - - +
114A ALA* 1.3 64.0 + - - +
116A ALA* 3.3 5.5 + - - +
117A THR* 3.0 27.8 + - - -
123A ALA* 5.0 2.0 - - + -
135A ILE* 3.7 25.6 - - + -
137A THR* 3.9 16.7 - - + +
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Residues in contact with ALA 114 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A PHE 2.9 17.0 + - - +
111A SER 3.7 4.0 - - - +
113A ALA* 1.3 80.2 - - - +
115A ILE* 1.3 57.6 - - - +
116A ALA 3.6 0.2 + - - -
117A THR* 3.6 5.9 + - - -
123A ALA* 3.8 23.1 - - + +
155A PHE* 4.2 8.1 - - + -
157A VAL* 3.6 17.7 - - + +
170A ARG* 2.9 22.5 + - - -
174A VAL* 3.9 24.0 - - + -
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Residues in contact with ILE 115 (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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111A SER* 2.9 32.3 + - - +
112A LYS* 3.8 7.2 - - - +
114A ALA* 1.3 77.3 - - - +
116A ALA* 1.3 61.9 + - - +
117A THR 4.0 0.7 - - - +
170A ARG* 3.3 20.6 + - + +
171A PRO* 3.9 50.5 - - + +
174A VAL* 4.1 13.2 - - + -
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Residues in contact with ALA 116 (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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112A LYS* 2.9 24.3 + - + +
113A ALA* 4.0 5.8 - - - +
115A ILE* 1.3 76.6 - - + +
117A THR* 1.3 64.2 + - - +
118A PHE* 3.2 8.0 + - - +
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Residues in contact with THR 117 (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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113A ALA 3.0 16.0 + - - -
114A ALA* 3.7 12.3 + - - -
115A ILE 3.3 2.1 - - - +
116A ALA* 1.3 74.2 - - - +
118A PHE* 1.3 71.2 + - - +
119A GLY 4.5 1.6 - - - +
120A SER 4.8 0.7 - - - +
121A GLY* 4.3 5.8 - - - -
122A TRP 4.4 3.1 + - - +
137A THR* 3.4 24.5 - - - +
138A THR 4.2 20.2 - - - +
139A SER* 5.6 0.9 - - - -
157A VAL* 3.9 21.2 - - + +
170A ARG* 2.7 28.2 + - - -
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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