Contacts of the helix formed by residues 114 - 129 (chain A) in PDB entry 1RPJ
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 ASN 114 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ASP* 4.3 3.4 + - - -
109A PHE* 6.1 0.2 - - - -
111A THR* 3.4 14.5 + - - +
112A THR* 2.9 26.8 + - - +
113A ASP* 1.3 69.1 + - - +
115A VAL* 1.3 63.3 - - - +
117A VAL* 3.8 11.2 - - - +
118A GLY 3.1 16.8 + - - -
147A SER* 3.6 22.5 - - - +
150A ALA* 3.4 24.2 - - + +
151A ARG* 3.0 50.6 + - + +
247A GLN* 5.1 0.2 + - - -
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Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASP* 3.0 9.5 + - - +
114A ASN* 1.3 74.5 - - - +
116A ALA* 1.3 57.9 + - - +
118A GLY 3.1 2.3 + - - -
119A ALA* 2.9 26.9 + - + +
150A ALA* 3.5 28.4 - - + +
153A ASN* 5.0 5.6 - - + +
154A GLY* 3.4 20.1 - - - +
157A GLU* 5.3 7.0 - - - +
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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
----------------------------------------------------------
113A ASP* 3.0 32.6 + - + +
115A VAL* 1.3 74.3 - - - +
117A VAL* 1.4 59.9 + - - +
119A ALA* 3.2 7.4 + - - +
120A LYS* 2.8 49.6 + - + +
283A SER* 5.3 1.8 - - - +
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Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A THR* 3.5 24.0 - - + -
113A ASP 3.1 14.7 + - - +
114A ASN* 3.5 17.9 - - - +
116A ALA* 1.4 76.2 - - - +
118A GLY* 1.4 63.7 + - - +
120A LYS* 3.3 1.8 + - - +
121A GLY* 3.0 18.7 + - - -
151A ARG* 3.8 7.2 - - + +
198A TYR* 3.5 7.7 + - - +
226A THR* 3.4 39.3 - - + +
245A VAL* 3.6 19.1 - - + +
247A GLN* 5.1 2.5 - - + -
283A SER* 3.9 14.8 + - - +
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Residues in contact with GLY 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASN 3.1 9.3 + - - -
115A VAL 3.7 0.9 - - - -
117A VAL* 1.4 79.9 - - - +
119A ALA* 1.3 57.8 + - - +
121A GLY* 3.4 0.9 + - - -
122A ALA 2.9 24.4 + - - -
151A ARG* 3.3 27.6 - - - +
155A ALA* 3.3 20.8 - - - +
198A TYR* 4.1 10.9 - - - -
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Residues in contact with ALA 119 (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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115A VAL* 2.9 18.8 + - + +
116A ALA* 3.7 8.5 - - - +
118A GLY* 1.3 76.0 - - - +
120A LYS* 1.3 55.7 + - - +
122A ALA* 4.0 0.3 - - - +
123A SER* 2.8 37.2 + - - -
154A GLY* 3.6 17.6 - - - +
158A ALA* 4.5 9.0 - - + +
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Residues in contact with LYS 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ALA* 2.8 37.4 + - - +
117A VAL 3.6 4.3 - - - +
119A ALA* 1.3 69.3 - - - +
121A GLY* 1.3 66.5 + - - +
123A SER* 3.8 3.9 - - - -
124A PHE* 2.9 26.0 + - - +
245A VAL* 4.1 17.5 - - + -
283A SER* 3.0 48.1 + - - +
284A ILE* 4.2 2.6 - - - +
285A LEU* 4.6 20.1 - - + +
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Residues in contact with GLY 121 (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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117A VAL 3.0 14.3 + - - -
118A GLY 3.9 2.2 - - - -
120A LYS* 1.3 77.4 - - - +
122A ALA* 1.3 60.8 + - - +
124A PHE* 3.5 5.5 + - - +
125A ILE* 3.1 31.4 + - - +
198A TYR* 4.2 7.9 - - - -
224A VAL* 4.1 14.9 - - - +
245A VAL* 3.8 14.2 - - - +
285A LEU* 5.0 1.3 - - - -
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Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLY 2.9 18.0 + - - +
119A ALA 4.0 0.2 - - - +
121A GLY* 1.3 73.7 - - - +
123A SER* 1.3 60.6 - - - +
125A ILE* 3.2 3.7 + - - +
126A ILE* 2.8 34.7 + - - +
155A ALA* 3.6 29.5 - - + +
158A ALA* 3.7 12.3 - - + -
159A PHE* 3.6 26.0 - - + -
198A TYR* 4.8 1.0 - - - -
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Residues in contact with SER 123 (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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119A ALA 2.8 24.4 + - - -
120A LYS* 3.8 5.4 - - - -
122A ALA* 1.3 73.6 - - - +
124A PHE* 1.3 61.7 + - - +
126A ILE* 3.3 12.1 + - - +
127A ASP* 2.9 35.1 + - - +
158A ALA* 4.7 3.6 - - - +
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Residues in contact with PHE 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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120A LYS 2.9 17.1 + - - +
121A GLY 3.7 2.2 - - - +
123A SER* 1.3 78.2 - - - +
125A ILE* 1.3 66.7 + - + +
127A ASP* 3.2 11.1 + - + +
128A LYS* 2.9 59.0 + - + +
222A LEU* 5.2 0.9 - - + -
224A VAL* 3.9 18.4 - - + -
242A THR* 3.5 33.7 - - + -
243A ALA* 3.7 17.7 - - + -
285A LEU* 3.6 31.0 - - + -
287A THR* 3.5 21.5 - - + -
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Residues in contact with ILE 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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121A GLY 3.1 20.2 + - - +
122A ALA 3.5 5.6 - - - +
124A PHE* 1.3 78.5 - - + +
126A ILE* 1.3 66.5 + - + +
128A LYS* 3.1 1.7 + - - +
129A LEU* 2.9 28.5 + - + +
136A VAL* 4.0 8.7 - - + -
159A PHE* 3.8 22.9 - - + -
165A ILE* 5.2 0.2 - - + -
196A ALA* 3.4 34.5 - - + -
197A ILE 4.1 1.3 - - - +
198A TYR* 3.9 35.4 - - + +
222A LEU* 4.4 8.5 - - + -
224A VAL* 3.7 24.5 - - + -
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Residues in contact with ILE 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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122A ALA 2.8 29.4 + - - +
123A SER* 3.6 9.6 - - - +
124A PHE 3.2 0.2 - - - -
125A ILE* 1.3 74.8 - - - +
127A ASP* 1.3 68.0 - - - +
129A LEU* 3.4 3.2 + - - +
130A GLY* 3.2 19.4 + - - +
158A ALA* 3.8 27.8 - - + +
159A PHE* 3.8 22.7 - - + -
162A ALA* 4.1 10.8 - - + -
164A GLN* 3.7 23.9 + - - +
165A ILE* 4.0 17.0 - - + +
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Residues in contact with ASP 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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123A SER* 2.9 25.8 + - - +
124A PHE* 3.4 14.5 - - + +
126A ILE* 1.3 81.7 - - - +
128A LYS* 1.3 65.7 + - - +
130A GLY* 3.0 20.1 + - - -
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Residues in contact with LYS 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 PHE* 2.9 57.9 + - + +
125A ILE 3.8 0.2 - - - +
127A ASP* 1.3 82.2 - - - +
129A LEU* 1.3 64.1 + - - +
130A GLY* 3.4 0.7 + - - -
222A LEU* 3.6 23.6 - - + -
242A THR* 5.0 3.1 - - + -
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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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125A ILE* 2.9 24.4 + - + +
126A ILE 3.9 4.0 - - - +
128A LYS* 1.3 78.5 - - - +
130A GLY* 1.3 64.2 + - - +
132A GLU* 4.0 5.4 + - - +
133A GLY* 3.5 34.4 + - - +
134A GLY* 4.3 0.9 - - - +
136A VAL* 3.9 27.4 - - + -
165A ILE* 3.9 14.6 - - + -
195A LYS* 3.7 32.8 - - + +
196A ALA* 4.3 0.9 - - + -
222A LEU* 3.8 20.6 - - + -
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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