Contacts of the helix formed by residues 146 - 161 (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 ALA 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A SER* 4.8 1.8 - - - -
92A GLU* 3.2 6.9 + - - +
93A LYS* 3.5 42.5 + - + +
144A GLY 3.3 5.5 + - - -
145A ASN* 1.3 71.7 - - - +
147A SER* 1.3 64.1 + - - +
149A GLU* 3.9 6.4 - - - +
150A ALA* 3.0 26.2 + - - +
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Residues in contact with SER 147 (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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91A ASP 4.6 6.3 - - - -
92A GLU* 2.7 29.5 + - - -
93A LYS 5.1 0.4 - - - +
114A ASN* 3.6 18.7 - - - +
145A ASN* 4.2 0.2 - - - +
146A ALA* 1.3 78.1 - - - +
148A GLY* 1.3 71.5 + - - +
150A ALA 3.4 0.2 + - - -
151A ARG* 3.1 39.6 + - - +
175A TRP* 3.3 10.2 - - - -
291A ALL 3.1 26.0 + - - -
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Residues in contact with GLY 148 (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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140A GLU* 5.4 2.3 - - - +
141A GLY* 4.6 7.7 + - - -
142A LYS 5.4 1.6 - - - -
145A ASN* 3.2 5.0 + - - -
147A SER* 1.3 81.8 + - - +
149A GLU* 1.3 56.0 + - - +
151A ARG* 3.2 3.0 + - - +
152A ARG* 2.7 35.6 + - - +
175A TRP* 3.6 22.7 - - - -
200A ALA* 4.4 12.8 - - - +
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Residues in contact with GLU 149 (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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140A GLU* 4.5 6.0 - - - +
142A LYS 4.7 1.0 + - - +
143A ALA* 3.7 10.4 - - - +
144A GLY* 2.8 36.2 + - - +
145A ASN 2.9 20.3 + - - +
146A ALA* 3.9 6.5 - - - +
148A GLY* 1.3 76.0 - - - +
150A ALA* 1.3 58.4 + - - +
152A ARG* 3.0 37.9 + - - +
153A ASN* 2.8 40.1 + - - +
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Residues in contact with ALA 150 (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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114A ASN* 3.4 25.4 - - + +
115A VAL* 3.5 26.4 - - + +
146A ALA 3.0 19.3 + - - +
149A GLU* 1.3 76.5 - - - +
151A ARG* 1.3 57.9 + - - +
153A ASN* 3.1 6.9 + - - +
154A GLY 2.8 27.2 + - - -
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Residues in contact with ARG 151 (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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114A ASN* 3.0 49.5 + - - +
117A VAL* 3.8 11.3 - - + +
118A GLY* 3.3 9.2 - - - -
147A SER* 3.1 19.1 + - - +
148A GLY* 3.2 6.3 + - - +
150A ALA* 1.3 74.1 - - - +
152A ARG* 1.3 58.3 + - - +
155A ALA* 2.9 29.3 + - - +
175A TRP* 3.8 13.3 - - - -
198A TYR* 3.5 24.7 - - + +
200A ALA* 2.7 43.1 + - + -
226A THR* 3.8 11.2 - - - +
247A GLN* 3.2 11.3 + - - +
291A ALL 2.8 44.6 + - - -
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Residues in contact with ARG 152 (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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138A ILE* 4.0 13.4 - - + +
140A GLU* 3.1 42.8 - - + +
148A GLY 2.7 21.2 + - - +
149A GLU* 3.0 28.6 + - - +
150A ALA 3.2 0.2 - - - -
151A ARG* 1.3 73.6 - - - +
153A ASN* 1.3 85.8 + - - +
155A ALA* 3.8 0.5 - - - +
156A THR* 2.6 58.3 + - - +
170A SER* 3.8 13.1 + - - +
198A TYR* 5.0 0.2 - - - -
200A ALA* 5.7 0.4 - - - +
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Residues in contact with ASN 153 (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* 5.0 6.5 - - + +
149A GLU* 2.8 30.5 + - - +
150A ALA* 3.6 6.1 - - - +
152A ARG* 1.3 104.5 + - - +
154A GLY* 1.3 62.4 + - - +
156A THR* 4.4 3.5 - - - -
157A GLU* 2.9 52.2 + - - +
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Residues in contact with GLY 154 (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* 3.4 36.4 - - - +
119A ALA* 3.6 12.9 - - - +
150A ALA 2.8 16.2 + - - -
151A ARG 3.8 0.7 - - - -
153A ASN* 1.3 76.2 - - - +
155A ALA* 1.3 59.6 + - - +
157A GLU* 4.2 3.7 - - - +
158A ALA* 3.2 22.9 + - - +
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Residues in contact with ALA 155 (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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118A GLY 3.3 21.8 - - - +
122A ALA* 3.6 11.9 - - + +
138A ILE* 3.9 12.3 - - + -
151A ARG 2.9 19.2 + - - +
154A GLY* 1.3 71.4 - - - +
156A THR* 1.3 60.6 + - - +
158A ALA 3.3 0.9 + - - -
159A PHE* 2.9 39.3 + - + -
198A TYR* 3.9 21.5 - - + -
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Residues in contact with THR 156 (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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138A ILE* 3.2 19.4 - - - +
152A ARG* 2.6 47.9 + - - +
153A ASN* 3.8 4.7 - - - -
155A ALA* 1.3 73.6 - - - +
157A GLU* 1.3 54.3 + - + +
159A PHE* 3.3 5.4 + - - +
160A LYS* 2.7 56.3 + - + +
167A LEU* 3.9 19.3 - - + +
170A SER* 4.8 0.9 + - - -
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Residues in contact with GLU 157 (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* 5.3 7.1 - - - +
153A ASN* 2.9 34.0 + - - +
154A GLY* 4.2 3.6 - - - +
156A THR* 1.3 75.5 - - + +
158A ALA* 1.3 66.1 + - - +
160A LYS* 3.5 6.3 + - - +
161A LYS* 3.4 35.5 + - - +
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Residues in contact with ALA 158 (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* 4.5 13.5 - - + +
122A ALA* 3.7 16.8 - - + -
123A SER* 4.7 2.9 - - - +
126A ILE* 3.8 15.1 - - + +
154A GLY 3.2 20.5 + - - +
155A ALA 3.6 4.0 - - - +
156A THR 3.2 0.2 - - - -
157A GLU* 1.3 78.4 - - - +
159A PHE* 1.3 64.3 + - - +
161A LYS* 3.1 30.0 + - - +
162A ALA* 3.6 3.6 + - - +
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Residues in contact with PHE 159 (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* 3.6 34.5 - - + -
125A ILE* 3.8 30.5 - - + -
126A ILE* 3.8 14.8 - - + -
136A VAL* 3.6 29.8 - - + -
137A ALA 4.8 1.3 - - - -
138A ILE* 4.0 22.9 - - + -
155A ALA* 2.9 26.9 + - + +
156A THR* 3.7 4.9 - - - +
158A ALA* 1.3 74.9 - - - +
160A LYS* 1.3 67.0 + - + +
162A ALA* 3.0 23.6 + - - +
165A ILE* 3.8 25.4 - - + +
167A LEU* 4.1 18.2 - - + -
198A TYR* 4.6 3.8 - - + -
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Residues in contact with LYS 160 (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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156A THR* 2.7 38.1 + - + +
157A GLU* 3.5 6.5 + - - +
158A ALA 3.2 0.6 - - - -
159A PHE* 1.3 76.2 - - - +
161A LYS* 1.3 59.2 + - + +
162A ALA 3.4 3.1 + - - -
163A SER* 4.7 2.6 + - - -
165A ILE 5.9 2.7 - - - +
167A LEU* 4.1 35.5 - - + +
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Residues in contact with LYS 161 (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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157A GLU* 3.4 27.8 + - - +
158A ALA* 3.1 16.6 + - - +
160A LYS* 1.3 77.2 - - - +
162A ALA* 1.3 58.1 + - - +
163A SER* 3.7 4.5 + - - -
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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