Contacts of the helix formed by residues 149 - 162 (chain A) in PDB entry 1RI4
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 THR 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A ALA 4.2 0.7 - - - +
147A PHE 4.5 2.1 - - - -
148A SER* 1.3 90.9 + - - +
150A SER* 1.3 66.0 + - - +
151A GLU* 3.5 11.5 + - - +
152A SER* 2.9 31.7 + - - +
153A LEU* 3.0 13.2 + - - +
210A ARG* 4.1 10.1 - - - +
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Residues in contact with SER 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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149A THR* 1.3 73.3 - - - +
151A GLU* 1.3 80.3 + - - +
153A LEU* 3.5 7.1 + - - +
154A ASP* 3.1 23.2 + - - +
210A ARG* 5.0 2.6 - - - +
232A ARG* 3.1 39.5 - - - +
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Residues in contact with GLU 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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149A THR* 3.1 9.3 - - - +
150A SER* 1.3 96.5 + - - +
152A SER* 1.3 59.3 - - - +
154A ASP* 3.4 8.0 + - - +
155A ILE* 2.9 44.4 + - + +
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Residues in contact with SER 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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124A TYR 3.2 8.5 - - - +
125A GLY* 4.1 21.7 - - - -
146A ALA* 3.4 15.1 - - - +
148A SER* 3.7 14.2 + - - -
149A THR* 2.9 27.2 + - - +
151A GLU* 1.3 77.6 - - - +
153A LEU* 1.3 59.1 + - - +
155A ILE* 4.6 2.0 - - - -
156A ALA* 3.0 26.3 + - - +
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Residues in contact with LEU 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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143A PHE* 4.5 8.5 - - + -
146A ALA* 3.2 13.8 + - + +
147A PHE* 3.7 48.9 - - + -
149A THR 3.0 9.9 + - - +
150A SER* 3.7 8.7 - - - +
151A GLU 3.2 0.2 - - - -
152A SER* 1.3 75.5 - - - +
154A ASP* 1.3 59.6 + - - +
156A ALA* 3.3 1.4 + - - +
157A GLN* 2.8 59.5 + - + +
232A ARG* 3.6 42.2 - - + +
233A MET* 4.7 1.1 - - + +
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Residues in contact with ASP 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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150A SER 3.1 14.9 + - - +
151A GLU* 3.7 9.8 - - - +
153A LEU* 1.3 79.9 - - - +
155A ILE* 1.3 64.1 + - - +
157A GLN* 4.0 9.1 - - - +
158A ARG* 2.9 66.8 + - - +
239A ARG* 4.9 1.9 + - - -
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Residues in contact with ILE 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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124A TYR 3.2 17.3 - - - +
125A GLY* 4.0 16.4 - - - +
126A ARG* 3.6 29.2 - - - +
127A HIS* 3.8 6.5 - - + +
151A GLU* 2.9 30.2 + - + +
152A SER* 3.9 1.3 - - - +
154A ASP* 1.3 81.3 - - - +
156A ALA* 1.3 60.4 + - - +
158A ARG* 3.2 8.4 + - - +
159A ASN* 3.0 24.5 + - - +
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Residues in contact with ALA 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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123A SER 4.2 5.1 - - - +
124A TYR* 3.1 30.7 + - + +
143A PHE* 4.4 8.7 - - + -
146A ALA* 3.8 19.5 - - + -
152A SER 3.0 20.0 + - - +
153A LEU 3.7 2.9 - - - +
155A ILE* 1.3 76.0 - - - +
157A GLN* 1.3 63.7 + - - +
159A ASN* 3.0 13.2 + - - +
160A ILE* 3.1 18.3 + - - +
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Residues in contact with GLN 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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143A PHE* 4.5 2.5 - - + -
153A LEU* 2.8 48.0 + - + +
154A ASP* 4.0 7.3 - - - +
156A ALA* 1.3 72.8 - - - +
158A ARG* 1.3 61.5 + - - +
160A ILE* 3.4 4.0 + - - +
161A ALA* 3.1 18.0 + - - +
232A ARG* 4.3 1.9 - - - +
233A MET* 2.9 36.5 + - - +
236A GLY* 3.5 19.4 - - - -
237A PHE* 3.2 45.9 - - + +
240A LEU* 3.2 18.2 - - + +
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Residues in contact with ARG 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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154A ASP* 2.9 56.8 + - - +
155A ILE* 3.5 7.9 - - - +
156A ALA 3.1 0.2 - - - -
157A GLN* 1.3 76.3 - - - +
159A ASN* 1.3 64.8 + - - +
161A ALA* 3.5 3.1 + - - +
162A ARG* 3.2 42.6 + - - +
239A ARG* 3.4 31.0 - - - +
240A LEU* 3.9 26.7 - - + +
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Residues in contact with ASN 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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69A LEU* 5.7 0.2 - - - +
71A LEU* 6.2 1.1 - - + -
123A SER 3.1 23.7 + - - +
126A ARG 2.8 28.9 + - - -
127A HIS* 3.7 4.9 - - - -
128A MET* 3.1 28.6 + - + +
155A ILE* 3.0 22.4 + - - +
156A ALA 3.0 7.2 + - - +
158A ARG* 1.3 74.2 - - - +
160A ILE* 1.3 65.5 + - + +
162A ARG* 2.5 32.9 + - - +
163A HIS* 2.7 30.5 + - - +
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Residues in contact with ILE 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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69A LEU* 6.4 0.2 - - - -
71A LEU* 3.9 22.7 - - + -
123A SER 6.1 0.2 - - - +
124A TYR* 5.9 0.4 - - + -
137A ILE* 3.4 15.8 - - + +
143A PHE* 3.5 23.6 - - + -
156A ALA* 3.1 11.1 + - + +
157A GLN 3.7 6.5 - - - +
158A ARG 3.3 0.2 - - - -
159A ASN* 1.3 78.7 - - + +
161A ALA* 1.3 63.9 + - - +
163A HIS 3.2 1.9 + - - -
164A LEU* 3.2 23.4 + - + +
170A PHE* 3.3 56.1 - - + -
237A PHE* 3.9 9.0 - - + -
242A LEU* 4.2 16.6 - - + -
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Residues in contact with ALA 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 GLN 3.1 13.6 + - - +
158A ARG* 4.0 3.6 - - - +
159A ASN 3.4 0.2 - - - -
160A ILE* 1.3 81.7 - - - +
162A ARG* 1.3 56.3 + - - +
163A HIS 3.2 1.1 + - - -
164A LEU* 3.5 5.6 + - - +
240A LEU* 3.9 33.2 - - + +
242A LEU* 4.1 19.5 - - + -
291A LYS* 2.7 32.0 + - - +
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Residues in contact with ARG 162 (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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127A HIS* 3.3 29.5 + - - -
128A MET 2.8 27.3 + - - -
129A ASP* 4.5 15.3 - - - -
132A LYS 4.5 1.6 - - - +
133A GLU* 4.3 14.5 - - - +
158A ARG* 3.2 33.3 + - - +
159A ASN* 2.5 35.5 + - - +
161A ALA* 1.3 75.3 - - - +
163A HIS* 1.3 79.9 + - + +
164A LEU 3.5 0.9 - - - -
291A LYS* 4.9 1.1 - - - +
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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