Contacts of the helix formed by residues 147 - 161 (chain B) in PDB entry 2R5S
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 ARG 147 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B MES 3.8 18.6 - - - +
118B LEU* 3.9 11.7 - - - +
143B GLU 3.3 5.5 + - - +
144B LEU* 3.1 39.5 + - - +
146B SER* 1.3 80.5 + - - +
148B GLY* 1.3 69.8 + - - +
149B ASP* 2.8 36.7 + - - +
150B VAL* 2.9 18.3 + - + +
151B LYS* 3.1 8.7 + - - -
178B TYR* 4.5 8.2 + - + +
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Residues in contact with GLY 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B SER 3.6 4.6 + - - -
147B ARG* 1.3 75.1 - - - +
149B ASP* 1.4 59.4 + - - +
151B LYS* 3.5 12.6 + - - +
152B LEU* 3.2 26.7 + - - +
174B ILE* 4.3 1.7 - - - +
175B PRO* 5.0 5.6 - - - -
178B TYR* 3.5 38.4 - - - -
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Residues in contact with ASP 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B MES 3.7 19.7 - - - +
147B ARG* 2.8 50.7 + - - +
148B GLY* 1.4 67.8 - - - +
150B VAL* 1.3 68.3 + - - -
152B LEU* 3.4 12.3 + - - +
153B ALA* 2.9 23.0 + - - +
178B TYR* 3.6 19.6 + - + -
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Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B MES 3.8 21.3 - - - +
118B LEU* 3.9 18.6 - - + -
137B ILE* 3.9 25.5 - - + +
140B LEU* 4.1 6.1 - - + -
144B LEU* 3.3 30.1 - - + +
145B GLN* 3.6 17.5 - - - +
147B ARG* 2.9 16.3 + - + +
149B ASP* 1.3 81.0 + - - +
151B LYS* 1.3 57.5 + - - +
153B ALA* 2.9 5.4 + - - +
154B LYS* 2.8 27.0 + - + +
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Residues in contact with LYS 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B GLN 3.8 15.7 - - - +
146B SER* 3.8 25.8 + - - +
147B ARG 3.1 9.4 + - - +
148B GLY* 3.6 10.3 - - - +
150B VAL* 1.3 76.5 - - - +
152B LEU* 1.3 50.6 + - - +
154B LYS* 3.1 8.0 + - + -
155B ALA* 2.7 32.4 + - - +
170B LEU* 3.4 25.8 - - + +
173B THR* 2.9 45.9 + - - +
174B ILE* 3.5 22.4 - - + -
175B PRO* 4.8 5.2 - - + +
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B GLY 3.2 25.9 + - - +
149B ASP* 3.6 11.4 - - - +
150B VAL 3.3 0.2 - - - -
151B LYS* 1.3 79.4 - - - +
153B ALA* 1.3 62.2 + - - +
155B ALA* 3.4 3.3 + - - -
156B ASP* 3.2 19.1 + - - +
171B LEU* 4.5 3.4 - - + -
174B ILE* 4.2 11.7 - - + -
178B TYR* 3.5 31.4 - - + +
180B ASP* 4.5 3.8 - - - +
182B SER* 4.5 13.7 - - - +
183B TYR* 3.8 41.1 - - + +
186B LEU* 3.5 21.0 - - + +
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B MES 3.8 20.0 - - - +
121B VAL* 4.9 0.2 - - + -
125B LEU* 4.1 22.4 - - + +
137B ILE* 4.8 10.1 - - + -
149B ASP 2.9 13.1 + - - +
150B VAL* 2.9 10.7 + - - +
152B LEU* 1.3 73.2 - - - +
154B LYS* 1.3 66.4 + - - +
156B ASP* 3.4 7.1 + - - +
157B CYS* 3.1 27.9 + - - -
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Residues in contact with LYS 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU* 3.7 21.5 - - + -
137B ILE* 4.3 27.5 - - + +
138B GLN* 6.2 3.8 - - - -
145B GLN* 4.8 14.5 + - + +
150B VAL* 2.8 12.3 + - + +
151B LYS* 3.4 10.3 - - + +
153B ALA* 1.3 77.6 - - - +
155B ALA* 1.3 58.0 + - - +
157B CYS* 3.0 10.0 + - - +
158B LEU* 2.7 40.0 + - + +
170B LEU* 3.6 26.6 - - + +
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Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B LYS 2.7 19.4 + - - +
152B LEU* 3.8 7.2 - - - +
153B ALA 3.3 0.2 - - - -
154B LYS* 1.3 72.9 - - - +
156B ASP* 1.3 55.8 + - - +
158B LEU* 3.4 8.0 + - - +
159B LEU* 3.0 28.9 + - - +
167B ALA* 3.8 5.6 - - - +
170B LEU* 3.6 15.7 - - + +
171B LEU* 3.7 36.8 - - + -
174B ILE* 5.8 0.4 - - + -
186B LEU* 4.3 4.7 - - + -
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Residues in contact with ASP 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A TYR 5.7 0.7 - - - +
125B LEU* 4.0 18.9 - - - +
130B HIS* 4.4 7.4 - - - -
152B LEU 3.2 12.7 + - - +
153B ALA* 3.6 11.0 - - - +
154B LYS 3.2 0.2 - - - -
155B ALA* 1.3 72.1 - - - +
157B CYS* 1.3 61.2 + - - +
159B LEU* 3.5 6.7 + - - +
160B GLU* 2.9 48.1 + - - +
186B LEU* 4.0 24.2 - - + +
189B LYS* 4.8 6.2 + - - -
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Residues in contact with CYS 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B VAL* 6.1 0.2 - - - -
125B LEU* 3.5 25.8 - - - -
130B HIS* 3.8 18.5 - - - +
133B ALA* 3.7 23.1 - - - -
134B LEU* 3.5 26.0 - - + -
137B ILE* 5.5 2.2 - - - -
153B ALA* 3.1 15.3 + - - +
154B LYS* 3.0 9.6 + - - +
156B ASP* 1.3 76.5 - - - +
158B LEU* 1.3 66.5 + - - +
159B LEU 3.2 0.5 + - - -
160B GLU* 3.2 3.8 + - - +
161B THR* 3.0 26.2 + - - -
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LEU* 3.6 21.8 - - + -
154B LYS* 2.7 27.8 + - + +
155B ALA* 3.7 6.5 - - - +
157B CYS* 1.3 71.8 - - - +
159B LEU* 1.3 56.5 + - - +
161B THR* 2.7 23.0 - - - +
162B LYS 2.9 2.4 + - - -
163B GLN* 2.8 34.7 + - - +
166B LEU* 3.5 45.5 - - + +
167B ALA* 3.5 18.4 - - + +
170B LEU* 3.8 24.0 - - + -
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B ALA 3.0 13.8 + - - +
156B ASP* 3.7 4.7 - - - +
157B CYS 3.2 0.2 - - - -
158B LEU* 1.3 76.6 - - - +
160B GLU* 1.3 64.1 + - - +
161B THR 2.9 4.4 + - - -
162B LYS* 3.1 10.6 + - - +
164B PHE* 3.4 33.4 - - + -
167B ALA* 4.3 13.0 - - + -
171B LEU* 5.3 1.3 - - + -
186B LEU* 3.7 50.5 - - + +
189B LYS* 4.1 16.8 - - + +
190B LEU* 4.3 9.9 - - + +
193B HIS* 3.6 34.9 + - + +
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Residues in contact with GLU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A TYR* 4.7 9.4 + - - -
130B HIS* 3.5 49.3 + - + -
156B ASP* 2.9 33.6 + - - +
157B CYS 3.8 1.3 - - - +
159B LEU* 1.3 79.9 - - - +
161B THR* 1.3 58.2 + - - +
162B LYS* 3.2 10.2 - - - +
189B LYS* 4.5 15.7 + - - +
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Residues in contact with THR 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B HIS* 5.1 6.6 - - - +
131B ALA* 5.2 8.0 + - - +
134B LEU* 4.6 8.9 - - + +
157B CYS 3.0 15.0 - - - +
158B LEU* 2.7 26.5 - - - +
159B LEU 2.9 0.4 - - - -
160B GLU* 1.3 77.8 - - - +
162B LYS* 1.3 70.8 - - - +
163B GLN* 2.7 43.4 + - + +
265B LEU* 5.2 12.8 + - - +
269B ASN* 5.2 1.0 + - - -
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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