Contacts of the helix formed by residues 147 - 158 (chain B) in PDB entry 2H5X
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 VAL 147 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146B ALA* 1.3 82.9 - - - +
148B ARG* 1.3 67.4 + - - +
149B SER 4.6 0.2 - - - +
150B PRO* 3.4 4.1 - - - +
151B VAL* 2.9 38.9 + - + +
173B LEU* 3.8 33.9 - - + -
178B ASP* 6.1 4.5 - - + -
179B ALA 5.5 8.1 - - - +
180B THR* 4.8 3.4 - - - +
181B THR* 3.6 26.2 - - + +
184B ALA* 4.7 1.3 - - + -
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Residues in contact with ARG 148 (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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147B VAL* 1.3 88.7 - - + +
149B SER* 1.3 67.6 + - - +
151B VAL* 3.1 2.4 + - - +
152B VAL* 3.0 30.5 + - + +
166B GLU* 3.5 31.3 + - - +
169B THR* 4.2 17.0 - - + -
170B ASP* 2.8 42.1 + - - +
173B LEU* 4.2 11.7 - - + -
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Residues in contact with SER 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ALA* 6.1 1.8 - - - -
147B VAL 4.6 0.2 - - - +
148B ARG* 1.3 80.3 - - - +
150B PRO* 1.3 57.8 - - - +
152B VAL* 3.0 9.5 + - - +
153B GLU* 2.6 48.9 + - - +
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Residues in contact with PRO 150 (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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14A LEU* 4.1 12.4 - - + +
146B ALA* 3.8 24.0 - - + +
147B VAL* 3.4 19.5 - - - +
149B SER* 1.3 94.7 - - - +
151B VAL* 1.3 50.5 + - - +
153B GLU* 2.8 12.3 + - + +
154B ALA* 2.7 35.0 + - - +
181B THR* 4.1 12.8 - - + -
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 4.4 6.3 - - + -
147B VAL* 2.9 24.0 + - + +
148B ARG 3.1 4.1 + - - +
150B PRO* 1.3 74.5 - - - +
152B VAL* 1.3 62.0 + - - +
154B ALA* 3.3 2.9 + - - +
155B LEU* 2.9 29.8 + - + +
169B THR* 3.8 24.0 - - + +
181B THR* 3.5 34.8 - - - +
184B ALA* 3.9 14.4 - - + +
185B LEU* 3.7 28.5 - - + +
188B ALA* 4.6 0.4 - - + -
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Residues in contact with VAL 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 ARG* 3.0 27.4 + - + +
149B SER* 3.4 8.1 - - - +
151B VAL* 1.3 75.1 - - - +
153B GLU* 1.3 57.6 + - - +
155B LEU* 2.9 6.8 + - - +
156B VAL* 2.7 47.7 + - + +
162B ALA* 4.4 4.9 - - + +
165B ALA* 3.7 19.5 - - + -
166B GLU* 4.0 27.8 - - + +
169B THR* 3.8 22.0 - - + +
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Residues in contact with GLU 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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149B SER* 2.6 35.7 + - - +
150B PRO* 2.9 17.7 - - + +
152B VAL* 1.3 75.4 - - - +
154B ALA* 1.3 54.2 - - - +
156B VAL* 3.3 13.8 + - - +
157B GLY* 2.8 24.3 + - - -
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Residues in contact with ALA 154 (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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14A LEU* 4.0 18.4 - - + +
15A ASP* 6.0 3.1 - - + -
150B PRO 2.7 16.8 + - - +
151B VAL 3.7 4.5 - - - +
152B VAL 3.2 0.2 - - - -
153B GLU* 1.3 70.9 - - - +
155B LEU* 1.3 62.3 + - - +
157B GLY* 3.1 2.7 + - - -
158B LEU* 2.8 36.2 + - + +
185B LEU* 3.9 28.3 - - + -
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Residues in contact with LEU 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 VAL* 2.9 18.8 + - + +
152B VAL 3.4 4.0 - - - +
154B ALA* 1.3 73.6 - - - +
156B VAL* 1.3 62.6 + - - +
158B LEU* 3.5 5.4 + - + +
160B PHE* 2.9 38.5 + - + +
165B ALA* 3.8 24.0 - - + +
168B ALA* 5.0 0.2 - - + -
169B THR* 3.5 24.0 - - - +
185B LEU* 3.9 15.3 - - + -
188B ALA* 3.9 14.1 - - + -
189B LEU* 3.5 34.3 - - + +
192B LEU* 3.7 25.1 - - + -
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Residues in contact with VAL 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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152B VAL* 2.7 38.1 + - + +
153B GLU* 3.5 15.5 - - - +
155B LEU* 1.3 74.2 - - - +
157B GLY* 1.3 60.9 + - - +
159B GLY* 2.9 21.3 + - - -
160B PHE 3.3 17.8 + - - +
162B ALA* 4.2 20.2 - - + +
165B ALA* 4.5 2.2 - - + -
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Residues in contact with GLY 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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153B GLU 2.8 15.4 + - - -
154B ALA* 3.1 6.5 + - - -
156B VAL* 1.3 79.5 - - - +
158B LEU* 1.3 57.0 + - - +
159B GLY* 3.2 4.7 + - - -
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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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15A ASP* 6.3 3.4 - - + -
32A PRO* 5.0 7.6 - - + -
83A ARG 5.8 0.2 - - - +
86A MET* 5.0 4.3 - - + -
87A ALA* 3.7 37.5 - - + +
90A ALA* 3.8 32.1 - - + -
91A VAL* 5.8 0.7 - - + -
113A PRO* 3.9 11.4 - - - +
154B ALA* 2.8 21.9 + - + +
155B LEU* 3.5 7.4 + - + +
156B VAL 3.2 0.6 - - - -
157B GLY* 1.3 75.0 - - - +
159B GLY* 1.3 58.7 + - - +
160B PHE* 3.6 10.5 - - + -
185B LEU* 5.0 2.5 - - + -
189B LEU* 4.0 26.0 - - + -
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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