Contacts of the helix formed by residues 147 - 158 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C ALA* 1.3 78.3 - - - +
148C ARG* 1.3 67.5 + - + +
149C SER 3.7 0.2 - - - -
150C PRO* 3.6 4.1 - - - +
151C VAL* 3.0 29.5 - - - +
173C LEU* 3.8 26.5 - - + -
178C ASP* 4.0 22.7 - - - +
179C ALA 4.6 13.0 - - - +
181C THR* 3.8 22.3 + - - +
184C ALA* 6.0 0.2 - - + -
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Residues in contact with ARG 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C ALA* 4.6 0.4 - - - +
147C VAL* 1.3 81.3 - - + +
149C SER* 1.3 70.6 + - - +
151C VAL* 3.9 1.2 - - - +
152C VAL* 3.3 24.7 + - + +
166C GLU* 4.1 29.9 + - - +
169C THR* 4.0 17.0 - - + +
170C ASP* 2.6 42.6 + - - -
173C LEU* 3.8 20.0 - - + -
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Residues in contact with SER 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C ALA* 4.7 12.4 - - - +
147C VAL 4.8 0.4 - - - +
148C ARG* 1.3 78.1 - - - +
150C PRO* 1.3 76.6 - - - +
152C VAL* 3.1 6.1 + - - +
153C GLU* 3.1 27.1 + - - +
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Residues in contact with PRO 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU* 4.2 13.5 - - + -
146C ALA* 3.2 28.3 - - + +
147C VAL* 3.6 3.4 - - - +
148C ARG 3.5 3.1 - - - -
149C SER* 1.3 94.3 - - - +
151C VAL* 1.3 51.9 - - - +
153C GLU* 2.6 37.6 + - + +
154C ALA* 2.7 16.3 + - - +
181C THR* 4.1 12.8 - - - +
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Residues in contact with VAL 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU* 4.2 3.1 - - + +
147C VAL 3.0 21.8 - - - +
148C ARG* 3.9 4.3 - - - +
149C SER 3.5 0.2 - - - -
150C PRO* 1.3 77.9 - - - +
152C VAL* 1.3 58.1 + - - +
154C ALA* 3.6 10.1 - - - +
155C LEU* 3.2 23.7 + - - +
169C THR* 3.6 25.8 - - + +
173C LEU* 6.0 0.2 - - + -
181C THR* 3.2 32.5 - - - +
184C ALA* 4.0 16.8 - - + +
185C LEU* 3.7 27.1 - - + +
188C ALA* 4.6 2.9 - - + -
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Residues in contact with VAL 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C ARG* 3.3 19.7 + - + +
149C SER* 3.1 10.0 + - - +
150C PRO 2.7 5.5 + - - -
151C VAL* 1.3 70.7 - - - +
153C GLU* 1.3 55.8 + - + +
154C ALA 3.0 1.3 - - - -
155C LEU* 2.9 4.1 + - - +
156C VAL* 2.7 51.9 + - + +
162C ALA* 4.9 2.2 - - + +
165C ALA* 3.3 33.2 - - + +
166C GLU* 4.0 26.5 - - + +
169C THR* 3.7 13.7 - - + +
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Residues in contact with GLU 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C SER* 3.1 18.0 + - - +
150C PRO* 2.6 19.3 + - + +
152C VAL* 1.3 73.2 - - + +
154C ALA* 1.3 51.3 + - - +
156C VAL* 3.4 11.6 - - + +
157C GLY* 2.5 32.2 + - - -
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Residues in contact with ALA 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU* 3.8 16.8 - - + +
15B ASP* 6.5 0.7 - - + -
150C PRO 2.7 10.4 + - - +
151C VAL 3.6 8.1 - - - +
153C GLU* 1.3 78.6 - - - +
155C LEU* 1.3 58.2 + - - +
157C GLY* 3.3 3.1 + - - -
158C LEU* 3.1 30.8 + - - +
185C LEU* 3.4 32.7 - - + +
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Residues in contact with LEU 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C VAL 3.2 10.7 + - - +
152C VAL 2.9 6.1 + - - +
154C ALA* 1.3 73.4 - - - +
156C VAL* 1.3 67.5 + - - +
157C GLY 2.9 1.6 - - - -
158C LEU* 3.0 9.3 + - + +
159C GLY 3.3 0.2 + - - -
160C PHE* 2.9 31.4 + - + +
165C ALA* 3.3 43.1 - - + +
168C ALA* 4.9 0.4 - - + -
169C THR* 3.5 13.0 - - - +
185C LEU* 3.6 17.3 - - + -
188C ALA* 3.9 14.1 - - + -
189C LEU* 3.5 32.8 - - + -
192C LEU* 3.8 17.0 - - + -
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Residues in contact with VAL 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C VAL* 2.7 39.6 + - + +
153C GLU* 3.6 9.4 - - + +
155C LEU* 1.3 71.4 - - - +
157C GLY* 1.3 58.3 + - - +
159C GLY* 3.1 18.0 + - - -
160C PHE 3.1 10.8 - - - +
161C ALA 3.0 25.4 - - - +
162C ALA* 4.4 5.4 - - + -
165C ALA* 4.3 1.8 - - + -
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Residues in contact with GLY 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C GLU 2.5 22.4 + - - -
154C ALA* 3.5 5.8 - - - -
155C LEU 2.9 0.6 - - - -
156C VAL* 1.3 71.7 - - - +
158C LEU* 1.3 58.2 + - - +
159C GLY* 3.0 8.5 + - - -
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Residues in contact with LEU 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ASP* 6.1 5.2 - - + -
32B PRO* 5.0 6.5 - - + -
86B MET* 5.0 4.7 - - + -
87B ALA* 3.7 41.7 - - + +
90B ALA* 3.7 24.5 - - + -
91B VAL* 5.8 0.9 - - + -
113B PRO* 3.7 14.5 - - + +
154C ALA 3.1 14.5 + - - +
155C LEU* 3.0 10.7 + - + +
157C GLY* 1.3 76.6 - - - +
159C GLY* 1.3 56.7 + - - +
160C PHE* 3.5 10.5 - - + -
185C LEU* 5.0 2.9 - - + -
189C LEU* 4.1 28.5 - - + -
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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