Contacts of the helix formed by residues 148 - 163 (chain C) in PDB entry 1H88
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 148 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145C THR* 5.0 7.2 - - + -
146C SER 4.0 7.6 - - - +
147C TRP* 1.3 75.8 - - - +
149C GLU* 1.3 69.5 + - - +
150C GLU* 3.3 8.8 + - - +
151C GLU* 3.1 40.8 + - + +
152C ASP* 2.9 30.5 + - - +
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Residues in contact with GLU 149 (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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147C TRP 4.4 5.4 - - - +
148C THR* 1.3 80.4 - - - +
150C GLU* 1.3 60.4 + - + +
152C ASP* 3.6 5.9 - - - +
153C ARG* 2.8 54.9 + - - +
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Residues in contact with GLU 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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148C THR* 3.3 7.5 + - - +
149C GLU* 1.3 75.5 - - - +
151C GLU* 1.3 63.6 + - + +
153C ARG* 2.8 37.1 + - - +
154C ILE* 2.8 22.3 + - + +
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Residues in contact with GLU 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C THR* 5.9 0.4 - - - -
146C SER 3.8 1.0 - - - +
147C TRP* 3.9 14.3 - - + -
148C THR* 3.1 32.9 + - + +
150C GLU* 1.3 80.2 - - + +
152C ASP* 1.3 64.8 + - - +
153C ARG 3.0 1.4 + - - -
154C ILE* 3.3 4.5 + - - +
155C ILE* 3.1 28.3 + - - +
173C LEU* 3.8 28.5 - - + +
174C PRO* 5.3 4.9 - - - +
175C GLY 5.7 1.2 + - - -
176C ARG* 3.1 42.4 + - - +
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Residues in contact with ASP 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C TRP* 4.7 3.1 - - + +
148C THR 2.9 23.2 + - - +
149C GLU* 3.7 6.7 - - - +
151C GLU* 1.3 76.2 - - - +
153C ARG* 1.3 56.9 + - - +
155C ILE* 3.8 9.4 - - - +
156C TYR* 3.2 26.3 + - - +
184C HIS* 3.0 32.0 + - - +
188C THR* 4.3 4.3 - - - +
189C MET* 3.8 18.6 - - - +
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Residues in contact with ARG 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 GLU* 2.8 42.3 + - - +
150C GLU* 2.8 25.9 + - - +
152C ASP* 1.3 73.8 - - - +
154C ILE* 1.3 54.8 + - + +
155C ILE 2.8 4.6 + - - -
156C TYR* 2.9 9.2 + - + +
157C GLN* 2.6 38.1 + - + +
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Residues in contact with ILE 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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150C GLU* 2.8 22.4 + - + +
151C GLU* 4.0 4.9 - - - +
153C ARG* 1.3 75.1 - - + +
155C ILE* 1.3 53.9 + - - +
157C GLN* 3.2 14.3 - - + +
158C ALA* 2.7 33.5 + - + +
169C ILE* 5.4 0.7 - - + +
172C LEU* 4.1 37.7 - - + +
173C LEU* 4.3 13.9 - - + -
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Residues in contact with ILE 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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147C TRP* 3.3 39.5 - - + -
151C GLU 3.1 17.4 + - - +
152C ASP* 3.8 3.8 - - - +
153C ARG 2.8 0.8 + - - -
154C ILE* 1.3 73.7 - - - +
156C TYR* 1.3 64.8 + - - +
157C GLN 3.0 1.3 + - - -
158C ALA 3.3 0.2 + - - -
159C HIS* 2.8 27.9 + - + +
166C TRP* 5.8 0.2 - - + -
169C ILE* 4.3 23.3 - - + +
173C LEU* 4.4 9.9 - - + -
181C ILE* 4.1 22.9 - - + +
184C HIS* 4.5 8.5 - - + -
185C TRP* 3.7 12.8 - - + -
189C MET* 3.3 23.8 - - + -
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Residues in contact with TYR 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 ASP* 3.2 17.7 + - - +
153C ARG* 2.9 11.0 + - + +
155C ILE* 1.3 77.9 - - - +
157C GLN* 1.3 66.4 + - - +
159C HIS* 4.3 1.0 - - - +
160C LYS* 3.4 31.9 + - + +
185C TRP* 3.7 24.5 - + - -
189C MET* 4.7 11.4 - - + -
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Residues in contact with GLN 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 ARG* 2.6 22.3 + - + +
154C ILE* 3.2 21.5 - - + +
156C TYR* 1.3 79.2 - - - +
158C ALA* 1.3 65.8 + - + +
160C LYS* 3.1 18.6 + - - +
161C ARG* 3.4 26.5 + - - +
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Residues in contact with ALA 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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154C ILE* 2.7 21.7 + - + +
155C ILE 4.0 1.1 - - - +
157C GLN* 1.3 74.4 - - + +
159C HIS* 1.3 55.7 + - - +
161C ARG* 2.7 18.6 + - - +
162C LEU* 2.6 42.5 + - + -
169C ILE* 4.2 21.1 - - + -
172C LEU* 4.5 19.3 - - + -
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Residues in contact with HIS 159 (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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155C ILE 2.8 13.7 + - - +
158C ALA* 1.3 73.8 - - - +
160C LYS* 1.3 60.1 + - - +
163C GLY* 2.8 44.4 + - - +
164C ASN* 3.1 27.6 + - - -
166C TRP* 3.5 20.8 - + - -
169C ILE* 4.3 7.0 - - + +
185C TRP* 3.2 64.1 + + + -
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Residues in contact with LYS 160 (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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156C TYR* 3.4 24.4 + - + +
157C GLN* 3.1 14.6 + - - +
158C ALA 3.0 0.2 - - - -
159C HIS* 1.3 82.9 + - - +
161C ARG* 1.3 61.7 + - - +
163C GLY* 4.7 0.5 + - - -
185C TRP* 5.1 1.3 - - + -
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Residues in contact with ARG 161 (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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157C GLN* 3.4 27.8 + - - +
158C ALA* 2.7 19.2 + - - +
160C LYS* 1.3 83.7 - - - +
162C LEU* 1.3 98.5 + - + +
163C GLY* 3.5 0.3 + - - -
172C LEU* 4.8 13.7 - - - +
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Residues in contact with LEU 162 (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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158C ALA* 2.6 24.6 + - + +
161C ARG* 1.3 112.6 - - + +
163C GLY* 1.3 58.9 + - - +
164C ASN 3.8 0.3 + - - -
165C ARG* 3.2 34.2 - - + +
168C GLU* 3.5 32.8 - - + +
169C ILE* 4.8 8.5 - - + +
172C LEU* 5.3 4.5 - - + -
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Residues in contact with GLY 163 (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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159C HIS* 2.8 46.8 + - - -
160C LYS 5.3 0.4 - - - -
161C ARG 3.4 2.4 - - - -
162C LEU* 1.3 75.3 - - - +
164C ASN* 1.3 61.5 + - - -
165C ARG 3.1 10.3 + - - -
169C ILE* 3.7 7.1 - - - +
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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