Contacts of the helix formed by residues 150 - 162 (chain C) in PDB entry 1D2H
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 GLN 150 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145C ASP* 3.5 15.8 + - - +
148C GLY 5.6 0.2 - - - +
149C ASP* 1.3 70.1 - - - +
151C SER* 1.3 55.3 + - - +
152C GLU 3.1 1.6 - - - -
153C HIS* 2.6 52.7 + - + +
154C ARG* 2.7 46.1 + - - +
243C TYR* 3.6 20.7 + - - -
245C HIS* 4.9 0.8 + - - -
249C SER* 3.7 21.4 + - - -
253C LEU* 4.3 14.3 - - + +
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Residues in contact with SER 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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147C LYS* 3.2 24.0 - - - +
149C ASP* 2.6 33.3 + - - +
150C GLN* 1.3 72.4 - - - +
152C GLU* 1.3 74.2 + - - +
154C ARG* 3.2 11.9 + - - +
155C LEU* 3.0 23.1 + - - +
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Residues in contact with GLU 152 (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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118C LEU* 3.7 24.4 - - + +
143C LEU* 4.3 10.8 - - + +
144C PRO* 3.1 28.7 - - - +
145C ASP* 4.9 2.0 - - - -
146C SER* 3.4 25.0 + - - +
147C LYS* 4.2 22.4 - - + +
149C ASP 3.8 3.1 + - - +
150C GLN 3.1 0.4 - - - -
151C SER* 1.3 88.2 + - - +
153C HIS* 1.3 66.7 + - - +
155C LEU* 3.3 9.8 + - - +
156C ALA* 3.0 22.3 + - - +
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Residues in contact with HIS 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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140C PHE* 4.6 4.7 - + - -
143C LEU* 3.2 35.9 + - + +
144C PRO 3.9 16.4 + - - -
145C ASP* 3.9 9.3 - - + +
150C GLN* 2.6 33.9 + - + +
152C GLU* 1.3 72.3 - - - +
154C ARG* 1.3 60.3 + - - +
156C ALA* 3.0 7.2 + - - +
157C LEU* 2.8 38.4 + - + +
243C TYR* 3.5 12.9 - + - -
245C HIS* 3.3 38.4 + + - -
253C LEU* 3.8 19.7 - - + -
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Residues in contact with ARG 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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149C ASP* 6.0 0.4 - - - +
150C GLN* 2.7 44.7 + - - +
151C SER* 3.6 11.1 - - - +
153C HIS* 1.3 73.0 - - - +
155C LEU* 1.3 54.6 + - - +
157C LEU* 4.0 4.8 - - - +
158C LYS* 2.7 42.4 + - + +
252C GLU* 5.2 7.9 + - - -
253C LEU* 3.2 22.0 - - + +
256C GLU* 2.8 39.9 + - - +
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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
----------------------------------------------------------
118C LEU* 3.4 39.3 - - + +
121C ASP* 5.2 1.8 - - - +
151C SER 3.0 12.1 + - - +
152C GLU* 3.5 10.8 - - - +
154C ARG* 1.3 76.0 - - - +
156C ALA* 1.3 58.5 + - - +
158C LYS* 4.1 17.5 - - - +
159C ASN* 2.8 67.2 + - - +
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Residues in contact with ALA 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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117C TRP* 3.9 13.6 - - + +
118C LEU* 3.9 9.2 - - + -
140C PHE* 3.6 20.4 - - + -
143C LEU* 3.7 20.4 - - + -
152C GLU 3.0 12.0 + - - +
153C HIS 3.0 9.7 + - - +
155C LEU* 1.3 73.5 - - - +
157C LEU* 1.3 69.9 + - - +
159C ASN* 3.1 11.8 + - - +
160C ILE* 3.2 18.6 + - - +
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Residues in contact with LEU 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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140C PHE* 3.0 40.8 - - + -
153C HIS 2.8 38.9 + - - +
154C ARG* 4.0 4.0 - - - +
156C ALA* 1.3 74.3 - - - +
158C LYS* 1.3 63.5 + - - +
160C ILE* 3.0 5.5 + - - +
161C ALA* 3.0 23.2 + - - +
170C LEU* 6.1 0.4 - - + +
172C ILE* 4.0 15.5 - - + -
250C PHE* 3.9 15.0 - - + -
253C LEU* 3.8 26.0 - - + +
254C VAL* 4.3 20.9 - - + +
256C GLU* 5.2 0.4 - - - +
257C ALA* 3.8 17.3 - - + +
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Residues in contact with LYS 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 ARG* 2.7 26.8 + - + +
155C LEU* 3.6 21.5 - - - +
157C LEU* 1.3 73.6 - - - +
159C ASN* 1.3 70.3 + - - +
161C ALA* 3.6 2.4 + - - +
162C SER* 3.3 21.6 + - - -
256C GLU* 4.9 6.7 - - - +
257C ALA* 4.1 19.5 - - - +
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Residues in contact with ASN 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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117C TRP 2.6 29.2 - - - +
118C LEU 2.9 22.9 - - - +
119C THR 3.7 0.7 + - - -
120C LEU* 2.7 26.1 - - + +
121C ASP* 3.5 21.2 + - - +
155C LEU* 2.8 39.2 + - - +
156C ALA 3.1 0.9 + - - +
158C LYS* 1.3 83.4 - - - +
160C ILE* 1.3 62.2 + - - +
162C SER* 3.4 18.8 + - - -
163C MET* 3.5 3.8 - - - +
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Residues in contact with ILE 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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63C VAL* 4.2 18.4 - - + -
117C TRP* 3.2 44.6 - - + +
120C LEU* 3.1 19.3 - - + +
133C VAL* 4.4 5.5 - - + +
135C CYS* 5.1 0.2 - - - -
140C PHE* 4.8 3.4 - - + -
156C ALA 3.2 18.8 + - - +
157C LEU* 3.0 7.4 + - - +
159C ASN* 1.3 73.4 - - - +
161C ALA* 1.3 56.1 + - - +
162C SER 3.0 5.2 - - - -
163C MET* 2.9 26.6 + - - +
164C VAL* 3.9 4.3 - - - +
170C LEU* 3.3 33.4 - - + -
172C ILE* 4.5 18.4 - - + -
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Residues in contact with ALA 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C LEU 3.0 15.0 + - - +
158C LYS 4.0 1.8 - - - +
160C ILE* 1.3 78.2 - - - +
162C SER* 1.3 57.1 + - - +
163C MET 3.0 4.0 + - - -
164C VAL* 3.3 16.8 + - - +
170C LEU* 5.2 1.3 - - + +
257C ALA* 3.8 23.8 - - + +
258C PHE* 3.4 39.1 - - + -
290C LYS* 3.4 16.6 + - - -
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Residues in contact with SER 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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121C ASP* 5.2 8.5 - - - +
126C ALA* 3.6 10.6 - - - +
129C GLY* 5.8 0.3 - - - -
158C LYS* 3.3 12.6 + - - -
159C ASN* 3.4 13.0 + - - -
160C ILE 3.0 0.8 - - - -
161C ALA* 1.3 76.8 - - - +
163C MET* 1.3 75.1 + - - +
164C VAL 3.3 4.5 - - - +
290C LYS* 4.8 4.5 - - - +
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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