Contacts of the helix formed by residues 154 - 162 (chain C) in PDB entry 2E52
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 154 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C GLN* 3.6 21.5 + - + +
153C SER* 1.3 73.6 + - - +
155C ILE* 1.3 57.3 + - - +
157C LYS* 3.3 4.6 + - - +
158C GLN* 2.9 46.5 + - + +
208C GLU* 3.9 14.2 - - - +
90D ASN* 3.1 28.1 + - - +
128D ALA* 4.0 7.4 - - - +
131D GLU* 6.2 0.2 - - - +
132D TRP* 3.1 25.3 + - - -
3H C 3.0 31.5 + - - +
4H A 2.9 25.4 + - - -
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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
----------------------------------------------------------
121C GLN* 3.7 32.1 - - + +
124C PHE* 3.9 21.5 - - + -
126C VAL* 4.1 8.7 - - + +
148C TYR* 3.8 15.3 - - + -
149C PRO* 3.7 27.6 - - + -
153C SER* 3.0 20.8 - - - +
154C GLN* 1.3 77.5 - - - +
156C PHE* 1.3 64.9 - - + +
158C GLN* 3.4 17.2 - - - +
159C SER* 2.9 29.3 + - - -
166C LEU* 3.7 23.7 - - + +
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Residues in contact with PHE 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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148C TYR* 5.0 3.1 - - + -
149C PRO* 3.3 46.4 - - + -
152C LYS 4.1 2.5 - - - -
153C SER* 3.1 19.0 + - - +
155C ILE* 1.3 77.8 - - + +
157C LYS* 1.3 63.1 + - - +
159C SER* 3.4 3.6 + - - -
160C LEU* 3.1 28.1 + - - +
166C LEU* 3.9 13.0 - - + -
207C ALA 3.6 5.6 - - - +
208C GLU 3.5 19.1 - - - +
209C ASN 3.5 15.9 - - - +
210C ASN* 3.5 29.2 - - + -
211C PHE* 3.6 43.2 - + + -
212C MET* 4.4 9.2 - - + -
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Residues in contact with LYS 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 SER 3.7 1.6 + - - -
154C GLN* 3.3 7.0 + - - +
156C PHE* 1.3 76.3 - - - +
158C GLN* 1.3 59.5 + - - +
160C LEU* 3.3 4.8 + - + +
161C ASP* 2.8 66.8 + - - +
204C VAL* 4.8 14.6 - - - +
207C ALA* 3.2 38.3 + - + +
208C GLU* 3.9 25.1 - - + +
131D GLU* 4.4 15.1 + - + -
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Residues in contact with GLN 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C GLN* 3.0 27.3 + - - +
126C VAL* 3.5 33.3 + - + +
127C LYS* 3.8 34.1 - - + +
154C GLN* 2.9 33.2 + - + +
155C ILE* 3.4 18.7 - - - +
157C LYS* 1.3 76.2 - - + +
159C SER* 1.3 58.2 + - - +
161C ASP* 5.1 0.2 - - - -
162C GLU* 2.9 37.4 + - - +
128D ALA* 5.0 8.3 - - - +
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Residues in contact with SER 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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126C VAL* 3.8 7.8 - - - +
155C ILE 2.9 18.6 + - - -
156C PHE 3.5 5.8 - - - -
158C GLN* 1.3 76.5 - - - +
160C LEU* 1.3 57.6 + - - +
163C ASN* 2.9 26.3 + - - -
164C VAL 2.6 34.6 + - - +
166C LEU* 3.8 11.8 + - - +
195C PRO* 3.3 10.0 - - - +
211C PHE* 3.5 24.0 - - - -
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Residues in contact with LEU 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 PHE 3.1 13.6 + - - +
157C LYS* 3.3 4.0 + - + +
159C SER* 1.3 80.8 - - - +
161C ASP* 1.3 66.8 + - - +
162C GLU 3.5 0.2 + - - -
163C ASN* 3.6 6.9 + - - +
195C PRO* 3.6 28.3 - - + +
196C LYS* 4.8 4.2 + - - +
198C GLN* 3.7 18.8 - - + -
199C SER* 4.0 24.4 + - - +
202C THR* 3.8 35.4 - - + +
207C ALA* 3.9 22.0 - - + +
211C PHE* 3.6 26.7 - - + -
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Residues in contact with ASP 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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127C LYS* 4.5 20.3 + - - +
157C LYS* 2.8 60.4 + - - +
158C GLN 4.0 2.5 - - - +
160C LEU* 1.3 80.6 - - - +
162C GLU* 1.3 64.8 + - - +
163C ASN 4.0 0.2 + - - -
199C SER* 6.1 0.2 - - - -
207C ALA* 5.7 1.6 - - - +
131D GLU* 5.5 0.9 - - - +
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Residues in contact with GLU 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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126C VAL* 5.1 0.2 - - + -
127C LYS* 3.8 41.5 + - + +
130C SER* 2.7 37.6 + - - +
131C GLU* 4.4 9.8 - - - +
133C ARG* 2.7 31.5 + - - -
158C GLN 2.9 16.2 + - - +
161C ASP* 1.3 83.3 - - - +
163C ASN* 1.3 60.0 + - - +
164C VAL* 3.9 6.3 - - + -
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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