Contacts of the helix formed by residues 154 - 162 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90C ASN* 3.1 36.8 + - - +
128C ALA* 4.0 6.4 - - - +
132C TRP* 3.4 20.3 + - - -
121D GLN* 3.6 21.4 + - + +
153D SER* 1.3 71.4 + - - +
155D ILE* 1.3 57.1 + - - +
157D LYS* 3.2 4.4 + - - +
158D GLN* 2.9 47.0 + - + +
208D GLU* 3.9 11.6 + - - +
3F C 3.0 33.0 + - - +
4F A 3.0 24.4 + - - -
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Residues in contact with ILE 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D GLN* 3.7 34.5 - - + +
124D PHE* 3.8 26.0 - - + -
126D VAL* 4.2 8.6 - - + +
148D TYR* 3.8 20.9 - - + -
149D PRO* 3.7 26.7 - - + -
153D SER* 3.0 17.5 + - - +
154D GLN* 1.3 77.6 - - - +
156D PHE* 1.3 63.8 - - + +
158D GLN* 3.4 15.2 - - - +
159D SER* 2.9 29.5 + - - -
166D LEU* 3.9 15.6 - - + +
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Residues in contact with PHE 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D TYR* 4.9 3.8 - - + -
149D PRO* 3.4 35.2 - - + -
152D LYS 4.5 1.3 - - - -
153D SER* 3.1 25.7 + - - -
155D ILE* 1.3 76.2 - - + +
157D LYS* 1.3 67.2 + - - +
159D SER 3.4 1.0 + - - -
160D LEU* 3.1 27.2 + - - +
166D LEU* 3.9 12.1 - - + -
207D ALA 3.5 8.3 - - - +
208D GLU 3.4 19.7 - - - +
209D ASN 3.5 17.0 - - - +
210D ASN* 3.5 28.9 - - + -
211D PHE* 3.5 45.4 - + + -
212D MET* 4.5 9.0 - - + -
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Residues in contact with LYS 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C GLU* 4.4 14.0 + - - +
153D SER 3.8 2.2 + - - -
154D GLN* 3.2 7.9 + - - +
156D PHE* 1.3 75.3 - - - +
158D GLN* 1.3 60.9 + - + +
160D LEU* 3.3 2.9 + - - +
161D ASP* 2.7 67.2 + - - +
204D VAL* 4.7 19.0 - - - +
207D ALA* 3.3 37.7 + - + +
208D GLU* 3.9 24.9 - - + +
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Residues in contact with GLN 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C ALA* 5.1 7.3 - - - +
131C GLU* 5.7 2.0 - - - +
121D GLN* 2.9 27.9 + - - +
126D VAL* 3.5 32.2 + - + +
127D LYS* 3.8 33.1 - - + +
154D GLN* 2.9 34.3 + - + +
155D ILE* 3.4 19.8 - - - +
156D PHE 3.3 0.2 - - - -
157D LYS* 1.3 76.1 - - + +
159D SER* 1.3 64.2 + - - +
161D ASP* 3.9 0.3 - - - +
162D GLU* 2.9 29.8 + - - +
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Residues in contact with SER 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D VAL* 3.7 8.0 - - - +
155D ILE 2.9 18.6 + - - -
156D PHE 3.5 5.4 - - - -
158D GLN* 1.3 76.7 - - - +
160D LEU* 1.3 57.1 + - - +
163D ASN* 2.8 27.7 + - - -
164D VAL 2.6 33.1 + - - +
166D LEU* 3.8 12.3 + - - +
195D PRO* 3.4 10.8 - - - +
211D PHE* 3.4 24.3 - - - -
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Residues in contact with LEU 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D PHE 3.1 13.2 + - - +
157D LYS* 3.7 4.0 - - - +
159D SER* 1.3 81.1 - - - +
161D ASP* 1.3 66.6 + - - +
162D GLU 3.5 0.5 + - - -
163D ASN* 3.7 6.2 + - - +
195D PRO* 3.4 29.2 - - + +
196D LYS* 4.9 2.1 + - - +
198D GLN* 3.7 22.7 - - + -
199D SER* 3.9 23.7 + - - +
202D THR* 3.7 35.7 - - + +
207D ALA* 4.0 22.0 - - + +
211D PHE* 3.8 20.2 - - + -
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Residues in contact with ASP 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C GLU* 4.4 2.4 - - - +
127D LYS* 4.1 24.3 + - - +
157D LYS* 2.7 60.5 + - - +
158D GLN 3.9 2.9 - - - +
160D LEU* 1.3 78.3 - - - +
162D GLU* 1.3 65.1 + - + +
163D ASN 4.0 0.2 + - - -
207D ALA* 5.6 1.4 - - - +
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Residues in contact with GLU 162 (chain D).
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* 5.7 3.3 + - - -
126D VAL* 5.1 0.2 - - + -
127D LYS* 3.8 42.7 + - + +
130D SER* 2.7 39.1 + - - +
131D GLU* 4.0 13.6 - - - +
133D ARG* 2.7 31.4 + - - -
158D GLN 2.9 13.7 + - - +
161D ASP* 1.3 83.8 - - - +
163D ASN* 1.3 55.8 + - - +
164D VAL* 4.0 6.1 - - + -
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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