Contacts of the helix formed by residues 154 - 162 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A GLN* 3.6 19.0 + - + +
153A SER* 1.3 71.2 - - - +
155A ILE* 1.3 56.4 + - - +
156A PHE 3.2 0.2 + - - -
157A LYS* 3.2 4.9 + - - +
158A GLN* 2.9 45.3 + - - +
208A GLU* 3.9 13.7 + - - +
90B ASN* 3.3 31.3 - - - +
128B ALA* 3.8 13.0 - - - +
132B TRP* 3.4 25.3 + - - -
3G C 3.0 29.6 + - - +
4G A 3.1 23.2 + - - -
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Residues in contact with ILE 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLN* 3.7 34.5 - - + +
124A PHE* 3.8 25.1 - - + -
126A VAL* 4.2 8.5 - - + +
148A TYR* 3.8 22.2 - - + -
149A PRO* 3.7 27.6 - - + -
153A SER* 3.0 16.4 + - - +
154A GLN* 1.3 77.0 - - - +
156A PHE* 1.3 66.0 + - + +
158A GLN* 3.3 16.8 - - - +
159A SER* 3.0 28.6 + - - -
166A LEU* 3.9 15.6 - - + +
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Residues in contact with PHE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A TYR* 4.8 3.4 - - + -
149A PRO* 3.3 35.4 - - + -
152A LYS 4.5 1.3 - - - -
153A SER* 3.1 24.2 + - - -
155A ILE* 1.3 79.5 - - + +
157A LYS* 1.3 66.0 + - - +
159A SER 3.4 0.7 + - - -
160A LEU* 3.2 27.2 + - - +
166A LEU* 3.9 16.2 - - + -
207A ALA 3.5 5.2 - - - +
208A GLU 3.4 21.5 - - - +
209A ASN 3.5 17.5 - - - +
210A ASN* 3.4 28.7 - - + -
211A PHE* 3.4 41.8 - + + -
212A MET* 4.2 10.8 - - + -
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Residues in contact with LYS 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A SER 3.8 1.6 + - - -
154A GLN* 3.2 8.3 + - - +
156A PHE* 1.3 75.9 - - - +
158A GLN* 1.3 60.6 + - + +
160A LEU* 3.2 3.2 + - - +
161A ASP* 2.7 69.3 + - - +
204A VAL* 5.1 15.8 - - - +
207A ALA* 3.2 38.7 + - + +
208A GLU* 3.9 24.7 - - + +
131B GLU* 4.4 18.9 + - - +
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Residues in contact with GLN 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A GLN* 3.0 27.6 + - - +
126A VAL* 3.5 32.2 + - + +
127A LYS* 3.9 32.9 - - + +
154A GLN* 2.9 33.7 + - - +
155A ILE* 3.3 19.1 - - - +
157A LYS* 1.3 77.1 - - + +
159A SER* 1.3 57.3 + - - +
161A ASP* 3.8 0.5 - - - +
162A GLU* 2.9 35.2 + - - +
128B ALA* 5.1 6.7 - - - +
131B GLU* 5.6 2.7 - - - +
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Residues in contact with SER 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A VAL* 3.8 7.4 - - - +
155A ILE 3.0 18.9 + - - -
156A PHE 3.5 6.3 - - - -
158A GLN* 1.3 77.9 - - - +
160A LEU* 1.3 56.5 + - - +
163A ASN* 2.9 26.5 + - - -
164A VAL 2.6 33.8 + - - +
166A LEU* 3.8 12.6 + - - +
195A PRO* 3.4 9.8 - - - +
211A PHE* 3.4 24.8 - - - -
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Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A PHE 3.2 11.1 + - - +
157A LYS* 3.7 6.3 - - - +
159A SER* 1.3 77.9 - - - +
161A ASP* 1.3 66.5 + - - +
162A GLU 3.5 0.5 + - - -
163A ASN* 3.7 5.7 + - - +
194A PHE* 5.4 0.2 - - + -
195A PRO* 3.5 28.3 - - + +
196A LYS* 5.2 1.2 - - - -
198A GLN* 3.6 22.7 - - + -
199A SER* 3.9 24.2 + - - +
202A THR* 3.8 37.5 - - + +
207A ALA* 4.0 20.4 - - + +
211A PHE* 3.8 19.3 - - + -
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Residues in contact with ASP 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LYS* 4.0 24.5 + - - +
157A LYS* 2.7 59.8 + - - +
158A GLN 3.9 3.4 - - - +
160A LEU* 1.3 78.5 - - - +
162A GLU* 1.3 65.4 + - + +
163A ASN 3.9 0.2 + - - -
207A ALA* 5.5 1.7 - - - +
131B GLU* 4.2 3.3 - - - +
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Residues in contact with GLU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A VAL 5.1 0.2 - - - +
127A LYS* 3.7 42.9 + - + +
130A SER* 2.6 38.3 + - - +
131A GLU* 4.0 14.1 - - - +
133A ARG* 2.7 31.9 + - - -
158A GLN 2.9 14.0 + - - +
161A ASP* 1.3 82.8 - - - +
163A ASN* 1.3 58.5 + - - +
164A VAL* 4.0 6.1 - - + -
127B LYS* 5.6 3.0 + - - -
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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