Contacts of the helix formed by residues 150 - 159 (chain A) in PDB entry 3E8N
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 SER 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A GLY* 1.3 74.3 - - - -
151A LEU* 1.3 65.1 + - - +
152A ASP* 2.7 25.7 + - - -
153A GLN* 2.9 24.9 + - - +
154A VAL* 3.1 14.9 + - - +
194A SER* 3.3 28.5 - - - -
196A ILE 3.4 5.8 - - - -
197A LEU* 3.8 6.1 - - - -
600A ATP 3.0 20.9 + - - -
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Residues in contact with LEU 151 (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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150A SER* 1.3 72.1 - - - +
152A ASP* 1.3 52.2 + - - +
154A VAL* 3.2 26.2 + - + +
155A LEU* 2.7 37.4 + - - +
161A ILE* 4.5 5.6 - - + +
165A ILE* 6.4 0.2 - - + -
169A VAL* 3.7 35.4 - - + -
193A PRO* 3.2 12.0 + - + +
196A ILE* 2.9 33.9 + - + +
198A VAL* 4.0 21.5 - - + -
256A MET* 3.5 32.3 - - + -
371A PHE* 5.1 6.7 - - + -
374A TRP* 5.8 1.6 - - + -
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Residues in contact with ASP 152 (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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150A SER* 2.7 27.7 + - - -
151A LEU* 1.3 78.4 - - - +
153A GLN* 1.3 63.5 + - - +
155A LEU* 3.4 10.2 + - - +
156A LYS* 3.3 45.0 + - - +
193A PRO* 3.5 26.2 + - + +
194A SER* 3.5 23.1 - - - +
227A ARG* 6.2 0.9 - - - +
255A GLU* 5.2 4.7 - - - +
600A ATP 3.8 4.7 + - - -
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Residues in contact with GLN 153 (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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74A LEU 4.1 13.4 + - - +
148A GLY 5.4 0.9 - - - +
149A GLY* 3.4 9.9 - - - -
150A SER* 2.9 30.9 + - - +
152A ASP* 1.3 84.8 + - - +
154A VAL* 1.3 66.7 + - + +
156A LYS* 3.1 29.0 + - - +
157A LYS* 3.5 11.2 + - - +
600A ATP 2.5 28.9 + - - +
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Residues in contact with VAL 154 (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 GLY 3.8 18.8 - - - +
150A SER 3.1 17.7 + - - +
151A LEU* 3.3 29.2 - - + +
153A GLN* 1.3 75.1 - - + +
155A LEU* 1.3 60.7 + - - +
157A LYS* 3.9 2.8 - - - +
158A ALA* 2.9 33.4 + - - +
161A ILE* 3.8 14.6 - - + -
198A VAL* 4.3 2.0 - - + -
374A TRP* 4.3 15.0 - - + -
375A LEU* 4.0 15.7 - - + -
378A THR* 5.6 0.4 - - - +
379A ILE* 4.2 21.3 - - + +
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Residues in contact with LEU 155 (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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151A LEU 2.7 22.3 + - - +
152A ASP* 3.4 12.3 - - - +
154A VAL* 1.3 78.3 - - - +
156A LYS* 1.3 52.7 + - + +
158A ALA* 4.5 1.1 - - - -
159A GLY* 2.6 38.4 + - - +
160A ARG* 3.9 17.5 - - - -
161A ILE* 4.0 10.8 - - + -
193A PRO* 5.3 0.4 - - + -
255A GLU* 4.0 30.5 - - + +
256A MET* 3.8 47.3 - - + +
259A GLY* 4.5 7.4 - - - +
260A ARG* 5.7 0.2 - - - -
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Residues in contact with LYS 156 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A ASP* 3.3 32.8 + - - +
153A GLN* 3.1 15.0 + - + +
155A LEU* 1.3 75.5 - - + +
157A LYS* 1.3 67.7 + - + +
159A GLY* 3.0 14.1 + - - -
227A ARG* 5.9 4.6 - - - +
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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 GLN 3.5 11.4 + - - +
154A VAL* 3.5 6.1 + - - +
156A LYS* 1.3 78.0 - - + +
158A ALA* 1.3 58.2 + - - +
378A THR 4.1 17.7 - - - +
379A ILE* 3.7 39.4 + - + +
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Residues in contact with ALA 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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154A VAL 2.9 20.6 + - - +
155A LEU* 4.1 2.7 - - - +
157A LYS* 1.3 77.8 - - - +
159A GLY* 1.3 53.8 + - - +
160A ARG* 2.7 35.4 + - - +
161A ILE* 4.6 0.4 - - + -
374A TRP* 4.3 20.4 - - + -
378A THR* 4.7 15.3 - - + +
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Residues in contact with GLY 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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155A LEU* 2.6 23.0 + - - +
156A LYS* 3.0 10.3 + - - -
158A ALA* 1.3 71.2 - - - +
160A ARG* 1.3 60.1 + - - +
259A GLY* 3.3 24.8 - - - +
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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