Contacts of the helix formed by residues 158 - 165 (chain B) in PDB entry 1A08
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 ARG 158 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157B THR* 1.3 70.9 - - - +
159B ARG* 1.3 58.1 + - - +
161B SER* 3.0 16.0 + - - -
162B GLU* 3.0 31.8 + - + +
178B ARG* 3.4 19.8 - - - +
181B GLU* 2.9 19.4 + - - +
204B HIS* 3.3 41.8 - - - +
100D ACE 2.9 45.5 + - - +
101D FTY 3.0 33.1 + - - +
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Residues in contact with ARG 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B THR* 3.2 7.2 + - - +
158B ARG* 1.3 77.4 - - - +
160B GLU* 1.3 68.2 + - - +
162B GLU* 3.1 9.5 + - - +
163B ARG* 3.0 43.1 + - - +
181B GLU* 4.7 0.4 + - - -
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Residues in contact with GLU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ARG* 6.3 1.1 - - - +
182A THR* 3.2 27.7 - - + +
206A LYS* 4.4 5.8 + - - -
156B ILE* 4.3 13.5 - - + -
157B THR* 3.0 38.3 + - + +
159B ARG* 1.3 75.6 - - - +
161B SER* 1.4 63.5 + - - +
163B ARG* 3.1 22.4 + - - +
164B LEU* 2.9 33.5 + - + +
100C ACE 4.9 9.2 - - + -
101C FTY 3.3 30.1 + - - +
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Residues in contact with SER 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ILE* 3.9 14.5 - - - +
157B THR 3.0 14.2 + - - -
158B ARG 3.0 15.2 + - - -
159B ARG 3.1 0.4 - - - -
160B GLU* 1.4 75.3 - - - +
162B GLU* 1.3 59.8 + - - +
164B LEU* 3.5 4.6 + - - +
165B LEU* 3.1 29.5 + - - +
176B LEU* 4.0 11.2 - - - +
178B ARG* 3.3 30.0 + - - -
190B SER* 3.5 3.3 + - - -
204B HIS* 3.4 14.9 - - - -
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Residues in contact with GLU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B ARG* 3.0 32.4 + - - +
159B ARG* 3.1 8.5 + - - +
161B SER* 1.3 74.5 - - - +
163B ARG* 1.3 56.1 + - + +
165B LEU 3.2 0.7 + - - -
166B LEU* 2.7 49.1 + - + +
202B VAL* 4.3 25.1 - - + +
204B HIS* 3.0 30.1 + - + +
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Residues in contact with ARG 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A GLU 5.6 1.8 - - - +
182A THR* 3.4 59.0 + - - +
183A THR* 4.4 6.7 + - - +
206A LYS* 5.2 2.2 - - - +
159B ARG* 3.0 28.6 + - - +
160B GLU* 3.7 16.7 + - - +
162B GLU* 1.3 75.1 - - + +
164B LEU* 1.3 63.7 + - - +
165B LEU 3.4 0.2 + - - -
166B LEU* 3.5 17.1 + - - +
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ARG* 4.4 16.6 - - + +
181A GLU* 3.2 41.1 - - + +
182A THR* 3.8 14.1 - - - +
153B PHE* 3.9 19.1 - - + -
156B ILE* 3.7 28.3 - - + -
160B GLU* 2.9 27.9 + - + +
161B SER* 3.8 5.2 - - - +
163B ARG* 1.3 78.7 - - - +
165B LEU* 1.3 58.3 + - - +
167B ASN* 4.9 3.8 - - - +
170B ASN* 4.5 6.1 + - - -
176B LEU* 4.4 1.6 - - + -
248B CYS* 3.6 23.7 - - - -
249B PRO* 5.2 2.9 - - - +
101C FTY 4.6 4.9 - - - +
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B SER 3.1 14.8 + - - +
162B GLU 3.2 0.2 + - - -
164B LEU* 1.3 80.8 - - - +
166B LEU* 1.3 62.1 + - - +
167B ASN 2.9 9.9 + - - +
170B ASN* 3.6 13.1 + - - +
174B THR* 3.6 40.6 - - + +
175B PHE* 3.9 4.3 - - - +
176B LEU* 4.0 9.9 - - + -
190B SER* 3.5 31.2 - - - +
191B VAL 4.1 3.1 - - - +
192B SER* 4.3 11.5 - - - +
202B VAL* 3.6 35.2 - - + -
248B CYS* 3.9 16.8 - - + -
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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