Contacts of the helix formed by residues 156 - 163 (chain F) in PDB entry 2JJD
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 LYS 156 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152F GLU 3.5 9.7 + - - +
153F LEU* 3.7 16.2 - - + +
154F ALA 3.4 2.0 - - - -
155F ASN* 1.3 79.4 - - - +
157F GLU* 1.3 68.5 + - - +
158F GLU* 4.3 6.3 - - + +
159F ASN* 2.9 25.6 + - - +
160F ARG* 3.2 9.0 + - - +
186F CYS* 5.7 2.2 - - + -
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Residues in contact with GLU 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F ASN 3.4 3.7 + - - -
156F LYS* 1.3 69.7 - - - +
158F GLU* 1.3 64.2 + - - +
160F ARG* 3.0 23.6 + - - +
161F GLU 4.7 0.7 + - - -
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Residues in contact with GLU 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156F LYS* 3.2 4.2 - - + +
157F GLU* 1.3 80.5 - - - +
159F ASN* 1.3 60.2 + - - +
160F ARG 3.6 0.2 + - - -
161F GLU* 4.5 5.5 + - - +
162F LYS* 4.0 13.4 - - - +
185F PRO* 4.9 3.8 - - + +
186F CYS* 3.3 31.2 - - + -
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Residues in contact with ASN 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F LEU* 2.8 34.9 + - - +
154F ALA 4.0 7.9 - - - +
156F LYS* 2.9 16.7 + - - +
158F GLU* 1.3 75.8 - - - +
160F ARG* 1.3 65.1 + - - +
161F GLU 3.3 3.4 - - - -
162F LYS* 3.1 42.9 + - - +
163F ASN* 3.6 10.4 + - - -
186F CYS* 3.4 15.5 + - - +
189F TYR* 3.3 36.2 - - + +
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Residues in contact with ARG 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F ALA 5.1 1.6 - - - -
155F ASN* 5.6 2.0 - - - +
156F LYS 3.2 7.2 + - - +
157F GLU* 3.0 18.5 + - - +
159F ASN* 1.3 77.5 - - - +
161F GLU* 1.3 59.2 + - - +
162F LYS 3.1 4.9 + - - -
163F ASN* 3.3 23.5 + - - +
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Residues in contact with GLU 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F GLU 4.7 0.2 + - - -
158F GLU 4.5 5.2 + - - +
159F ASN 3.3 1.0 - - - -
160F ARG* 1.3 77.2 - - - +
162F LYS* 1.3 60.3 + - + +
163F ASN 3.4 0.9 - - - -
211F LYS* 3.0 28.1 + - - +
213F GLU* 4.2 14.1 - - + +
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Residues in contact with LYS 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F GLU 4.0 11.9 - - - +
159F ASN* 3.3 32.5 + - - +
160F ARG 3.1 0.8 - - - -
161F GLU* 1.3 81.8 - - + +
163F ASN* 1.3 61.2 + - - +
185F PRO 5.2 0.8 + - - -
186F CYS* 2.7 31.9 + - - +
187F SER* 4.3 6.1 - - - +
189F TYR* 3.9 32.3 + - + +
190F ILE* 6.1 0.7 - - - -
191F ASN* 4.5 3.3 + - - +
208F GLN* 2.8 18.9 + - - -
211F LYS* 4.2 3.4 - - - -
213F GLU* 5.8 1.8 - - + +
214F THR* 3.7 29.3 - - + +
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Residues in contact with ASN 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F ALA 3.2 25.3 + - - -
159F ASN 3.6 11.3 + - - -
160F ARG* 3.3 16.0 + - - +
162F LYS* 1.3 79.2 - - - +
164F ARG* 1.3 64.4 + - - +
165F TYR 4.2 7.7 - - - +
166F PRO* 4.9 3.7 - - + +
169F LEU* 3.3 21.7 - - + +
189F TYR* 2.7 28.6 + - - -
191F ASN* 2.7 22.5 + - - +
208F GLN* 3.6 2.9 - - - +
211F LYS* 3.6 13.2 + - - -
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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