Contacts of the helix formed by residues 182 - 194 (chain w) in PDB entry 6AH0
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 TYR 182 (chain w).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180w ALA 3.2 8.1 + - - -
181w GLU* 1.3 72.8 - - - +
183w LYS* 1.3 66.9 + - - +
184w ARG 3.3 2.0 - - - -
185w TYR* 3.2 7.7 + - - +
186w LEU* 2.9 18.2 + - - -
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Residues in contact with LYS 183 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181w GLU* 3.6 1.4 - - - +
182w TYR* 1.3 77.7 - - - +
184w ARG* 1.3 55.4 + - - +
186w LEU* 2.7 21.9 + - - +
187w GLU* 2.9 11.1 + - - -
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Residues in contact with ARG 184 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85i PRO* 4.5 21.1 - - - +
86i PRO 5.9 1.6 - - - -
181w GLU 4.9 2.7 + - - -
182w TYR* 3.3 1.0 - - - +
183w LYS* 1.3 75.2 - - - +
185w TYR* 1.3 55.6 + - - +
187w GLU* 3.1 5.0 + - - +
188w MET* 3.0 23.7 + - - -
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Residues in contact with TYR 185 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181w GLU 5.3 0.8 + - - -
182w TYR* 3.2 11.3 + - - +
184w ARG* 1.3 73.4 - - - +
186w LEU* 1.3 59.1 + - - +
188w MET* 3.9 2.8 - - - +
189w LEU* 2.9 24.9 + - - -
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Residues in contact with LEU 186 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182w TYR 2.9 9.6 + - - -
183w LYS* 2.7 16.3 + - - +
185w TYR* 1.3 68.9 - - - +
187w GLU* 1.3 64.3 + - - +
189w LEU* 3.2 2.4 + - - +
190w LEU* 2.9 19.8 + - - -
200w VAL* 6.1 5.2 - - - +
203w LEU* 6.4 2.7 - - - +
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Residues in contact with GLU 187 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183w LYS 2.9 11.4 + - - -
184w ARG* 3.1 4.9 + - - +
186w LEU* 1.3 71.1 - - - +
188w MET* 1.3 66.8 + - - +
190w LEU* 2.8 15.2 + - - +
191w GLU* 3.0 9.0 + - - -
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Residues in contact with MET 188 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83i GLU 5.7 2.0 - - - -
84i GLY* 5.3 13.7 - - - -
85i PRO* 5.2 3.6 - - - +
184w ARG 3.0 12.8 + - - -
185w TYR* 4.0 3.8 - - - +
187w GLU* 1.3 73.1 - - - +
189w LEU* 1.3 56.4 + - - +
191w GLU* 3.1 5.6 + - - +
192w TYR* 2.9 23.6 + - - -
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Residues in contact with LEU 189 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185w TYR 2.9 16.3 + - - -
186w LEU* 3.6 3.8 - - - +
187w GLU 3.0 0.4 - - - -
188w MET* 1.3 74.3 - - - +
190w LEU* 1.3 60.1 + - - +
192w TYR* 2.8 17.8 + - - +
193w LEU* 2.9 13.0 + - - -
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Residues in contact with LEU 190 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56j GLU* 4.6 1.4 - - - -
186w LEU 2.9 10.0 + - - -
187w GLU 2.8 7.7 + - - -
189w LEU* 1.3 75.5 - - - +
191w GLU* 1.3 60.3 + - - +
193w LEU* 3.4 1.2 + - - +
194w GLN* 3.2 19.4 + - - -
195w ASP 3.6 21.6 + - - +
196w TYR* 6.1 0.2 - - - +
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Residues in contact with GLU 191 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82i VAL 5.7 4.3 - - - -
54j GLN 5.0 2.1 - - - +
55j LEU* 4.4 2.3 - - - -
56j GLU* 3.4 30.3 + - - +
57j THR 5.5 0.4 - - - +
187w GLU 3.0 11.8 + - - -
188w MET* 3.4 6.5 - - - +
190w LEU* 1.3 76.9 - - - +
192w TYR* 1.3 58.8 + - - +
194w GLN 4.0 0.3 + - - -
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Residues in contact with TYR 192 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54j GLN 5.6 1.9 - - - +
188w MET 2.9 10.0 + - - -
189w LEU* 2.8 9.8 + - - +
191w GLU* 1.3 76.6 - - - +
193w LEU* 1.3 57.2 + - - +
194w GLN 3.2 5.2 + - - -
232w GLU* 5.8 11.9 - - - +
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Residues in contact with LEU 193 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189w LEU 2.9 12.8 + - - -
190w LEU* 4.1 1.3 - - - +
192w TYR* 1.3 75.9 - - - +
194w GLN* 1.3 66.4 + - - +
195w ASP* 3.2 4.1 + - - -
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Residues in contact with GLN 194 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42j ALA* 3.8 20.4 - - - +
55j LEU 4.6 3.1 - - - -
56j GLU* 3.5 31.2 - - - +
190w LEU 3.2 5.6 + - - -
191w GLU 4.0 0.8 + - - -
192w TYR 3.2 4.8 + - - -
193w LEU* 1.3 79.8 - - - +
195w ASP* 1.3 56.5 + - - +
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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