Contacts of the helix formed by residues 201 - 212 (chain B) in PDB entry 1ESG
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 201 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B SER* 3.0 8.4 + - - +
200B LYS* 1.3 79.8 - - - +
202B SER* 1.3 67.0 + - - +
203B ILE 3.2 1.3 - - - -
204B LYS* 3.2 11.3 + - - +
205B LYS* 3.1 62.4 + - + +
208B ASP* 4.7 7.1 + - - -
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Residues in contact with SER 202 (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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198B MET* 4.3 18.0 - - - +
199B SER* 3.1 25.3 + - - -
201B ARG* 1.3 79.6 - - - +
203B ILE* 1.3 61.8 + - - +
205B LYS* 3.4 10.3 + - - +
206B TRP* 3.0 30.0 + - - +
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Residues in contact with ILE 203 (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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59B PRO* 3.7 23.6 - - + +
62B GLU* 3.9 22.7 - - + +
63B LEU* 4.3 11.2 - - + +
66B THR* 3.9 26.7 - - + +
198B MET* 3.8 34.3 - - + +
199B SER 3.1 17.3 + - - +
200B LYS* 4.5 9.6 - - + +
202B SER* 1.3 78.3 - - - +
204B LYS* 1.3 58.0 + - + +
206B TRP* 3.4 11.3 + - + +
207B LYS* 2.9 28.3 + - + +
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Residues in contact with LYS 204 (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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66B THR* 3.6 16.2 - - + +
70B ASP* 3.0 31.1 + - - -
200B LYS* 3.9 21.4 + - + +
201B ARG* 3.2 20.7 + - - +
203B ILE* 1.3 79.2 - - + +
205B LYS* 1.3 60.0 + - - +
207B LYS* 3.3 15.7 + - - +
208B ASP* 2.9 40.9 + - - +
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Residues in contact with LYS 205 (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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201B ARG* 3.1 58.6 + - + +
202B SER* 3.7 10.5 - - - +
204B LYS* 1.3 75.7 - - - +
206B TRP* 1.3 63.4 + - - +
208B ASP* 3.3 11.7 + - - +
209B LYS* 3.1 25.4 + - - +
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Residues in contact with TRP 206 (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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37B ILE* 2.9 30.6 + - + +
38B TRP* 3.8 22.3 - + - -
40B ALA* 4.1 23.3 - - + +
45B PHE* 4.2 5.2 - + - -
59B PRO 3.7 21.5 - - - -
60B ILE* 3.3 31.4 - - + -
63B LEU* 3.7 27.6 - - + -
191B ILE* 4.6 1.8 - - + -
198B MET* 3.7 33.4 - - + -
202B SER 3.0 17.2 + - - +
203B ILE* 3.6 11.7 - - + +
205B LYS* 1.3 77.3 - - - +
207B LYS* 1.3 62.9 + - - +
209B LYS* 3.0 6.2 + - + +
210B VAL* 2.9 32.3 + - + +
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Residues in contact with LYS 207 (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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63B LEU* 3.8 16.7 - - + +
66B THR* 3.6 25.8 - - + +
67B LEU* 4.1 17.0 - - + +
70B ASP* 3.5 36.3 + - - +
71B THR* 4.2 6.3 - - - -
203B ILE 2.9 19.0 + - - +
204B LYS* 3.3 16.8 + - + +
206B TRP* 1.3 74.7 - - - +
208B ASP* 1.3 73.5 + - - +
210B VAL* 3.1 5.8 + - - +
211B GLU* 3.0 44.8 + - - +
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Residues in contact with ASP 208 (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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201B ARG* 4.7 8.0 + - - -
204B LYS* 2.9 30.1 + - - +
205B LYS* 3.3 12.6 - - - +
206B TRP 3.2 0.2 - - - -
207B LYS* 1.3 90.6 + - - +
209B LYS* 1.3 61.7 + - + +
211B GLU* 5.0 2.8 - - - +
212B ASN* 2.5 40.2 + - - +
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Residues in contact with LYS 209 (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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37B ILE* 4.2 8.2 - - + +
40B ALA* 3.5 40.2 - - + +
41B THR* 4.6 18.4 - - - +
43B LYS* 5.9 0.9 + - - -
205B LYS 3.1 14.3 + - - +
206B TRP 3.0 9.4 + - - +
208B ASP* 1.3 74.3 - - + +
210B VAL* 1.3 67.8 + - - +
211B GLU 3.4 0.5 + - - -
212B ASN 3.5 18.8 + - - +
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Residues in contact with VAL 210 (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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35B SER* 3.6 40.6 - - - +
37B ILE* 3.9 28.6 - - + +
63B LEU* 4.1 15.7 - - + -
67B LEU* 4.5 8.5 - - + -
206B TRP* 2.9 29.1 + - + +
207B LYS* 3.1 10.3 + - - +
209B LYS* 1.3 78.3 - - - +
211B GLU* 1.3 65.9 + - + +
212B ASN 3.7 0.2 + - - -
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Residues in contact with GLU 211 (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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67B LEU* 3.6 23.7 - - + +
71B THR* 2.4 40.7 + - - +
207B LYS* 3.0 35.6 + - - +
208B ASP* 4.9 1.8 - - - +
210B VAL* 1.3 79.6 - - + +
212B ASN* 1.3 66.6 + - - +
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Residues in contact with ASN 212 (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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43B LYS* 4.4 15.8 + - - -
208B ASP* 2.5 33.4 + - - +
209B LYS* 3.5 17.5 + - - +
210B VAL 3.5 0.4 + - - -
211B GLU* 1.3 86.6 - - - +
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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