Contacts of the helix formed by residues 209 - 220 (chain B) in PDB entry 2A1H
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 PRO 209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A SER* 5.6 1.3 - - - +
106A ARG* 2.9 38.3 + - - +
107A LEU* 4.2 12.1 - - + -
198A VAL* 3.9 39.3 - - + -
203A LEU* 4.6 3.6 - - + -
191B ILE 6.2 0.2 - - - +
205B GLY 3.3 21.8 - - - +
206B ASN 4.2 4.3 - - - +
207B TYR 3.6 3.6 - - - +
208B GLY* 1.4 87.8 - - - +
210B THR* 1.3 60.4 + - + +
211B VAL 3.4 0.6 + - - -
212B LEU 4.2 0.2 + - - -
213B VAL* 3.7 6.4 - - - +
227B TRP* 5.7 0.4 - - - -
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Residues in contact with THR 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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155A VAL* 3.8 13.5 - - - +
192B ARG* 4.4 12.3 - - + -
206B ASN 3.4 23.8 - - - +
207B TYR* 2.7 20.0 + - - +
209B PRO* 1.3 77.5 - - + +
211B VAL* 1.3 58.7 + - - +
212B LEU 3.4 0.2 - - - -
213B VAL* 3.3 4.0 + - - +
214B GLN* 2.9 31.4 + - - +
227B TRP* 3.8 35.1 - - + -
240B THR* 5.0 13.4 - - + +
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Residues in contact with VAL 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 4.5 13.2 - - + -
107A LEU 4.8 3.8 - - - +
108A CYS* 3.8 21.3 - - + -
155A VAL* 4.1 24.2 - - + -
156A SER* 3.7 16.4 - - - +
157A GLN* 3.5 31.0 - - + +
158A PRO* 5.2 0.2 - - + -
207B TYR 4.1 1.8 - - - +
208B GLY* 3.3 18.1 + - - +
210B THR* 1.3 75.4 - - - +
212B LEU* 1.3 62.9 + - - +
214B GLN* 3.3 8.0 + - - +
215B GLN* 3.1 26.0 + - + +
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Residues in contact with LEU 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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105A MET 4.0 14.1 - - - +
106A ARG* 3.7 49.7 + - - +
108A CYS* 3.6 22.6 - - - -
209B PRO 4.2 1.8 + - - -
210B THR 3.4 0.2 - - - -
211B VAL* 1.3 78.0 - - - +
213B VAL* 1.3 62.7 + - + +
215B GLN* 3.3 9.3 + - + +
216B GLU* 3.1 21.8 + - - +
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Residues in contact with VAL 213 (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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106A ARG* 4.3 11.7 - - - +
185B LEU* 5.2 1.4 - - + +
190B PHE* 3.6 48.7 - - + -
209B PRO 3.7 18.4 - - - +
210B THR 3.3 6.2 + - - +
212B LEU* 1.3 74.2 - - + +
214B GLN* 1.3 61.6 - - - +
216B GLU* 3.2 8.3 + - - +
217B ALA* 3.0 26.0 + - - +
225B VAL* 3.8 14.6 - - + -
227B TRP* 3.7 29.6 - - + -
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Residues in contact with GLN 214 (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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155A VAL 5.3 8.5 - - - +
156A SER* 6.5 0.2 - - - -
210B THR* 2.9 17.7 + - - +
211B VAL* 3.3 7.6 + - - +
213B VAL* 1.3 77.6 - - - +
215B GLN* 1.3 60.2 + - - +
217B ALA* 3.2 3.8 + - - +
218B LEU* 3.0 54.0 + - + +
223B GLU 2.7 30.0 + - - +
224B GLN* 3.6 23.7 + - - +
225B VAL* 4.0 13.2 - - + +
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Residues in contact with GLN 215 (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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108A CYS* 4.6 6.1 - - - -
156A SER* 5.8 2.4 - - - -
157A GLN* 4.3 33.4 + - - +
211B VAL* 3.1 23.3 + - + +
212B LEU* 3.6 13.2 - - + +
213B VAL 3.3 0.2 - - - -
214B GLN* 1.3 78.1 - - - +
216B GLU* 1.3 57.7 + - - +
218B LEU* 3.4 25.2 + - - +
219B LYS* 3.0 27.9 + - - +
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Residues in contact with GLU 216 (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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185B LEU* 4.5 1.3 - - + -
190B PHE* 4.1 26.0 - - + -
212B LEU 3.1 12.4 + - - +
213B VAL* 3.2 12.5 + - - +
215B GLN* 1.3 72.9 - - - +
217B ALA* 1.3 65.2 + - - +
219B LYS* 3.4 20.7 + - - +
220B ARG* 3.1 46.0 + - - +
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Residues in contact with ALA 217 (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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185B LEU* 3.8 22.2 - - + +
213B VAL 3.0 13.2 + - - +
214B GLN* 3.2 11.2 + - - +
216B GLU* 1.3 76.9 - - - +
218B LEU* 1.3 60.2 + - - +
220B ARG* 3.2 9.9 + - - +
221B GLY 3.3 0.3 + - - -
222B CYS* 2.9 33.1 + - - +
224B GLN 4.0 13.9 - - - +
225B VAL* 3.9 19.1 - - + -
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Residues in contact with LEU 218 (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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214B GLN* 3.0 39.3 + - + +
215B GLN* 3.6 31.9 - - - +
217B ALA* 1.3 74.9 - - - +
219B LYS* 1.3 59.0 + - - +
221B GLY* 3.0 18.9 + - - -
222B CYS 3.3 15.3 - - - +
223B GLU* 4.1 11.9 - - + +
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Residues in contact with LYS 219 (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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215B GLN 3.0 17.1 + - - +
216B GLU* 3.7 25.6 - - - +
217B ALA 3.3 0.2 - - - -
218B LEU* 1.3 76.2 - - - +
220B ARG* 1.3 58.5 + - + +
221B GLY 3.2 3.5 + - - -
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Residues in contact with ARG 220 (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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185B LEU* 3.5 31.1 - - + +
187B ASP* 5.7 3.9 + - - -
216B GLU* 3.1 35.4 + - - +
217B ALA 3.2 4.7 + - - +
218B LEU 3.2 0.2 - - - -
219B LYS* 1.3 76.4 - - + +
221B GLY* 1.3 58.6 - - - +
222B CYS* 3.5 2.9 + - - -
322B ARG* 5.2 2.8 + - - -
324B LEU* 3.8 41.5 - - + +
327B ASP* 3.7 36.1 + - - +
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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