Contacts of the helix formed by residues 201 - 211 (chain B) in PDB entry 2QJ3
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 ALA 201 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B GLU* 3.4 43.3 - - + +
120B MET* 3.8 8.7 - - + +
123B ALA* 3.8 7.8 - - + +
198B MET* 3.1 14.9 + - + +
199B ALA 2.9 1.6 + - - -
200B PRO* 1.3 78.2 - - - +
202B LEU* 1.3 61.7 + - - +
203B ASP 3.7 0.2 - - - -
204B GLY 4.8 1.6 - - - -
205B PHE* 3.3 23.8 + - - +
244B LEU* 3.5 10.8 - - + +
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Residues in contact with LEU 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 3.8 0.4 + - - -
199B ALA* 2.9 21.1 + - + +
200B PRO 3.3 0.4 - - - -
201B ALA* 1.3 78.1 - - - +
203B ASP* 1.3 64.7 + - - +
205B PHE* 3.3 2.3 + - + +
206B ALA* 2.8 39.6 + - + +
241B VAL* 3.8 36.6 - - + +
242B SER* 5.3 2.2 - - - -
244B LEU* 3.8 12.8 - - + -
245B THR* 4.5 13.2 - - + -
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Residues in contact with ASP 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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199B ALA 4.7 2.6 - - - +
200B PRO* 4.5 6.1 + - - +
201B ALA 3.7 0.2 - - - -
202B LEU* 1.3 87.4 + - - +
204B GLY* 1.3 59.1 + - - +
206B ALA* 3.6 5.0 + - - +
207B ALA* 3.0 28.4 + - - +
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Residues in contact with GLY 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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115B THR* 4.4 4.2 - - - +
119B GLU* 3.4 27.1 + - - -
200B PRO 5.4 0.8 + - - -
201B ALA 4.5 1.2 + - - -
202B LEU 3.4 0.2 - - - -
203B ASP* 1.3 77.0 - - - +
205B PHE* 1.3 59.9 + - - +
207B ALA* 3.3 6.5 + - - +
208B ALA* 2.9 31.0 + - - +
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Residues in contact with PHE 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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95B ILE* 4.5 3.1 - - + -
112B LEU* 3.5 36.8 - - + -
115B THR* 5.0 1.3 - - - -
116B ARG* 3.6 44.6 - - + -
119B GLU* 4.3 9.9 - - + +
201B ALA 3.3 22.2 + - - +
202B LEU* 3.3 3.9 + - - +
204B GLY* 1.3 75.5 - - - +
206B ALA* 1.3 61.5 + - - +
208B ALA* 3.4 4.1 + - + +
209B ALA* 3.1 21.8 + - + +
240B LEU* 3.7 38.6 - - + -
241B VAL* 4.1 20.6 - - + -
244B LEU* 3.7 24.2 - - + -
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Residues in contact with ALA 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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202B LEU* 2.8 25.3 + - + +
203B ASP* 3.7 5.4 - - - +
205B PHE* 1.3 70.8 - - - +
207B ALA* 1.3 53.8 + - - +
209B ALA* 3.0 5.5 + - - +
210B ALA* 2.8 34.3 + - - +
241B VAL* 4.0 28.4 - - + +
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Residues in contact with ALA 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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203B ASP 3.0 19.4 + - - +
204B GLY* 3.3 7.2 + - - +
206B ALA* 1.3 75.3 - - - +
208B ALA* 1.3 61.0 + - - +
210B ALA* 3.4 9.3 + - - +
211B ASN* 3.4 25.6 + - - +
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Residues in contact with ALA 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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112B LEU* 3.5 21.3 - - + -
115B THR* 3.8 23.3 - - + +
204B GLY 2.9 16.6 + - - +
205B PHE* 3.6 2.5 - - - +
206B ALA 3.2 0.2 - - - -
207B ALA* 1.3 76.8 - - - +
209B ALA* 1.3 60.7 + - - +
210B ALA 3.6 0.2 + - - -
211B ASN* 3.7 6.6 + - - +
212B ILE* 3.5 22.5 - - - +
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Residues in contact with ALA 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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112B LEU* 3.7 10.9 - - + +
205B PHE* 3.1 15.8 + - + +
206B ALA 3.0 8.8 + - - +
208B ALA* 1.3 75.7 - - - +
210B ALA* 1.3 64.0 + - - +
212B ILE* 3.7 14.5 + - - +
237B MET* 3.9 32.4 - - + +
240B LEU* 6.0 0.9 - - + -
241B VAL* 3.6 22.0 - - + -
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Residues in contact with ALA 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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206B ALA 2.8 12.1 + - - +
207B ALA* 3.6 14.1 - - - +
208B ALA 3.3 0.2 - - - -
209B ALA* 1.3 78.2 - - - +
211B ASN* 1.3 67.4 + - - +
212B ILE 3.0 9.9 + - - +
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Residues in contact with ASN 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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108B ASP* 5.1 0.9 - - - +
207B ALA* 3.4 13.4 + - - +
208B ALA* 3.7 3.8 + - - +
209B ALA 3.4 0.4 - - - -
210B ALA* 1.3 88.8 + - - +
212B ILE* 1.3 64.8 + - - +
213B ALA 4.3 0.2 - - - -
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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