Contacts of the helix formed by residues 249 - 261 (chain A) in PDB entry 2QPA
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 SER 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A VAL* 4.2 8.8 - - - +
207A MET* 3.3 22.2 - - - +
237A LEU* 4.9 21.7 - - - +
238A THR* 5.0 8.7 + - - -
248A ALA* 1.3 74.4 - - - +
250A ARG* 1.3 57.6 + - - +
251A ARG 2.7 6.1 - - - -
252A ILE* 2.8 29.0 + - - +
253A LYS* 3.1 12.0 + - - +
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Residues in contact with ARG 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A ALA* 3.3 8.9 - - + +
249A SER* 1.3 77.2 - - - +
251A ARG* 1.3 57.4 + - - +
252A ILE 3.4 0.4 - - - -
253A LYS* 4.1 10.6 - - - +
254A THR* 3.7 19.1 + - - -
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Residues in contact with ARG 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A GLU* 5.1 6.4 - - - +
248A ALA 3.3 25.1 - - - +
249A SER 2.7 0.6 - - - -
250A ARG* 1.3 81.6 - - - +
252A ILE* 1.3 63.8 + - + +
253A LYS 3.5 0.2 - - - -
254A THR* 4.3 5.3 - - - -
255A GLU* 4.2 12.6 + - - +
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Residues in contact with ILE 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A LEU* 4.9 7.0 - - + +
207A MET* 4.3 17.0 - - + -
210A SER* 3.6 31.4 - - - -
211A GLU* 4.7 4.3 - - + +
214A VAL* 4.5 18.9 - - + +
237A LEU* 4.6 24.6 - - + +
248A ALA 2.9 27.4 - - - +
249A SER* 2.8 15.3 + - - +
251A ARG* 1.3 84.3 - - + +
253A LYS* 1.3 64.6 + - - +
254A THR 3.2 2.2 + - - -
255A GLU* 3.6 6.7 + - + +
256A LEU* 3.5 17.8 + - - +
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Residues in contact with LYS 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A LEU* 4.8 12.9 - - - +
249A SER 3.1 12.7 + - - +
250A ARG* 4.3 10.8 - - - +
251A ARG 3.5 0.2 - - - -
252A ILE* 1.3 79.4 - - - +
254A THR* 1.3 61.6 + - - +
256A LEU* 3.4 7.1 + - - +
257A LEU* 3.1 28.2 + - + +
283A ASP* 5.6 5.4 - - + +
286A ILE* 4.6 23.7 - - + +
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Residues in contact with THR 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ARG 3.7 14.8 + - - -
251A ARG* 4.7 5.2 - - - -
252A ILE* 3.2 0.6 - - - +
253A LYS* 1.3 75.2 - - - +
255A GLU* 1.3 57.2 + - - +
256A LEU 3.0 1.8 - - - -
257A LEU* 2.9 12.9 + - + +
258A VAL* 2.6 55.9 + - + +
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Residues in contact with GLU 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A GLU* 3.8 28.3 - - + +
214A VAL* 3.7 21.8 - - + -
215A LYS* 2.9 36.7 + - + +
251A ARG 4.2 10.0 + - - +
252A ILE* 3.6 10.0 + - - +
253A LYS 3.5 0.8 - - - -
254A THR* 1.3 76.7 - - - +
256A LEU* 1.3 62.1 + - - +
258A VAL* 3.4 13.2 + - - +
259A GLN* 2.9 57.2 + - - +
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Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A VAL* 4.5 9.8 - - + +
218A PHE* 3.9 12.8 - - + -
231A ILE* 3.9 29.2 - - + -
234A VAL* 6.1 1.6 - - + -
237A LEU* 4.2 23.1 - - + -
252A ILE 3.5 8.9 + - - +
253A LYS* 3.4 10.7 + - - +
254A THR 3.0 0.6 - - - -
255A GLU* 1.3 75.0 - - - +
257A LEU* 1.3 67.7 + - + +
259A GLN* 2.8 15.5 + - - +
260A MET* 2.8 53.0 + - + +
286A ILE* 4.3 26.0 - - + -
290A PHE* 5.6 1.8 - - + -
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Residues in contact with LEU 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A LYS* 3.1 16.9 + - + +
254A THR* 2.9 17.6 + - + +
256A LEU* 1.3 79.5 - - + +
258A VAL* 1.3 63.7 + - - +
260A MET* 4.7 4.7 - - + +
261A ASN* 3.1 54.1 + - - +
285A ALA* 4.4 21.8 - - + +
286A ILE* 4.6 20.2 - - + +
289A ARG* 4.3 15.5 - - + -
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Residues in contact with VAL 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LYS* 6.4 0.2 - - - -
254A THR* 2.6 42.9 + - + +
255A GLU* 3.6 19.3 - - - +
257A LEU* 1.3 73.6 - - + +
259A GLN* 1.3 67.9 + - - +
261A ASN 4.3 1.6 - - - +
262A GLY* 4.1 9.7 + - - -
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Residues in contact with GLN 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A VAL* 4.4 6.3 - - + -
215A LYS* 3.8 17.9 + - - +
218A PHE* 3.0 54.8 - - + +
219A ALA 5.0 0.2 + - - -
222A ARG* 3.2 20.3 + - - +
255A GLU* 2.9 45.1 + - - +
256A LEU 2.8 11.8 + - - +
258A VAL* 1.3 73.5 - - - +
260A MET* 1.3 66.9 + - - +
262A GLY* 3.0 23.7 + - - +
263A VAL* 3.3 3.1 + - - +
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Residues in contact with MET 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A SER* 5.4 1.1 - - - -
168A GLY* 4.0 9.6 - - - -
218A PHE* 3.9 13.0 - - + -
256A LEU* 2.8 47.3 + - + +
257A LEU* 4.4 3.6 - - - +
259A GLN* 1.3 67.8 - - - +
261A ASN* 1.3 60.5 + - - +
262A GLY 2.3 19.4 + - - -
263A VAL* 2.7 25.0 + - - +
272A VAL* 3.4 34.5 - - + -
286A ILE* 5.5 1.3 - - - -
289A ARG* 3.7 28.7 - - + +
290A PHE* 3.9 23.1 - - + -
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Residues in contact with ASN 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A LEU* 3.1 47.2 + - - +
258A VAL 4.3 2.1 - - - +
259A GLN 4.0 0.7 - - - -
260A MET* 1.3 76.2 - - - +
262A GLY* 1.3 52.4 + - - +
289A ARG* 3.2 26.5 - - - +
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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