Contacts of the helix formed by residues 247 - 258 (chain A) in PDB entry 2QPS
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 ASP 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A LEU* 4.7 3.4 - - - -
245A VAL 3.4 2.7 + - - -
246A PHE* 1.3 68.1 - - - +
248A PHE* 1.3 58.9 + - - +
249A THR* 3.4 4.7 - - - -
250A THR* 2.7 47.0 + - - +
251A LYS* 3.0 24.1 + - - +
275A VAL* 3.0 22.4 + - - +
276A MET* 2.9 26.3 + - - +
283A ALA* 3.7 10.3 - - + +
284A VAL 3.0 17.4 + - - +
285A THR* 4.1 13.1 - - + +
286A PHE* 3.5 7.5 + - - -
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Residues in contact with PHE 248 (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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205A GLU* 3.9 21.5 - - + -
206A VAL 3.6 21.5 - - - +
207A TRP* 3.5 57.7 - + + -
210A MET* 4.2 0.7 - - - +
225A HIS* 3.8 18.8 - - + +
229A LEU* 4.1 2.7 - - + +
246A PHE* 2.8 42.1 + + + +
247A ASP* 1.3 70.3 - - - +
249A THR* 1.3 57.1 + - - +
251A LYS* 3.7 4.4 - - + +
252A GLY* 2.7 31.0 + - - -
286A PHE* 3.6 23.6 - + - -
289A ASN* 4.3 12.1 - - - -
292A THR* 4.6 2.7 - - + -
299A TRP* 4.1 15.9 - + + -
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Residues in contact with THR 249 (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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210A MET* 3.4 4.5 - - + +
222A GLN* 3.6 37.2 - - + +
225A HIS* 2.9 25.6 + - - +
226A ARG* 3.4 17.5 - - + +
229A LEU* 3.5 10.2 - - - +
247A ASP* 3.4 6.3 - - - -
248A PHE* 1.3 80.0 - - - +
250A THR* 1.3 58.1 + - - +
253A ILE* 2.9 38.1 + - + +
273A PRO 4.4 0.2 - - - +
274A GLY* 3.7 18.4 - - - -
275A VAL* 3.7 1.7 - - - +
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Residues in contact with THR 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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247A ASP* 2.7 41.9 + - - -
249A THR* 1.3 73.2 - - - +
251A LYS* 1.3 66.5 + - - +
253A ILE* 4.5 4.9 - - + -
254A LEU* 2.8 38.0 + - + +
265A LEU* 6.3 1.3 - - + -
273A PRO* 5.9 2.7 - - + -
274A GLY* 3.2 18.5 + - - +
276A MET* 4.3 9.7 - - + +
285A THR* 4.9 6.3 - - + -
286A PHE 6.1 0.9 - - - +
312A TYR* 3.7 35.2 + - + +
313A ILE* 5.3 2.5 - - + -
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Residues in contact with LYS 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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247A ASP 3.0 17.9 + - - +
248A PHE* 3.7 4.7 - - + +
250A THR* 1.3 77.8 - - - +
252A GLY* 1.3 63.6 + - - +
254A LEU* 4.0 4.0 - - - +
255A ASN* 2.7 56.4 + - - +
286A PHE* 3.8 38.3 + - + +
287A VAL 2.8 30.8 + - - +
288A ASP* 2.9 17.1 + - - -
292A THR* 4.3 8.3 - - + -
299A TRP* 3.0 37.3 + - + -
301A PHE* 3.6 7.1 - - + +
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Residues in contact with GLY 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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210A MET* 3.5 16.2 - - - -
218A PRO* 4.2 9.9 - - - +
248A PHE 2.7 15.0 + - - -
251A LYS* 1.3 76.0 - - - +
253A ILE* 1.3 61.1 + - - +
255A ASN* 3.4 13.0 - - - +
256A ALA* 3.7 3.3 + - - +
299A TRP* 3.4 33.2 + - - -
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Residues in contact with ILE 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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210A MET* 4.0 9.6 - - + -
218A PRO* 5.0 8.1 - - + -
219A ASN 5.6 1.6 - - - +
220A TYR 5.3 4.9 - - - +
222A GLN* 4.1 14.6 - - + -
249A THR* 2.9 41.0 + - + +
250A THR* 3.8 3.8 - - + +
252A GLY* 1.3 72.9 - - - +
254A LEU* 1.3 55.2 + - - +
256A ALA* 2.9 7.4 + - - +
257A ALA 2.8 30.5 + - - -
264A ARG* 3.8 36.1 - - + +
265A LEU* 4.1 10.8 - - + -
273A PRO* 3.4 30.7 - - + -
274A GLY* 3.9 4.9 - - - +
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Residues in contact with LEU 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 THR* 2.8 26.2 + - + +
251A LYS* 4.0 2.9 - - - +
253A ILE* 1.3 73.3 - - - +
255A ASN* 1.3 63.6 + - - +
256A ALA 3.1 1.2 + - - -
257A ALA* 3.1 13.1 + - + -
258A VAL* 3.2 39.1 + - + +
265A LEU* 4.1 26.9 - - + +
286A PHE 5.3 5.4 - - - +
287A VAL* 5.9 1.1 - - + -
301A PHE* 3.5 23.5 - - + -
309A GLY* 4.3 9.2 - - - +
312A TYR* 3.7 40.4 - - + -
313A ILE* 4.6 7.4 - - + -
376A ILE* 4.8 3.1 - - + -
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Residues in contact with ASN 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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251A LYS* 2.7 43.0 + - - +
252A GLY* 3.4 10.5 - - - +
253A ILE 3.1 0.2 - - - -
254A LEU* 1.3 77.4 - - - +
256A ALA* 1.3 57.9 + - + +
258A VAL* 4.2 0.2 - - - +
259A GLU* 3.7 5.7 - - - +
299A TRP* 3.5 30.0 + - - +
300A PRO 3.0 23.0 + - - -
301A PHE* 2.9 28.5 - - - -
302A PRO* 3.4 25.4 - - - +
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Residues in contact with ALA 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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217A LYS* 5.5 3.6 - - + -
218A PRO* 3.9 33.2 - - + -
252A GLY 3.7 1.1 + - - +
253A ILE 2.9 7.4 + - - +
255A ASN* 1.3 79.0 - - - +
257A ALA* 1.3 67.0 + - - +
258A VAL 3.4 0.9 - - - -
259A GLU* 3.1 22.8 + - - +
261A GLU* 3.9 11.1 - - - +
264A ARG* 3.9 14.3 + - - +
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Residues in contact with ALA 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 ILE 2.8 12.2 + - - +
254A LEU* 3.1 4.4 + - + +
256A ALA* 1.3 72.7 - - - +
258A VAL* 1.3 58.3 + - - +
259A GLU 2.8 10.9 + - - -
260A GLY 3.5 0.2 + - - -
261A GLU 2.8 42.9 + - - +
262A LEU* 3.2 7.4 + - - +
264A ARG* 3.9 8.0 - - + +
265A LEU* 3.3 41.7 - - + -
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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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254A LEU* 3.2 36.3 + - + +
255A ASN 4.2 0.7 - - - +
257A ALA* 1.3 72.8 - - - +
259A GLU* 1.3 50.5 + - - +
260A GLY 3.2 6.0 + - - -
262A LEU* 4.7 8.7 - - + +
301A PHE* 4.0 15.9 - - + -
302A PRO* 3.6 37.5 - - + -
305A LYS* 2.7 40.9 + - + +
308A GLN* 4.2 28.3 - - + +
376A ILE* 4.8 5.6 - - + -
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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