Contacts of the helix formed by residues 240 - 254 (chain B) in PDB entry 2PQG
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 LYS 240 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236B LYS 3.3 15.2 + - - +
237B GLN 2.9 12.9 + - - +
239B GLN* 1.3 96.6 + - - +
241B TRP* 1.3 63.5 + - - +
242B ASP* 3.2 3.6 - - - +
243B ARG* 2.4 68.3 + - + +
244B ILE* 3.0 23.0 + - + +
265B LEU* 3.7 28.7 - - + -
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Residues in contact with TRP 241 (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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62B LEU* 3.6 27.4 - - + -
92B ASN* 3.5 28.7 - - + -
210B ARG* 3.3 40.2 - - + +
211B PHE* 3.6 34.8 - + + -
237B GLN 3.6 0.4 + - - -
238B VAL 3.4 8.6 + - - +
239B GLN 3.5 1.6 - - - -
240B LYS* 1.3 75.8 - - - +
242B ASP* 1.3 77.5 + - - +
244B ILE* 3.8 2.9 - - - +
245B SER* 2.8 39.8 + - - -
277B VAL* 3.9 12.3 - - + +
279B LEU 2.8 26.1 + - - -
280B VAL* 4.1 0.2 - - - +
281B LYS* 3.4 44.4 - - + -
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Residues in contact with ASP 242 (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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239B GLN 5.4 0.4 + - - +
240B LYS* 3.2 0.6 - - - -
241B TRP* 1.3 88.8 - - - +
243B ARG* 1.3 67.6 + - + +
245B SER* 3.3 8.4 + - - -
246B LYS* 3.1 32.6 + - - +
281B LYS* 3.4 34.6 - - - +
283B GLN* 4.5 1.2 + - - -
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Residues in contact with ARG 243 (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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240B LYS* 2.4 63.6 + - + +
242B ASP* 1.3 81.8 - - + +
244B ILE* 1.3 57.6 + - - +
246B LYS* 3.1 13.3 + - + +
247B ALA* 3.0 23.2 + - - +
261B ASP* 4.7 23.7 + - + +
262B MET* 3.9 12.0 - - + +
265B LEU* 5.8 0.9 - - - -
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Residues in contact with ILE 244 (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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211B PHE* 5.1 2.0 - - + -
237B GLN* 4.7 5.4 - - + +
240B LYS* 3.0 18.9 + - + +
241B TRP* 4.0 5.6 - - - +
243B ARG* 1.3 71.8 - - - +
245B SER* 1.3 62.6 + - - +
246B LYS 3.2 0.2 - - - -
247B ALA* 3.6 2.5 - - - +
248B ALA* 3.0 24.2 + - + +
251B TRP* 5.6 0.7 - - + -
262B MET* 3.6 33.0 - - + -
265B LEU* 4.1 13.0 - - + -
267B ILE* 4.7 10.3 - - + -
273B ALA* 4.3 17.9 - - + +
276B ILE* 5.5 3.6 - - + -
277B VAL* 3.0 53.8 - - + +
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Residues in contact with SER 245 (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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241B TRP* 2.8 31.0 + - - -
242B ASP 3.5 5.6 - - - -
244B ILE* 1.3 77.6 - - - +
246B LYS* 1.3 63.1 + - - +
248B ALA* 3.4 2.4 + - - +
249B PHE* 3.2 29.8 + - - -
280B VAL* 3.5 17.8 - - - +
281B LYS* 3.0 44.3 + - - +
283B GLN* 3.9 3.8 - - - -
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Residues in contact with LYS 246 (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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242B ASP* 3.1 18.7 + - - +
243B ARG* 3.1 13.9 + - + +
245B SER* 1.3 77.2 - - - +
247B ALA* 1.3 59.6 + - - +
249B PHE* 3.2 4.0 + - - +
250B GLU* 2.9 28.4 + - - +
283B GLN* 3.0 31.9 - - + +
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Residues in contact with ALA 247 (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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243B ARG 3.0 8.9 + - - +
244B ILE 3.7 4.9 - - - +
245B SER 3.3 0.2 - - - -
246B LYS* 1.3 74.2 - - - +
248B ALA* 1.3 60.7 + - - +
250B GLU* 3.2 5.1 + - - +
251B TRP* 2.8 40.2 + - + -
259B ILE* 3.6 18.1 - - + +
262B MET* 3.5 43.1 - - + -
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Residues in contact with ALA 248 (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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56B GLY 4.5 2.1 - - - +
57B ILE* 3.7 19.5 - - + +
59B GLN* 4.1 13.0 - - - +
244B ILE* 3.0 16.5 + - + +
245B SER 3.5 10.5 - - - +
246B LYS 3.2 0.4 - - - -
247B ALA* 1.3 77.3 - - - +
249B PHE* 1.3 62.8 + - + +
251B TRP* 3.5 12.1 + - - +
252B ALA* 3.3 14.4 + - - -
270B LYS* 6.2 0.4 - - - -
273B ALA* 6.2 2.5 - - + -
280B VAL* 4.1 21.1 - - + -
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Residues in contact with PHE 249 (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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54B HIS* 4.3 15.3 - + - -
57B ILE* 3.9 25.8 - - + -
61B VAL* 3.9 24.7 - - + -
245B SER 3.2 16.6 + - - -
246B LYS 3.2 8.8 + - - +
248B ALA* 1.3 78.5 - - + +
250B GLU* 1.3 60.6 + - - +
252B ALA* 2.8 26.1 + - + +
253B ASP* 3.5 7.9 + - - +
280B VAL* 4.5 3.6 - - + -
281B LYS 3.4 15.9 - - - -
282B ASN* 4.0 4.5 - - - -
283B GLN* 3.2 51.6 - - + -
284B THR* 5.1 4.7 - - - -
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Residues in contact with GLU 250 (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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246B LYS 2.9 13.1 + - - +
247B ALA* 3.2 8.3 + - - +
249B PHE* 1.3 76.2 - - - +
251B TRP* 1.3 58.5 + - - +
252B ALA 3.2 0.2 + - - -
253B ASP* 3.3 7.5 + - - +
254B HIS* 2.9 32.6 + - - +
257B ALA* 3.5 25.7 - - + +
258B VAL 5.5 0.7 - - - +
259B ILE* 3.6 31.9 - - + +
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Residues in contact with TRP 251 (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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56B GLY* 4.5 1.1 - - - -
244B ILE 5.6 0.4 - - - -
247B ALA* 2.8 37.4 + - + +
248B ALA* 3.9 9.6 - - - +
249B PHE 3.2 0.4 - - - -
250B GLU* 1.3 75.1 - - - +
252B ALA* 1.3 63.6 + - - +
253B ASP 3.3 0.2 - - - -
254B HIS 3.4 17.7 - - - -
255B PRO* 3.2 30.0 + - - +
257B ALA* 2.8 21.6 + - + -
259B ILE* 3.4 21.9 - - + +
262B MET* 3.5 25.4 - - + -
267B ILE* 4.2 2.9 - - + -
268B LYS 3.0 28.7 + - - -
269B ASP* 3.6 12.2 - - - +
270B LYS* 3.1 59.1 + - + +
273B ALA* 4.1 14.1 - - + -
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Residues in contact with ALA 252 (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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55B LYS 3.8 13.5 - - - +
56B GLY* 3.7 17.9 - - - +
57B ILE* 3.7 29.6 - - + -
248B ALA 3.3 3.0 + - - -
249B PHE* 2.8 16.2 + - + +
251B TRP* 1.3 79.7 - - - +
253B ASP* 1.3 63.8 + - - +
255B PRO* 4.7 2.8 - - - +
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Residues in contact with ASP 253 (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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249B PHE 3.5 6.4 + - - +
250B GLU* 3.3 6.8 + - - +
252B ALA* 1.3 84.1 - - - +
254B HIS* 1.3 89.4 + - + +
255B PRO* 3.5 7.1 - - - +
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Residues in contact with HIS 254 (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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250B GLU* 2.9 18.1 + - + +
251B TRP* 3.4 10.6 - - - -
253B ASP* 1.3 103.2 - - + +
255B PRO* 1.3 65.1 - - - +
256B THR* 3.1 9.2 + - - +
257B ALA* 3.1 28.6 + - + +
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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