Contacts of the helix formed by residues 240 - 254 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A LYS 3.5 13.4 + - - +
237A GLN 2.8 12.6 + - - +
239A GLN* 1.3 90.3 + - - +
241A TRP* 1.3 63.5 + - - +
242A ASP* 3.1 3.6 - - - -
243A ARG* 2.8 57.8 + - + +
244A ILE* 2.9 12.7 + - + +
265A LEU* 3.7 31.0 - - + -
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Residues in contact with TRP 241 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A LEU* 3.7 21.5 - - + -
92A ASN* 3.5 32.1 - - + -
210A ARG* 3.4 44.2 + - + +
211A PHE* 3.4 38.6 - + + -
237A GLN 3.4 0.8 + - - -
238A VAL 3.4 8.8 + - - +
239A GLN 3.5 1.6 + - - -
240A LYS* 1.3 77.5 - - - +
242A ASP* 1.3 72.2 + - - +
244A ILE* 3.5 4.1 + - - +
245A SER* 2.8 43.4 + - - -
277A VAL* 4.2 8.9 - - + +
279A LEU 2.9 28.7 + - - -
281A LYS* 3.2 41.1 - - + -
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Residues in contact with ASP 242 (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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240A LYS 3.1 1.0 - - - -
241A TRP* 1.3 85.8 - - - +
243A ARG* 1.3 59.6 + - - +
245A SER* 3.3 7.7 + - - -
246A LYS* 3.0 41.7 + - - +
281A LYS* 3.2 35.0 - - + +
283A GLN* 4.9 0.9 - - - +
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Residues in contact with ARG 243 (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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240A LYS* 2.8 53.4 + - + +
242A ASP* 1.3 78.7 - - - +
244A ILE* 1.3 60.0 + - - +
245A SER 3.1 0.2 - - - -
246A LYS* 3.2 13.2 + - + +
247A ALA* 3.0 23.2 + - - +
261A ASP* 2.9 63.2 + - + +
262A MET* 3.6 12.3 - - + +
264A LYS* 3.8 19.0 - - - +
265A LEU* 3.8 13.3 - - - +
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Residues in contact with ILE 244 (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 PHE* 5.0 1.3 - - + -
237A GLN* 4.3 9.2 - - + +
240A LYS* 2.9 25.1 + - + +
241A TRP* 4.1 6.7 - - - +
243A ARG* 1.3 75.4 - - - +
245A SER* 1.3 59.1 + - - +
247A ALA* 3.8 1.6 - - - +
248A ALA* 3.0 24.9 + - + +
251A TRP* 5.3 1.7 - - + -
262A MET* 3.4 29.8 - - + +
265A LEU* 5.0 4.0 - - + -
267A ILE* 4.5 13.9 - - + -
273A ALA* 3.7 26.2 - - + +
276A ILE* 4.8 2.2 - - + -
277A VAL* 3.4 45.5 - - + -
280A VAL* 4.9 0.2 - - - +
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Residues in contact with SER 245 (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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241A TRP* 2.8 28.4 + - - -
242A ASP 3.4 5.6 - - - -
243A ARG 3.1 0.2 - - - -
244A ILE* 1.3 77.0 - - - +
246A LYS* 1.3 65.4 + - - +
248A ALA* 3.1 20.9 - - - +
249A PHE* 3.3 14.6 + - - -
277A VAL* 5.8 0.2 - - - +
280A VAL* 3.6 10.8 - - - +
281A LYS* 2.9 47.5 + - - +
283A GLN* 4.1 3.8 - - - -
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Residues in contact with LYS 246 (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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242A ASP* 3.0 27.2 + - - +
243A ARG* 3.2 13.7 + - + +
245A SER* 1.3 73.7 - - - +
247A ALA* 1.3 64.1 + - - +
249A PHE* 3.1 6.8 + - - +
250A GLU* 2.9 21.7 + - - +
283A GLN* 3.6 35.7 - - + +
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Residues in contact with ALA 247 (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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243A ARG 3.0 14.8 + - - +
244A ILE 3.8 5.6 - - - +
245A SER 3.3 0.2 - - - -
246A LYS* 1.3 73.9 - - - +
248A ALA* 1.3 60.0 + - - +
250A GLU* 3.0 6.4 + - - +
251A TRP* 2.8 43.9 + - + +
259A ILE* 3.5 29.6 - - + -
262A MET* 3.7 21.1 - - + -
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Residues in contact with ALA 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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56A GLY 4.5 2.4 - - - +
57A ILE* 3.7 22.2 - - + +
59A GLN* 4.7 4.9 - - - +
244A ILE* 3.0 16.7 + - + +
245A SER 3.1 12.1 + - - +
247A ALA* 1.3 77.4 - - - +
249A PHE* 1.3 61.6 + - + +
251A TRP* 3.5 11.4 + - - +
252A ALA 3.3 14.2 + - - -
270A LYS* 5.6 0.4 - - - -
277A VAL* 6.0 0.4 - - + -
280A VAL* 3.8 25.1 - - + -
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Residues in contact with PHE 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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54A HIS* 4.0 24.5 - + - -
57A ILE* 3.7 27.6 - - + -
61A VAL* 3.7 25.1 - - + -
245A SER 3.3 13.4 + - - -
246A LYS 3.1 8.6 + - - +
248A ALA* 1.3 78.9 - - + +
250A GLU* 1.3 63.9 + - - +
252A ALA* 3.1 16.8 - - - +
253A ASP* 3.4 11.4 + - - -
280A VAL* 4.2 7.0 - - + -
281A LYS 3.6 18.6 - - - -
282A ASN* 4.0 4.9 - - - -
283A GLN* 3.5 40.4 - - + -
284A THR* 4.5 6.1 - - - -
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Residues in contact with GLU 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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246A LYS 2.9 13.5 + - - +
247A ALA* 3.0 10.0 + - - +
249A PHE* 1.3 76.3 - - - +
251A TRP* 1.3 57.9 + - - +
253A ASP* 3.2 7.9 + - - +
254A HIS* 2.9 32.8 + - - +
257A ALA* 3.6 25.2 - - + +
258A VAL 4.7 2.8 - - - +
259A ILE* 3.7 28.5 - - + +
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Residues in contact with TRP 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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244A ILE* 5.3 1.1 - - + -
247A ALA* 2.8 36.1 + - + +
248A ALA* 3.9 8.5 - - - +
250A GLU* 1.3 69.1 - - - +
252A ALA* 1.3 65.3 + - - +
254A HIS 3.4 19.3 - - - -
255A PRO* 3.3 25.9 + - + +
257A ALA* 2.8 24.3 + - + -
259A ILE* 3.4 25.7 - - + +
262A MET* 3.7 24.7 - - + -
267A ILE* 4.6 3.4 - - + -
268A LYS 2.9 32.5 + - - -
269A ASP* 3.8 9.9 - - - +
270A LYS* 3.0 60.5 + - + +
273A ALA* 4.0 16.6 - - + -
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Residues in contact with ALA 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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54A HIS* 4.4 6.3 - - + +
55A LYS 3.7 14.3 - - - +
56A GLY* 3.6 18.2 - - - +
57A ILE* 3.7 29.6 - - + -
248A ALA 3.3 4.0 + - - +
249A PHE* 3.1 15.5 + - - +
250A GLU 3.1 0.2 - - - -
251A TRP* 1.3 81.2 - - - +
253A ASP* 1.3 64.4 + - - +
255A PRO* 4.8 2.6 - - - +
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Residues in contact with ASP 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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54A HIS* 5.6 2.6 + - - -
249A PHE 3.4 8.5 + - - +
250A GLU* 3.2 7.7 + - - +
252A ALA* 1.3 85.7 - - - +
254A HIS* 1.3 88.0 + - + +
255A PRO* 3.7 6.5 - - - +
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Residues in contact with HIS 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 GLU* 2.9 19.8 + - - +
251A TRP* 3.4 11.0 - - - -
253A ASP* 1.3 98.1 + - + +
255A PRO* 1.3 61.7 - - - +
256A THR* 3.0 13.3 + - - +
257A ALA* 3.1 29.4 + - + +
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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