Contacts of the helix formed by residues 244 - 254 (chain B) in PDB entry 2PKG
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 VAL 244 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B ILE* 4.7 2.2 - - + -
209B PHE* 4.8 6.7 - - + -
228B CYS* 3.6 29.6 - - - +
231B ILE* 4.7 9.4 - - + -
232B ALA* 4.4 17.3 - - + -
235B LEU* 3.6 15.7 - - + -
240B LEU* 2.7 43.1 + - + +
243B LEU* 1.3 73.4 - - + +
245B MET* 1.3 70.3 + - - +
246B PRO* 3.4 0.7 - - - -
247B THR* 2.9 21.1 + - - -
248B LEU* 3.1 19.4 + - + -
274B VAL* 6.2 0.2 - - + -
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Residues in contact with MET 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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240B LEU* 3.1 19.8 + - + +
241B GLU* 3.8 15.7 - - - +
244B VAL* 1.3 76.8 - - - +
246B PRO* 1.3 64.5 - - + +
248B LEU* 2.9 28.4 + - + -
249B ARG* 2.5 60.0 + - + +
274B VAL* 4.1 11.9 - - + -
278B ILE* 3.1 35.2 - - + +
282B ASP* 3.3 30.3 - - + +
283B LEU* 4.6 3.8 - - + -
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Residues in contact with PRO 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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241B GLU* 3.5 19.1 - - - +
242B ALA* 5.1 5.4 - - - +
243B LEU 4.3 8.1 - - - +
244B VAL 3.4 6.3 - - - -
245B MET* 1.3 95.4 - - + +
247B THR* 1.3 57.8 + - - +
249B ARG* 3.5 21.5 - - + +
250B GLN* 2.9 26.7 + - - +
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Residues in contact with THR 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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209B PHE* 3.4 30.3 - - + -
210B SER* 4.2 16.3 + - - -
213B ALA* 3.4 33.9 - - + -
243B LEU 4.1 7.3 + - - -
244B VAL 2.9 10.9 + - - -
246B PRO* 1.3 79.6 - - - +
248B LEU* 1.3 57.9 + - - +
250B GLN* 3.1 8.5 + - - +
251B ALA* 2.8 29.0 + - + +
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Residues in contact with LEU 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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225B VAL* 6.4 0.9 - - + -
228B CYS* 3.7 28.2 - - + -
244B VAL* 3.1 6.5 + - + +
245B MET* 2.9 39.4 + - + +
247B THR* 1.3 79.3 - - - +
249B ARG* 1.3 62.7 + - + +
251B ALA* 3.0 22.6 - - + +
252B ALA* 3.1 8.5 + - + +
263B VAL* 4.2 11.2 - - + -
267B PHE* 6.3 0.2 - - + -
270B LEU* 4.0 31.4 - - + -
274B VAL* 4.1 20.4 - - + -
283B LEU* 4.8 10.5 - - + -
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Residues in contact with ARG 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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241B GLU* 2.6 45.2 + - - -
245B MET* 2.5 32.7 + - + +
246B PRO* 3.5 26.0 - - + +
248B LEU* 1.3 71.3 - - + +
250B GLN* 1.3 67.7 + - - +
251B ALA 3.1 0.5 + - - -
252B ALA* 3.2 8.6 + - - +
253B GLU* 3.2 34.6 + - - +
282B ASP* 3.2 31.4 + - + +
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Residues in contact with GLN 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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213B ALA 6.0 2.0 - - - +
214B SER* 6.4 1.6 - - - -
246B PRO 2.9 13.4 + - - +
247B THR* 3.5 10.3 - - + +
249B ARG* 1.3 76.8 - - - +
251B ALA* 1.3 52.2 + - - +
253B GLU* 3.1 20.5 + - - +
254B ASP* 2.6 56.2 + - - +
255B LYS* 4.8 1.2 - - - +
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Residues in contact with ALA 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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213B ALA* 6.5 0.9 - - + -
225B VAL* 4.1 24.7 - - + -
228B CYS* 6.6 0.2 - - + -
247B THR* 2.8 13.9 + - + +
248B LEU* 3.0 18.2 - - + +
250B GLN* 1.3 75.3 - - - +
252B ALA* 1.3 58.4 + - - +
254B ASP* 2.7 37.0 + - - +
259B VAL* 4.0 7.0 - - + +
260B ARG* 4.1 1.0 - - - +
263B VAL* 4.0 11.6 - - + +
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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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248B LEU* 3.1 7.5 + - + +
249B ARG* 3.2 9.8 + - - +
251B ALA* 1.3 79.8 - - - +
253B GLU* 1.3 59.3 + - + +
260B ARG* 3.1 26.4 - - - +
263B VAL* 3.9 24.4 - - + +
267B PHE* 6.3 0.2 - - + -
286B ALA* 4.6 21.3 - - + +
290B LEU* 4.4 14.4 - - + +
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Residues in contact with GLU 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 ARG* 3.2 25.2 + - - +
250B GLN* 3.1 24.3 + - - +
251B ALA 3.0 0.8 - - - -
252B ALA* 1.3 77.0 - - + +
254B ASP* 1.3 71.3 + - - +
255B LYS* 4.3 1.4 - - - +
260B ARG* 4.2 3.2 - - - +
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Residues in contact with ASP 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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213B ALA 4.6 3.3 - - - +
221B ARG* 2.9 37.8 + - - +
250B GLN* 2.6 27.5 + - - +
251B ALA* 2.7 21.6 + - - +
253B GLU* 1.3 79.9 - - - +
255B LYS* 1.3 60.4 + - - +
256B SER 2.8 26.0 + - - -
259B VAL* 3.4 31.0 - - + +
260B ARG* 2.8 25.4 + - + -
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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