Contacts of the helix formed by residues 238 - 251 (chain Y) in PDB entry 2Q4G
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 LEU 238 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210Y VAL* 3.4 33.4 - - + +
211Y THR 4.0 2.7 - - - +
212Y SER* 3.1 16.2 + - - +
215Y CYS* 3.6 25.8 - - - -
233Y LEU* 4.0 27.8 - - + -
236Y ASN* 2.9 26.5 + - + +
237Y LYS* 1.3 72.8 - - - +
239Y GLY* 1.3 65.6 + - - +
241Y VAL* 4.4 0.3 + - - +
242Y GLY* 2.9 23.6 + - - -
243Y MET* 4.5 2.2 - - - +
246Y LEU* 4.3 9.4 - - + -
262Y ILE* 4.5 4.0 - - + -
265Y CYS* 3.3 27.8 + - + +
267Y ILE* 5.4 3.6 - - + -
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Residues in contact with GLY 239 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212Y SER* 5.1 0.4 - - - -
237Y LYS 3.5 1.8 - - - -
238Y LEU* 1.3 73.3 - - - +
240Y ASP* 1.3 63.4 + - - -
241Y VAL* 3.2 0.7 - - - -
243Y MET* 2.8 28.9 + - - +
265Y CYS 2.7 15.4 + - - -
266Y GLY* 3.2 22.2 - - - -
267Y ILE* 3.9 5.3 - - - +
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Residues in contact with ASP 240 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239Y GLY* 1.3 69.4 - - - -
241Y VAL* 1.3 63.3 + - + +
243Y MET* 3.7 1.7 - - - +
244Y ALA* 2.8 31.6 + - - +
266Y GLY 3.9 1.9 + - - -
267Y ILE* 3.5 2.4 - - - -
268Y THR* 2.5 49.9 + - - +
270Y LYS* 3.3 22.6 - - + +
271Y GLY* 2.9 30.6 + - - +
274Y ASP* 4.6 1.6 - - - +
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Residues in contact with VAL 241 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212Y SER* 5.0 12.1 - - - +
216Y ARG* 6.2 0.4 - - - +
238Y LEU 4.8 1.8 - - - +
239Y GLY 3.2 0.4 - - - -
240Y ASP* 1.3 78.9 - - + +
242Y GLY* 1.3 60.3 + - - +
244Y ALA* 3.4 6.5 + - - +
245Y GLU* 3.1 40.6 + - - +
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Residues in contact with GLY 242 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212Y SER* 4.3 3.5 + - - -
215Y CYS* 3.7 27.4 - - - -
238Y LEU 2.9 23.6 + - - -
241Y VAL* 1.3 75.7 - - - +
243Y MET* 1.3 65.6 + - - +
245Y GLU* 2.9 16.1 + - - +
246Y LEU* 3.1 18.2 + - - +
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Residues in contact with MET 243 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238Y LEU* 4.5 3.4 - - - +
239Y GLY 2.8 21.0 + - - +
240Y ASP* 3.7 6.7 - - - +
242Y GLY* 1.3 70.9 - - - +
244Y ALA* 1.3 63.3 + - - +
246Y LEU* 3.3 23.3 + - + +
247Y CYS* 3.2 21.6 + - - -
250Y LEU* 4.0 17.7 - - + -
260Y LEU* 4.8 0.2 - - + -
262Y ILE* 3.8 17.0 - - + -
267Y ILE* 3.5 31.6 - - + -
271Y GLY* 3.3 26.5 - - - +
274Y ASP* 4.8 0.7 - - + -
275Y LEU* 3.5 39.3 - - + +
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Residues in contact with ALA 244 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240Y ASP 2.8 17.9 + - - +
241Y VAL* 3.6 7.4 - - - +
242Y GLY 3.1 0.2 - - - -
243Y MET* 1.3 77.8 - - - +
245Y GLU* 1.3 64.2 + - + +
246Y LEU 3.3 0.2 + - - -
247Y CYS* 3.3 11.2 + - - +
248Y PRO* 3.2 16.5 - - - +
274Y ASP* 3.1 28.0 + - - +
277Y ARG* 5.2 1.4 + - - +
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Residues in contact with GLU 245 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212Y SER 3.4 21.7 - - - +
215Y CYS* 4.3 12.3 - - + +
216Y ARG* 3.1 42.8 + - + -
219Y CYS* 3.3 17.7 - - - +
241Y VAL* 3.1 32.3 + - + +
242Y GLY* 2.9 6.8 + - - +
244Y ALA* 1.3 77.8 - - + +
246Y LEU* 1.3 58.0 + - - +
248Y PRO* 3.0 18.1 - - - +
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Residues in contact with LEU 246 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215Y CYS* 3.4 36.3 - - + +
218Y LEU* 4.7 10.1 - - + -
219Y CYS* 4.2 7.9 - - - +
222Y VAL* 5.4 4.5 - - + +
231Y LEU* 5.7 5.8 - - + -
233Y LEU* 4.4 13.9 - - + -
238Y LEU* 4.3 20.4 - - + -
242Y GLY 3.1 15.0 + - - +
243Y MET* 3.5 31.4 - - + +
244Y ALA 3.2 0.4 - - - -
245Y GLU* 1.3 76.5 - - - +
247Y CYS* 1.3 53.9 + - - +
249Y GLY* 2.6 29.6 + - - -
250Y LEU* 3.1 16.8 + - + +
260Y LEU* 5.6 5.2 - - + -
262Y ILE* 5.3 4.5 - - + -
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Residues in contact with CYS 247 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243Y MET* 3.2 23.8 - - - -
244Y ALA* 3.4 11.7 - - - +
246Y LEU* 1.3 76.7 - - - +
248Y PRO* 1.3 61.7 - - + +
249Y GLY 2.7 0.5 + - - -
250Y LEU* 2.8 4.4 + - - +
251Y LEU* 2.6 44.8 + - + +
274Y ASP* 3.9 31.2 - - - -
277Y ARG* 4.2 13.5 - - - +
278Y VAL* 3.9 20.2 - - + -
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Residues in contact with PRO 248 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219Y CYS* 4.0 12.1 - - - -
223Y ALA* 5.2 1.1 - - - +
244Y ALA 3.2 8.3 - - - +
245Y GLU* 3.0 23.3 - - - +
247Y CYS* 1.3 89.1 - - + +
249Y GLY* 1.3 58.0 + - - +
251Y LEU* 3.9 11.5 - - + +
252Y HIS* 3.4 18.2 + - - +
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Residues in contact with GLY 249 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219Y CYS* 3.6 22.4 - - - -
222Y VAL* 3.0 25.0 - - - +
223Y ALA* 4.4 4.5 - - - -
246Y LEU 2.6 17.4 + - - -
248Y PRO* 1.3 71.8 - - - +
250Y LEU* 1.3 55.7 + - - -
251Y LEU 3.0 4.0 - - - -
252Y HIS* 2.9 25.5 + - - +
255Y SER* 3.7 1.9 - - - -
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Residues in contact with LEU 250 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222Y VAL* 3.5 19.0 - - + +
231Y LEU* 5.4 1.6 - - + -
243Y MET* 4.0 21.8 - - + -
246Y LEU* 3.1 15.8 + - + +
247Y CYS* 2.8 10.3 + - - +
249Y GLY* 1.3 74.1 - - - +
251Y LEU* 1.3 60.0 + - - +
252Y HIS 3.4 0.4 + - - -
255Y SER* 4.4 6.0 + - - +
257Y LEU* 3.8 33.4 - - + -
260Y LEU* 4.2 18.2 - - + -
278Y VAL* 3.9 35.9 - - + -
282Y LYS* 3.4 29.8 + - + +
285Y LEU* 6.5 0.7 - - + -
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Residues in contact with LEU 251 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247Y CYS* 2.6 35.9 + - + +
248Y PRO* 3.9 9.6 - - + +
249Y GLY 3.0 0.2 - - - -
250Y LEU* 1.3 77.0 - - - +
252Y HIS* 1.3 62.5 + - - +
253Y PRO* 3.4 6.6 - - - +
277Y ARG* 4.3 14.8 - - + +
278Y VAL* 3.9 24.0 - - + +
280Y ARG* 5.8 0.9 - - - +
281Y ALA* 3.9 28.3 - - + -
282Y LYS* 4.7 7.1 + - + +
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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