Contacts of the helix formed by residues 227 - 239 (chain G) in PDB entry 4HHM
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 ASN 227 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221G GLU* 5.6 0.2 - - - +
226G LEU* 1.3 74.8 - - - +
228G PHE* 1.3 64.5 + - - +
229G PRO* 3.0 15.4 - - - +
230G HIS* 2.7 53.5 + - + +
231G GLY* 3.1 16.8 + - - -
270G TRP* 6.4 0.2 - - - -
190H ASP* 3.1 38.5 + - + -
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Residues in contact with PHE 228 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196G ILE* 4.1 1.3 - - + -
216G PRO* 3.6 22.2 - - + -
217G GLU 3.4 17.7 - - - -
218G VAL* 3.4 45.8 - - + +
221G GLU* 3.3 34.5 - - + -
222G GLN* 4.6 16.4 + - + +
226G LEU 3.6 5.1 + - - -
227G ASN* 1.3 68.5 - - - +
229G PRO* 1.3 77.4 - - + +
231G GLY* 3.0 2.7 + - - +
232G ILE* 2.8 57.1 + - + +
244G ILE* 4.2 5.2 - - + -
267G ALA* 5.6 1.3 - - + +
271G LEU* 3.8 19.7 - - + -
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Residues in contact with PRO 229 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227G ASN* 3.0 17.7 - - - +
228G PHE* 1.3 90.8 - - + +
230G HIS* 1.3 61.8 + - + +
232G ILE* 3.2 5.1 + - + -
233G ALA* 2.8 26.7 + - - +
267G ALA* 3.5 33.9 - - + +
270G TRP* 3.8 20.0 - - + +
271G LEU* 3.8 15.5 - - + +
274G LEU* 3.1 23.9 - - + +
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Residues in contact with HIS 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227G ASN* 2.7 47.7 + - + +
229G PRO* 1.3 76.9 - - + +
231G GLY* 1.3 62.4 + - - +
233G ALA* 3.2 4.9 + - - +
234G GLN* 3.1 20.3 + - - +
142H GLY* 5.3 0.2 - - - -
143H ALA* 4.8 17.2 - - + +
145H SER 5.7 2.2 + - - -
146H GLY* 5.7 5.7 + - - -
149H LYS* 5.0 4.6 + - + +
151H VAL* 3.4 37.1 - - + +
190H ASP* 3.8 27.0 - - + +
191H ILE 5.2 2.4 + - - -
192H LEU* 4.1 19.5 - - + +
194H PRO* 6.4 2.0 - - + -
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Residues in contact with GLY 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196G ILE* 3.9 26.7 - - - +
221G GLU* 5.6 0.9 - - - -
227G ASN 3.1 9.1 + - - -
228G PHE* 3.0 5.8 + - - -
230G HIS* 1.3 72.9 - - - +
232G ILE* 1.3 65.4 + - - +
234G GLN* 2.9 18.3 + - - +
235G ALA* 3.0 13.0 + - - +
198H HIS* 4.8 13.0 - - - -
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Residues in contact with ILE 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G ILE* 4.1 0.4 - - + +
216G PRO* 3.8 21.3 - - + -
228G PHE* 2.8 61.0 + - + +
229G PRO 3.5 7.6 - - - +
231G GLY* 1.3 71.4 - - - +
233G ALA* 1.3 64.0 + - - +
235G ALA* 3.0 6.4 + - - +
236G LEU* 3.0 25.0 + - + +
241G LEU* 4.0 24.0 - - + -
244G ILE* 3.9 12.3 - - + -
271G LEU* 3.8 15.3 - - + -
274G LEU* 3.9 14.8 - - + -
275G LEU* 4.2 7.9 - - + -
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Residues in contact with ALA 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229G PRO 2.8 16.2 + - - +
230G HIS* 3.4 9.4 - - - +
231G GLY 3.1 0.2 - - - -
232G ILE* 1.3 74.1 - - - +
234G GLN* 1.3 57.2 + - - +
236G LEU* 3.3 5.7 + - - +
237G TRP* 2.8 31.7 + - - +
274G LEU* 3.6 17.9 - - + +
151H VAL* 3.5 29.4 - - + -
152H ARG* 3.7 15.8 - - + +
155H LEU* 4.7 1.1 - - - -
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Residues in contact with GLN 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196G ILE* 5.5 0.2 - - + -
200G LEU* 4.4 11.4 - - + +
230G HIS 3.1 10.6 + - - +
231G GLY* 2.9 11.9 + - - +
233G ALA* 1.3 77.2 - - - +
235G ALA* 1.3 61.0 + - - +
237G TRP* 3.5 7.9 + - + +
238G ALA* 3.1 24.0 + - + +
151H VAL* 5.6 0.4 - - + -
155H LEU* 3.8 24.8 - - + +
193H LEU* 3.7 17.9 + - - +
194H PRO* 5.0 0.2 - - - +
198H HIS* 3.0 60.3 + - + +
201H ALA* 3.8 9.1 - - - +
202H PHE* 3.8 14.5 - - - +
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Residues in contact with ALA 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196G ILE* 4.7 5.6 - - + -
200G LEU* 4.5 11.8 - - - +
214G VAL* 4.0 25.6 - - + -
216G PRO* 5.1 1.6 - - + -
231G GLY 3.0 10.6 + - - +
232G ILE* 3.3 11.0 - - - +
234G GLN* 1.3 77.2 - - - +
236G LEU* 1.3 56.6 + - - +
238G ALA* 3.2 3.3 + - - +
239G GLY 2.8 22.7 + - - -
240G LYS 2.8 12.1 + - - -
241G LEU* 4.1 20.4 - - + +
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Residues in contact with LEU 236 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232G ILE* 3.0 21.7 + - + +
233G ALA* 3.6 6.5 - - - +
235G ALA* 1.3 73.5 - - - +
237G TRP* 1.3 65.6 + - - +
238G ALA 3.0 1.8 - - - -
239G GLY* 2.9 16.1 + - - +
241G LEU* 3.4 32.3 - - + -
274G LEU* 4.0 29.2 - - + +
275G LEU* 5.2 3.1 - - + -
278G ALA* 3.9 26.7 - - + -
280G TRP* 3.8 20.9 - - + -
152H ARG* 4.2 11.0 - - - -
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Residues in contact with TRP 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233G ALA 2.8 21.0 + - - +
234G GLN* 3.7 12.1 - - + +
235G ALA 3.4 0.2 - - - -
236G LEU* 1.3 72.8 - - - +
238G ALA* 1.3 65.3 + - + +
152H ARG* 3.6 31.6 - - + +
155H LEU* 3.6 44.5 - - + +
156H ASP* 3.1 24.3 + - - +
159H LYS* 3.9 21.7 - - + +
201H ALA 5.7 0.2 - - - -
202H PHE* 3.5 37.5 - + - -
205H ARG* 3.5 36.1 - - + +
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Residues in contact with ALA 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200G LEU* 4.6 9.2 - - + -
234G GLN* 3.1 17.3 + - + +
235G ALA* 3.6 5.6 - - - +
236G LEU 3.0 0.8 - - - -
237G TRP* 1.3 87.0 - - + +
239G GLY* 1.3 59.2 + - - +
240G LYS* 3.6 13.5 + - + +
201H ALA* 6.5 0.2 - - + -
205H ARG* 2.9 46.9 + - + +
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Residues in contact with GLY 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235G ALA 2.8 4.0 + - - -
236G LEU* 2.9 14.1 + - - -
237G TRP 3.4 0.2 - - - -
238G ALA* 1.3 78.3 - - - +
240G LYS* 1.3 63.5 + - - +
241G LEU 3.6 2.9 - - - -
242G PHE* 3.5 16.6 - - - -
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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