Contacts of the helix formed by residues 244 - 257 (chain G) in PDB entry 6D6Q
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 ILE 244 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A PHE* 3.6 33.0 - - + -
16A ARG* 4.0 43.3 - - + +
17A ALA* 4.4 13.0 - - + +
20A GLU* 3.5 36.8 - - - +
22A LYS* 5.2 4.0 - - + -
196G ASP* 5.7 1.8 - - - +
242G LYS 5.6 0.7 - - - +
243G THR* 1.3 85.2 + - - +
245G GLN* 1.3 65.1 + - - +
246G GLN 3.1 1.8 - - - -
247G THR* 3.0 6.2 + - - -
248G LEU* 2.9 33.2 + - + +
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Residues in contact with GLN 245 (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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22A LYS* 3.1 39.8 - - - +
243G THR* 3.9 9.7 + - + +
244G ILE* 1.3 76.6 - - - +
246G GLN* 1.3 64.2 + - - +
248G LEU* 3.2 14.6 + - - +
249G ILE* 3.0 55.4 + - + +
275G SER* 4.6 16.6 - - - -
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Residues in contact with GLN 246 (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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225G HIS* 3.4 49.4 + - + +
226G PRO* 4.7 2.8 - - - +
241G ALA* 4.0 13.2 - - + +
242G LYS* 4.4 5.6 + - - +
243G THR* 3.4 28.3 + - + +
244G ILE 3.1 0.6 - - - -
245G GLN* 1.3 77.6 - - - +
247G THR* 1.3 62.7 + - - +
249G ILE* 3.3 7.1 + - - +
250G LEU* 2.9 24.9 + - - +
272G LEU* 4.6 3.7 + - + -
275G SER* 3.5 40.9 + - - +
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Residues in contact with THR 247 (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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13A PHE* 3.9 15.6 - - + -
197G GLY* 5.2 0.7 - - - -
198G LEU* 3.6 34.1 - - + +
239G VAL* 3.7 16.9 - - + +
240G LYS* 4.7 0.6 - - - -
241G ALA* 3.8 19.4 + - - +
243G THR 3.0 17.5 + - - -
244G ILE* 3.0 10.1 + - - -
246G GLN* 1.3 76.7 - - - +
248G LEU* 1.3 58.5 + - - +
250G LEU* 3.3 9.0 + - - +
251G ALA* 2.9 27.5 + - - +
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Residues in contact with LEU 248 (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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13A PHE* 3.2 34.8 - - + -
17A ALA* 5.0 1.6 - - + -
22A LYS* 4.1 20.0 - - + +
23A ARG 3.3 23.1 - - - +
24A LEU* 3.4 31.0 - - + +
198G LEU* 4.3 4.5 - - + -
244G ILE* 2.9 25.3 + - + +
245G GLN* 3.6 14.8 - - - +
247G THR* 1.3 73.0 - - - +
249G ILE* 1.3 65.0 + - + +
251G ALA* 3.2 5.2 + - - +
252G ASN* 2.6 34.1 + - - +
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Residues in contact with ILE 249 (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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245G GLN* 3.0 40.7 + - + +
246G GLN 3.7 0.4 - - - +
248G LEU* 1.3 76.9 - - + +
250G LEU* 1.3 58.1 + - - +
252G ASN* 3.4 9.7 + - - +
253G ILE* 3.0 33.2 + - + +
268G ILE* 3.1 38.5 - - + +
271G ARG* 4.9 15.5 - - + -
272G LEU* 3.1 34.5 - - + +
275G SER* 6.0 1.6 - - - +
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Residues in contact with LEU 250 (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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221G VAL* 3.8 33.4 - - + -
225G HIS* 4.8 11.0 - - + +
227G LEU* 4.1 22.9 - - + -
229G ILE* 4.2 8.5 - - + -
239G VAL* 4.0 28.3 - - + -
240G LYS 5.2 2.2 - - - +
241G ALA* 5.6 1.6 - - + -
246G GLN 2.9 17.1 + - - +
247G THR* 3.4 7.4 - - - +
248G LEU 3.1 0.2 - - - -
249G ILE* 1.3 74.4 - - - +
251G ALA* 1.3 65.9 + - - +
253G ILE* 3.2 13.4 + - + +
254G LEU* 2.9 45.0 + - + +
272G LEU* 4.8 1.3 - - + +
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Residues in contact with ALA 251 (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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198G LEU* 3.5 32.3 - - + -
200G PHE* 3.7 30.9 - - + -
239G VAL* 5.1 1.5 - - + +
247G THR 2.9 10.8 + - - +
248G LEU* 3.7 4.3 - - - +
250G LEU* 1.3 75.6 - - - +
252G ASN* 1.3 64.7 + - - +
254G LEU* 3.3 1.8 + - - +
255G GLU* 3.0 27.3 + - - +
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Residues in contact with ASN 252 (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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24A LEU 3.5 22.8 + - - +
25A ASP* 4.0 20.2 + - - +
26A GLY* 5.7 0.2 - - - -
248G LEU* 2.6 25.0 + - - +
249G ILE* 3.6 10.3 + - + +
251G ALA* 1.3 74.7 - - - +
253G ILE* 1.3 66.6 + - + +
255G GLU* 3.1 24.5 + - - +
256G ALA* 3.0 23.2 + - - +
268G ILE* 5.9 7.2 - - + -
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Residues in contact with ILE 253 (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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217G ILE* 4.0 26.2 - - + -
221G VAL* 5.1 7.0 - - + -
249G ILE* 3.0 21.6 + - + +
250G LEU* 3.4 14.4 - - + +
252G ASN* 1.3 75.9 - - - +
254G LEU* 1.3 58.7 + - + +
256G ALA* 2.9 3.3 + - - -
257G CYS* 2.7 35.9 + - - +
260G MET* 3.8 21.4 - - + +
268G ILE* 3.3 35.4 - - + +
269G PHE* 4.8 12.8 - - + -
272G LEU* 3.6 25.1 - - + -
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Residues in contact with LEU 254 (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 PHE* 3.5 34.5 - - + -
202G VAL* 4.8 0.7 - - - -
206G LEU* 3.3 12.4 - - - +
210G LEU* 4.5 20.6 - - + -
217G ILE* 5.2 6.3 - - + -
218G ILE* 6.0 6.3 - - + -
221G VAL* 6.1 1.8 - - + -
229G ILE* 5.1 10.5 - - + -
231G PHE* 5.2 7.2 - - + -
237G ILE* 4.3 12.8 - - + -
239G VAL* 4.1 16.6 - - + -
250G LEU* 2.9 34.2 + - + +
252G ASN 3.3 0.2 - - - -
253G ILE* 1.3 83.5 - - + +
255G GLU* 1.3 62.5 + - - +
256G ALA 3.1 1.6 + - - -
257G CYS* 3.1 26.3 + - - -
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Residues in contact with GLU 255 (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 PHE* 4.3 6.4 - - + -
201G LYS 5.3 2.2 - - - +
202G VAL* 3.9 23.3 - - + -
206G LEU* 4.7 3.8 - - - +
251G ALA 3.0 22.2 + - - +
252G ASN* 3.1 30.6 + - - +
254G LEU* 1.3 75.0 - - - +
256G ALA* 1.3 64.4 + - - +
258G GLU* 5.3 1.7 + - - +
259G HIS* 5.4 3.3 - - - -
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Residues in contact with ALA 256 (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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252G ASN 3.0 15.5 + - - +
253G ILE* 2.9 3.8 + - - +
255G GLU* 1.3 89.3 - - - +
257G CYS* 1.3 52.5 + - - +
258G GLU* 2.7 18.1 + - - -
259G HIS* 3.2 24.5 + - + +
260G MET* 3.2 24.6 + - + +
264G GLN* 5.7 3.4 - - - +
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Residues in contact with CYS 257 (chain G).
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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206G LEU* 3.7 18.4 - - - -
209G LYS* 3.9 8.1 + - - -
210G LEU* 4.0 22.4 - - - -
217G ILE* 4.3 27.6 - - + +
253G ILE 2.7 17.6 + - - +
254G LEU* 3.1 31.8 + - - -
256G ALA* 1.3 70.2 - - - +
258G GLU* 1.3 61.1 + - - +
259G HIS 3.3 1.1 - - - -
260G MET* 3.6 21.0 + - - +
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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