Contacts of the helix formed by residues 229 - 239 (chain M) 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 THR 229 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188M THR* 3.8 14.8 - - + -
190M PRO* 4.4 9.2 - - - +
228M THR* 1.3 76.3 - - - +
230M GLU* 1.3 62.5 + - - +
231M ILE 3.2 1.8 - - - -
232M LEU* 2.9 21.7 + - + +
233M ARG* 2.9 12.0 + - - +
251M PHE* 4.7 6.5 - - + -
262M ARG* 5.5 2.6 - - - +
265M VAL* 3.5 22.2 - - + -
266M TRP* 3.7 39.9 + - + +
269M THR* 3.9 19.1 - - + +
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Residues in contact with GLU 230 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228M THR* 4.1 1.2 + - - -
229M THR* 1.3 73.7 - - - +
231M ILE* 1.3 65.0 + - - +
233M ARG* 3.1 15.0 + - + +
234M SER* 3.0 22.5 + - - -
262M ARG* 3.6 18.2 + - - +
265M VAL* 3.9 26.4 - - + +
21O A 2.1 53.7 + - - +
22O C 2.5 54.2 + - - +
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Residues in contact with ILE 231 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212M MET* 4.2 0.9 - - - -
213M THR* 4.9 10.5 - - - +
227M MET* 3.5 29.4 - - - -
228M THR* 3.3 23.1 - - - +
229M THR 3.2 0.2 - - - -
230M GLU* 1.3 77.5 - - - +
232M LEU* 1.3 55.9 + - - +
234M SER* 2.6 23.9 + - - -
235M MET* 3.0 18.7 + - + +
22O C 2.9 37.5 - - - +
23O A 2.9 49.8 - - + +
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Residues in contact with LEU 232 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186M ILE* 3.7 24.0 - - + -
188M THR* 3.7 26.2 - - + -
227M MET* 4.3 11.2 - - + +
228M THR 4.3 1.7 + - - +
229M THR* 2.9 17.0 + - + +
231M ILE* 1.3 77.0 - - - +
233M ARG* 1.3 60.5 + - - +
235M MET* 3.3 4.1 + - - +
236M LEU* 2.9 59.0 + - + +
243M MET* 3.8 18.8 - - + -
249M VAL* 4.8 11.0 - - + -
251M PHE* 5.1 1.1 - - + -
269M THR* 3.6 22.0 - - + -
273M LEU* 5.1 6.3 - - + -
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Residues in contact with ARG 233 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229M THR 2.9 11.4 + - - +
230M GLU* 3.1 16.3 + - - +
232M LEU* 1.3 74.0 - - - +
234M SER* 1.3 65.8 + - - +
236M LEU* 3.3 7.5 + - - +
237M TYR* 3.0 60.6 + - + -
264M VAL* 5.4 2.6 - - - +
265M VAL* 4.3 25.1 - - + +
268M GLU* 2.7 31.2 + - + +
269M THR* 4.1 15.2 + - - +
272M LEU* 5.3 1.1 - - + -
566M THR* 4.2 5.9 + - - -
568M ASN* 4.6 11.1 - - - +
569M MET* 3.7 22.8 - - - +
572M ASN* 5.3 1.2 - - - +
881M SER* 5.4 6.9 - - - -
22O C 5.1 8.3 + - - -
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Residues in contact with SER 234 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230M GLU 3.0 11.2 + - - -
231M ILE* 2.6 22.0 + - - -
233M ARG* 1.3 76.9 - - - +
235M MET* 1.3 62.4 + - - +
237M TYR* 3.3 13.5 + - - +
238M ARG* 2.9 29.5 + - - +
22O C 4.7 8.7 + - - -
23O A 3.0 27.8 + - - -
24O C 5.2 6.3 - - - -
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Residues in contact with MET 235 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212M MET* 3.3 39.7 - - + -
225M LEU* 5.6 0.7 - - + -
227M MET* 3.7 23.8 - - + -
231M ILE* 3.0 9.7 + - + +
232M LEU* 3.5 9.0 - - - +
234M SER* 1.3 81.1 + - - +
236M LEU* 1.3 56.6 + - - +
238M ARG 2.9 3.2 + - - +
239M GLY* 2.7 35.2 + - - -
240M SER* 3.6 8.6 + - - +
242M VAL* 4.5 15.3 - - + -
243M MET* 3.8 31.6 - - + -
23O A 3.3 40.2 - - + +
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Residues in contact with LEU 236 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159H ARG* 3.1 14.0 + - - -
232M LEU* 2.9 57.6 + - + +
233M ARG* 3.7 2.2 - - - +
235M MET* 1.3 73.0 - - - +
237M TYR* 1.3 65.5 + - - +
239M GLY* 3.7 3.3 + - - +
243M MET* 4.2 22.2 - - + -
269M THR* 4.2 9.4 - - + +
272M LEU* 3.4 60.9 - - + +
273M LEU* 3.8 20.6 - - + +
274M PRO* 4.9 2.2 - - + -
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Residues in contact with TYR 237 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159H ARG* 2.6 40.4 + - - +
233M ARG* 3.0 42.1 + - + -
234M SER* 3.3 13.9 - - - +
236M LEU* 1.3 75.7 - - - +
238M ARG* 1.3 56.4 + - + +
239M GLY 3.2 0.2 - - - -
268M GLU* 1.8 39.1 + - - -
272M LEU* 3.6 25.8 - - + -
569M MET* 3.8 2.9 - - - +
572M ASN* 3.7 42.4 - - + +
573M LEU* 3.8 26.0 - - + +
575M ARG* 6.0 1.8 - - - +
576M VAL* 5.0 5.2 - - + +
584M MET* 5.8 0.2 - - + -
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Residues in contact with ARG 238 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H VAL* 3.6 18.1 - - + +
146H GLN* 3.6 39.1 + - + +
147H ALA* 3.6 12.1 - - - +
157H HIS* 4.4 3.7 - - - -
159H ARG* 4.3 5.2 - - - +
234M SER* 2.9 19.4 + - - +
235M MET* 2.9 7.4 + - - +
237M TYR* 1.3 74.8 - - + +
239M GLY* 1.3 66.8 + - - +
240M SER* 2.9 7.5 + - - +
575M ARG* 3.5 29.4 - - - +
879M GLU* 4.0 14.6 + - - -
23O A 5.2 4.0 - - - +
24O C 3.5 31.5 + - - +
25O C 2.8 29.2 + - - -
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Residues in contact with GLY 239 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146H GLN* 3.7 5.4 + - - -
157H HIS* 4.2 17.0 - - - -
159H ARG* 4.1 6.0 - - - +
235M MET 2.7 14.3 + - - -
236M LEU* 3.7 5.1 + - - -
237M TYR 3.2 6.1 + - - -
238M ARG* 1.3 71.0 - - - +
240M SER* 1.3 68.4 + - - +
243M MET* 5.0 7.2 - - - -
244M ARG* 3.2 21.9 + - - -
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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