Contacts of the helix formed by residues 211 - 222 (chain M) in PDB entry 5IYB
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 211 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210M THR* 1.3 72.4 - - - +
212M GLY* 1.3 66.1 + - - +
213M ASP 3.1 1.0 + - - -
214M PHE* 3.2 18.6 + - - +
215M MET* 3.7 11.9 + - - +
236M ALA* 3.7 26.5 - - + +
237M ARG* 4.8 1.2 + - - -
240M VAL* 4.4 18.5 - - + +
250M PRO* 3.9 34.1 - - + +
253M VAL* 4.3 19.1 - - + -
254M ALA* 4.8 7.8 - - - +
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Residues in contact with GLY 212 (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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210M THR* 3.5 6.2 + - - -
211M THR* 1.3 80.8 + - - +
213M ASP* 1.3 56.4 + - - +
214M PHE 3.1 5.5 + - - -
215M MET* 3.4 24.9 + - - +
216M SER* 4.4 4.0 + - - -
233M THR* 5.0 11.9 - - - -
236M ALA* 6.1 0.7 - - - -
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Residues in contact with ASP 213 (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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102B ASP* 5.8 0.5 - - - +
172M GLY* 4.0 10.0 - - - +
173M VAL* 5.6 1.6 - - - -
174M PRO* 3.6 38.5 - - + +
209M ILE* 5.0 0.3 - - - -
210M THR* 2.5 45.1 + - - +
211M THR 3.1 0.8 + - - -
212M GLY* 1.3 76.0 - - - +
214M PHE* 1.3 66.3 + - + +
216M SER* 4.3 9.0 + - - -
217M ARG* 4.5 9.2 + - - +
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Residues in contact with PHE 214 (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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174M PRO* 3.7 39.0 - - + -
175M ARG* 4.2 5.2 - - - -
176M THR* 3.9 23.8 - - + -
209M ILE* 5.0 15.7 - - + -
210M THR 3.4 23.8 - - - -
211M THR* 3.2 8.4 + - - +
212M GLY 3.1 0.4 - - - -
213M ASP* 1.3 83.5 - - + +
215M MET* 1.3 67.5 + - - +
216M SER* 3.2 4.4 + - - -
217M ARG* 3.4 24.2 + - - +
218M PHE* 3.0 50.8 + + + -
250M PRO* 5.5 3.4 - - + -
251M ILE* 4.1 19.3 - - + -
254M ALA* 5.1 7.9 - - + -
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Residues in contact with MET 215 (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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211M THR 3.7 12.5 + - - +
212M GLY* 3.4 16.1 + - - +
214M PHE* 1.3 78.9 - - - +
216M SER* 1.3 63.1 + - - +
218M PHE* 3.8 2.4 + - - +
219M CYS* 3.4 28.7 + - - +
229M GLN* 3.9 7.1 - - + +
232M ALA* 3.6 41.7 - - + +
233M THR* 3.5 25.1 - - - +
236M ALA* 3.6 19.7 - - + -
254M ALA* 4.1 20.4 - - + +
257M ALA* 3.9 14.4 - - + -
258M ILE* 4.1 12.6 - - - -
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Residues in contact with SER 216 (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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102B ASP* 3.8 31.0 + - - +
104B ALA* 4.7 4.3 - - - -
212M GLY 4.4 2.3 + - - -
213M ASP 4.3 12.5 + - - -
215M MET* 1.3 78.8 - - - +
217M ARG* 1.3 62.1 + - - +
219M CYS* 4.2 1.9 - - - +
220M SER* 2.8 33.1 + - - -
229M GLN* 3.2 20.7 + - - +
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Residues in contact with ARG 217 (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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102B ASP* 2.9 24.4 + - + +
103B GLY* 4.3 15.6 - - - +
104B ALA* 4.5 6.3 - - - -
173M VAL 4.9 0.2 - - - -
174M PRO 2.8 27.3 + - - -
175M ARG* 3.1 21.1 - - - +
179M GLU* 2.7 47.0 + - - -
213M ASP 4.5 7.8 + - - +
214M PHE* 3.4 25.6 + - - +
216M SER* 1.3 81.3 + - - +
218M PHE* 1.3 76.6 + - + +
220M SER* 3.4 7.9 - - - -
221M ASN* 3.2 34.2 + - - +
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Residues in contact with PHE 218 (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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176M THR* 5.2 7.9 - - + -
179M GLU* 5.9 2.5 - - - -
214M PHE* 3.0 54.8 + + + +
215M MET 4.2 0.4 - - - +
216M SER 3.4 0.8 - - - -
217M ARG* 1.3 85.8 - - + +
219M CYS* 1.3 67.0 + - - +
220M SER 3.1 1.6 - - - -
221M ASN* 3.1 7.4 + - - +
222M LEU* 2.9 31.9 + - + +
251M ILE* 5.3 5.6 - - + -
254M ALA* 5.1 9.2 - - + -
255M ALA 6.2 0.2 - - - -
258M ILE* 3.5 29.4 - - + -
274M ILE* 6.3 1.8 - - + -
277M ILE* 3.6 24.6 - - + +
278M ALA* 3.5 39.7 - - + -
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Residues in contact with CYS 219 (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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215M MET* 3.4 13.6 + - - +
216M SER 4.2 1.3 - - - +
218M PHE* 1.3 78.0 - - - +
220M SER* 1.3 61.4 + - - +
222M LEU* 3.3 1.1 + - - -
223M CYS 3.1 3.3 + - - -
224M LEU* 3.0 61.5 + - + +
228M VAL* 5.0 0.4 - - - -
229M GLN* 3.6 49.6 - - + +
232M ALA* 4.9 4.5 - - - -
258M ILE* 4.6 17.5 - - - -
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Residues in contact with SER 220 (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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104B ALA* 3.3 25.3 - - - +
105B PRO* 4.0 20.6 + - - +
216M SER 2.8 17.9 + - - -
217M ARG 3.4 9.4 - - - -
218M PHE 3.1 0.2 - - - -
219M CYS* 1.3 77.3 - - - +
221M ASN* 1.3 58.3 + - - +
223M CYS* 2.8 26.7 + - - +
224M LEU 5.5 1.3 - - - -
229M GLN* 5.4 3.3 + - - +
149T VAL* 5.0 1.0 - - - +
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Residues in contact with ASN 221 (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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103B GLY 4.8 1.7 - - - +
105B PRO* 3.6 21.8 - - - +
217M ARG* 3.2 21.6 + - - +
218M PHE* 3.1 8.3 + - - +
220M SER* 1.3 75.7 - - - +
222M LEU* 1.3 63.7 + - - +
223M CYS* 3.3 3.4 + - - -
277M ILE* 4.3 26.4 - - + +
149T VAL* 3.6 52.7 + - + +
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Residues in contact with LEU 222 (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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218M PHE* 2.9 23.6 + - + +
219M CYS 3.3 0.2 + - - -
220M SER 3.0 0.6 - - - -
221M ASN* 1.3 80.5 - - - +
223M CYS* 1.3 57.9 + - - +
224M LEU* 3.0 21.3 + - + +
258M ILE* 3.8 28.5 - - + -
269M ARG* 2.5 51.1 + - + +
273M GLU* 4.1 27.4 - - + +
274M ILE* 3.9 22.4 - - + -
277M ILE* 4.2 20.0 - - + -
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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