Contacts of the helix formed by residues 210 - 219 (chain B) in PDB entry 2M8L
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 210 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208B GLY 3.2 7.6 + - - +
209B ALA* 1.3 76.9 - - - +
211B LEU* 1.3 60.0 + - - +
212B GLU* 3.8 9.3 + - - +
213B GLU* 2.8 43.8 + - - +
214B MET* 2.8 26.9 + - - +
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B PHE* 5.2 1.2 - - - -
165B VAL* 5.3 12.1 - - + -
186B THR* 4.4 29.4 - - + +
190B LEU* 4.8 13.5 - - + -
209B ALA 5.2 2.5 - - - +
210B THR* 1.3 75.0 - - - +
212B GLU* 1.3 57.1 + - - +
214B MET* 3.2 23.3 + - + +
215B MET* 2.9 28.2 + - - +
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Residues in contact with GLU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B THR* 3.1 9.1 + - - +
211B LEU* 1.3 78.0 - - - +
213B GLU* 1.3 58.8 + - + +
215B MET* 3.4 17.7 + - + +
216B THR* 3.0 37.1 + - - +
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Residues in contact with GLU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B LEU* 4.7 4.2 - - + +
208B GLY 4.4 1.9 - - - +
209B ALA* 3.3 23.9 - - + +
210B THR* 2.8 40.3 + - - +
212B GLU* 1.3 75.6 - - + +
214B MET* 1.3 60.2 + - - +
216B THR* 3.3 8.1 + - - -
217B ALA* 2.8 31.0 + - - +
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Residues in contact with MET 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B PHE* 4.2 11.0 - - + -
186B THR 5.9 2.9 - - - +
187B GLU* 5.7 3.1 - - - +
190B LEU* 4.8 13.2 - - - -
191B VAL* 4.1 24.5 - - + -
202B LEU* 3.7 28.5 - - + +
205B LEU* 4.2 13.0 - - + +
209B ALA* 4.0 24.2 - - + +
210B THR 2.8 13.8 + - - +
211B LEU* 3.3 28.3 - - + +
213B GLU* 1.3 76.4 - - - +
215B MET* 1.3 56.7 + - - +
217B ALA* 3.2 1.6 + - - +
218B CYS* 2.9 34.5 + - - -
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Residues in contact with MET 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B PHE* 4.0 15.9 - - + +
162B ARG* 3.6 57.7 - - + +
165B VAL* 5.8 2.0 - - + -
211B LEU 2.9 14.9 + - - +
212B GLU* 3.8 18.6 - - + +
213B GLU 3.3 0.2 - - - -
214B MET* 1.3 74.9 - - - +
216B THR* 1.3 65.0 + - - +
218B CYS 3.3 1.2 + - - -
219B GLN* 3.0 27.8 + - + +
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Residues in contact with THR 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B GLU* 3.0 20.0 + - - +
213B GLU* 3.5 11.5 - - - -
215B MET* 1.3 81.7 - - - +
217B ALA* 1.3 64.0 + - - +
219B GLN* 3.5 21.3 + - - +
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Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B ILE* 3.7 29.2 - - + +
205B LEU* 4.0 26.2 - - + -
213B GLU 2.8 21.2 + - - +
214B MET 3.2 4.7 + - - +
216B THR* 1.3 76.4 - - - +
218B CYS* 1.3 60.1 + - - +
219B GLN 3.7 1.7 + - - +
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Residues in contact with CYS 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B PHE* 3.8 24.2 + - + +
198B CYS* 3.0 47.8 - - + -
201B ILE* 4.6 6.7 - - - -
202B LEU* 3.3 29.4 - - - -
214B MET 2.9 12.8 + - - +
215B MET 3.3 1.8 + - - -
217B ALA* 1.3 77.8 - - - +
219B GLN* 1.3 65.3 + - - +
220B GLY 3.2 0.9 + - - -
221B VAL* 3.2 26.2 - - + +
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Residues in contact with GLN 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B PHE* 5.7 2.2 - - - +
215B MET* 3.0 17.8 + - + +
216B THR* 3.5 15.7 + - - +
217B ALA 3.4 3.8 - - - +
218B CYS* 1.3 76.4 - - - +
220B GLY* 1.3 67.6 + - - +
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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