Contacts of the helix formed by residues 211 - 218 (chain B) in PDB entry 4O8M
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 PRO 211 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B TYR* 3.5 43.7 - - + +
148B GLY* 3.7 21.3 - - - +
149B THR 3.2 17.3 - - - +
150B ARG* 4.0 7.4 - - + -
210B ASN* 1.3 101.2 - - + +
212B THR* 1.3 66.2 + - - +
213B VAL* 4.2 11.2 - - + +
214B VAL* 3.0 7.8 + - + +
215B LEU* 3.0 18.8 + - - +
276B GLU* 4.0 4.7 - - - +
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Residues in contact with THR 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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149B THR 4.3 1.8 + - - -
151B HIS* 4.3 15.2 - - + +
210B ASN 3.8 0.6 + - - -
211B PRO* 1.3 72.0 - - - +
213B VAL* 1.3 58.7 + - - +
215B LEU* 3.3 5.2 + - - +
216B PHE* 2.9 31.9 + - - +
227B LEU* 4.0 27.1 - - + -
276B GLU* 2.8 42.4 + - + +
279B ALA* 3.6 8.9 - - - +
280B LEU* 4.0 11.2 - - + -
283B LEU* 4.0 13.4 - - + +
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Residues in contact with VAL 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLU* 3.6 13.3 - - - +
40B PRO* 3.8 29.8 - - + -
41B ILE* 6.5 0.7 - - + -
147B TYR 4.5 3.4 - - - +
211B PRO* 4.2 9.8 - - + +
212B THR* 1.3 76.5 + - - +
214B VAL* 1.3 71.6 + - + +
216B PHE* 4.2 1.0 - - - +
217B GLY* 2.9 22.0 + - - -
272B ILE* 4.4 12.6 - - + -
275B ALA* 3.5 45.1 - - + +
276B GLU* 4.1 4.9 - - + +
279B ALA* 3.8 9.6 - - + -
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Residues in contact with VAL 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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35B ASN* 3.4 26.2 - - - +
39B GLU* 3.5 10.2 - - - +
41B ILE* 6.2 0.2 - - + -
147B TYR* 3.6 29.6 - - + +
193B LEU* 5.0 11.9 - - + -
210B ASN* 3.7 29.4 - - + +
211B PRO* 3.0 11.8 + - + +
213B VAL* 1.3 87.5 - - + +
215B LEU* 1.3 58.9 + - - +
216B PHE 3.2 0.4 - - - -
218B GLY* 2.9 27.7 + - - -
220B PHE* 3.7 7.7 - - + -
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Residues in contact with LEU 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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151B HIS 4.4 2.2 - - - +
153B LEU* 3.9 32.1 - - + -
208B LEU* 4.0 20.4 - - + -
209B GLU 4.6 0.2 - - - -
210B ASN* 3.4 37.9 - - + +
211B PRO 3.0 14.6 + - - +
212B THR* 3.7 8.5 - - - +
214B VAL* 1.3 78.9 - - - +
216B PHE* 1.3 60.5 + - - +
219B LYS 3.4 1.4 + - - -
220B PHE* 3.2 31.6 + - + +
221B PHE* 4.3 2.6 + - - -
227B LEU* 3.5 31.2 - - + -
283B LEU* 4.3 12.6 - - + -
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Residues in contact with PHE 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 THR 2.9 16.7 + - - +
213B VAL* 4.2 2.5 - - - +
215B LEU* 1.3 75.0 - - - +
217B GLY* 1.3 69.0 + - - +
219B LYS* 3.0 16.8 + - - +
221B PHE* 3.4 37.8 - + - -
279B ALA* 4.4 10.1 - - + -
282B ASN* 3.6 52.0 - - + -
283B LEU* 4.0 19.7 - - + +
286B ALA* 4.5 3.1 - - + -
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Residues in contact with GLY 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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36B GLN* 3.3 23.3 - - - +
39B GLU* 3.7 18.4 - - - -
213B VAL 2.9 19.3 + - - -
216B PHE* 1.3 79.8 - - - +
218B GLY* 1.3 58.6 + - - +
219B LYS* 3.2 7.8 + - - +
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Residues in contact with GLY 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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36B GLN* 4.5 11.0 - - - -
39B GLU* 4.4 1.2 + - - -
197B TYR* 3.9 12.8 - - - +
214B VAL 2.9 18.0 + - - -
216B PHE 3.2 0.2 - - - -
217B GLY* 1.3 74.1 - - - +
219B LYS* 1.3 69.5 + - - +
220B PHE* 3.1 24.5 + - - -
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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