Contacts of the helix formed by residues 212 - 221 (chain A) in PDB entry 3O8C
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 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A GLY* 3.1 14.8 + - - -
210A LYS 3.4 0.2 - - - -
211A SER* 1.3 84.5 - - - +
213A LYS* 1.3 73.8 + - - +
214A VAL 3.3 0.9 - - - -
215A PRO* 3.2 3.2 - - - +
216A ALA* 3.0 25.8 + - - +
238A PHE* 3.8 27.6 - - + +
241A TYR* 3.7 41.3 + - + -
242A MET* 4.8 2.8 - - + +
246A HIS* 4.0 5.6 + - - -
267A TYR* 3.8 8.3 + - - +
850A SO4 5.1 1.3 + - - +
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Residues in contact with LYS 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A SER 4.1 14.3 + - - +
209A GLY* 3.0 14.8 + - - +
212A THR* 1.3 80.0 + - - +
214A VAL* 1.3 61.4 + - + +
216A ALA* 3.4 1.6 + - - +
217A ALA* 2.9 34.0 + - + +
246A HIS* 3.8 19.7 - - + +
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Residues in contact with VAL 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A PRO* 3.8 30.5 - - + -
191A PRO* 6.2 0.2 - - + -
202A LEU* 4.0 16.4 - - + -
208A SER 5.5 1.6 - - - +
209A GLY 3.0 16.3 + - - +
210A LYS* 3.5 17.0 - - + +
213A LYS* 1.3 79.7 - - + +
215A PRO* 1.4 70.9 - - + +
217A ALA* 3.2 8.1 + - - +
218A TYR* 3.1 46.9 + - + +
288A ILE* 4.0 9.2 - - + -
319A VAL* 6.1 1.1 - - + -
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Residues in contact with PRO 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A LYS 3.4 13.9 - - - +
211A SER 3.1 22.4 - - - +
212A THR 3.2 14.8 - - - +
214A VAL* 1.4 97.6 - - + +
216A ALA* 1.3 54.3 + - - -
218A TYR* 3.4 12.8 + - + +
219A ALA* 2.9 29.6 + - - +
225A VAL* 3.9 15.4 - - + +
227A VAL* 3.7 25.1 - - + -
242A MET* 5.8 0.4 - - + -
265A VAL* 4.2 7.6 - - + +
267A TYR* 3.7 8.5 - - - +
288A ILE* 4.0 3.6 - - + -
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Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A THR 3.0 20.0 + - - +
213A LYS 3.6 4.5 - - - +
215A PRO* 1.3 77.0 - - - +
217A ALA* 1.3 57.6 + - - +
219A ALA* 3.1 9.0 + - - +
220A ALA* 2.8 29.0 + - - +
242A MET* 4.5 11.5 - - - -
246A HIS* 3.6 37.7 - - + +
248A ILE* 6.0 0.9 - - + -
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Residues in contact with ALA 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A PRO* 6.5 0.9 - - + -
213A LYS* 2.9 23.2 + - + +
214A VAL* 3.6 6.3 - - - +
216A ALA* 1.3 75.8 - - - +
218A TYR* 1.3 62.6 + - - +
220A ALA* 3.2 10.4 + - - +
221A GLN* 3.2 36.8 + - - +
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Residues in contact with TYR 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A PRO* 3.8 8.0 - - + +
191A PRO* 2.6 47.9 + - - +
192A ALA* 5.4 0.4 - - - -
193A VAL* 4.1 11.2 - - + -
214A VAL* 3.1 42.1 + - + -
215A PRO* 3.6 10.3 - - + +
217A ALA* 1.3 76.5 - - + +
219A ALA* 1.3 63.2 + - - +
221A GLN* 3.0 37.2 + - - +
223A TYR* 3.3 15.6 + + - -
225A VAL* 3.7 13.7 - - + -
286A ILE* 3.4 32.8 - - + -
288A ILE* 4.3 11.9 - - + -
317A LEU* 3.9 11.1 - - + +
319A VAL* 4.1 5.3 - - + +
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Residues in contact with ALA 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A PRO 2.9 14.7 + - - +
216A ALA* 3.3 11.0 - - - +
218A TYR* 1.3 78.3 - - - +
220A ALA* 1.3 55.3 + - - +
222A GLY* 2.9 21.5 + - - -
223A TYR 3.6 15.9 + - - +
225A VAL* 4.2 0.8 - - + +
248A ILE* 5.3 3.8 - - + -
264A PRO* 4.6 11.3 - - + +
265A VAL* 3.6 25.1 - - + -
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Residues in contact with ALA 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ALA 2.8 13.5 + - - +
217A ALA* 3.4 13.7 - - - +
219A ALA* 1.3 77.0 - - - +
221A GLN* 1.3 59.2 + - + +
222A GLY 3.2 1.2 + - - -
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Residues in contact with GLN 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A VAL* 4.7 2.4 + - - +
217A ALA* 3.2 27.0 + - - +
218A TYR* 3.0 27.7 + - - +
220A ALA* 1.3 79.6 - - - +
222A GLY* 1.3 57.9 + - - +
223A TYR* 3.6 27.7 - - + -
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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