Contacts of the helix formed by residues 213 - 218 (chain A) in PDB entry 3N51
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 GLY 213 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LYS* 5.1 2.0 - - - -
211A LYS 3.3 1.0 + - - -
212A ILE* 1.3 75.4 - - - +
214A THR* 1.3 63.1 - - - +
215A ALA* 3.1 4.5 + - - -
216A TYR* 3.2 18.1 - - - -
217A TYR* 3.1 28.8 - - - -
337A GLN* 3.5 20.9 - - - +
469A VAL* 5.3 2.0 - - - +
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Residues in contact with THR 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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174A ASP* 6.1 1.8 - - + +
176A LYS* 3.8 32.1 - - + -
210A ASP 4.6 2.9 - - - +
211A LYS* 2.8 50.5 + - + +
212A ILE 3.1 2.2 - - - +
213A GLY* 1.3 76.7 - - - +
215A ALA* 1.3 64.8 + - - +
216A TYR 3.2 1.6 + - - -
217A TYR* 3.3 12.1 + - - +
218A ILE* 3.6 14.7 + - - +
255A GLU* 5.0 2.1 + - - +
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Residues in contact with ALA 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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211A LYS 4.6 0.4 + - - -
213A GLY* 3.1 1.6 + - - +
214A THR* 1.3 81.3 + - - +
216A TYR* 1.3 63.6 + - + +
217A TYR 3.3 0.7 + - - -
218A ILE* 3.6 14.5 - - - +
255A GLU* 4.3 15.7 - - + -
258A ILE* 3.6 28.2 - - + +
259A LEU* 3.5 30.3 - - + +
262A VAL* 3.7 14.4 - - - +
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Residues in contact with TYR 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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213A GLY* 3.2 26.2 - - - -
214A THR 3.2 1.4 + - - -
215A ALA* 1.3 79.2 - - + +
217A TYR* 1.3 76.7 + + + +
218A ILE 5.0 0.2 - - - +
238A VAL* 3.4 20.0 - - + +
248A PRO* 3.8 22.2 - - + -
249A PRO* 5.4 0.3 - - - +
250A PHE* 3.5 23.6 - - - +
251A ASN* 3.6 19.6 + - - -
252A GLY 5.1 1.0 + - - -
258A ILE* 3.5 32.7 - - + +
262A VAL* 4.5 8.5 - - - +
333A PHE* 4.0 16.1 - + - -
337A GLN* 3.1 40.3 + - - -
469A VAL* 3.8 17.9 - - + +
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Residues in contact with TYR 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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175A LEU 3.4 18.6 - - - +
176A LYS* 3.6 17.0 - - + -
177A PRO* 3.2 35.3 - - + +
213A GLY* 3.1 32.3 - - - -
214A THR 3.3 5.1 + - - +
215A ALA 3.2 0.4 - - - -
216A TYR* 1.3 87.7 - + + +
218A ILE* 1.3 59.2 + - - +
219A ALA 3.6 0.3 + - - -
234A TRP* 3.6 4.9 - - - -
235A SER* 2.7 35.5 + - - -
238A VAL* 3.4 20.9 - - + -
239A ILE* 3.9 17.3 - - + -
242A ILE* 3.5 24.2 - - + +
333A PHE* 3.4 27.4 - - - -
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Residues in contact with ILE 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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173A ARG* 4.9 10.5 - - - +
174A ASP* 5.5 5.6 - - - +
214A THR* 3.6 12.7 + - - +
215A ALA* 3.6 16.8 - - - +
216A TYR 3.7 0.4 - - - -
217A TYR* 1.3 78.4 - - - +
219A ALA* 1.3 69.1 + - - +
222A VAL* 3.5 32.5 - - + -
223A LEU* 3.8 22.0 - - + -
234A TRP* 3.6 3.9 + - - -
235A SER* 4.6 1.6 - - - -
259A LEU* 3.9 20.2 - - + -
262A VAL* 3.2 18.7 - - + +
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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