Contacts of the helix formed by residues 213 - 221 (chain A) in PDB entry 4E70
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 ASN 213 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PRO 5.4 1.4 + - - -
180A ALA* 2.8 37.6 + - + +
181A GLY* 5.0 0.2 - - - -
183A SER* 3.7 18.8 - - - -
184A TRP* 3.8 27.5 - - - +
187A SER* 3.5 13.4 + - - -
188A ARG* 5.0 1.1 + - - -
209A GLY 4.5 1.4 + - - -
211A THR* 3.5 4.8 + - - +
212A GLY* 1.3 77.6 - - - +
214A THR* 1.3 62.4 + - - +
216A LYS* 4.2 1.7 - - - +
217A VAL* 3.6 15.1 + - - +
241A GLN* 2.8 36.3 + - - +
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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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183A SER* 3.5 23.3 + - - -
186A PHE* 5.7 1.1 - - + -
187A SER* 3.7 17.5 + - - -
190A LEU* 4.5 10.5 - - + -
206A ASP* 3.6 11.7 - - - -
209A GLY* 5.3 4.4 + - - -
212A GLY* 3.2 0.6 - - - -
213A ASN* 1.3 77.1 - - - +
215A SER* 1.3 66.0 + - - +
217A VAL* 3.3 5.5 + - - +
218A ILE* 3.1 28.3 + - + +
265A LEU* 3.9 26.7 - - + -
267A LYS* 4.1 18.1 - - + +
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Residues in contact with SER 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 4.3 4.0 - - - +
206A ASP* 2.8 36.6 + - - +
212A GLY 3.4 3.7 + - - -
214A THR* 1.3 75.6 - - - +
216A LYS* 1.3 61.1 + - - +
218A ILE* 3.7 9.2 - - - +
219A ALA* 2.8 32.7 + - - +
227A CYS* 3.9 14.3 - - - +
228A THR 4.8 0.7 + - - -
229A VAL* 3.7 9.1 - - - +
246A LEU* 3.6 26.0 - - - -
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Residues in contact with LYS 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 GLY 2.8 19.0 + - - +
213A ASN 4.2 3.6 - - - +
214A THR 3.3 0.2 - - - -
215A SER* 1.3 75.8 - - - +
217A VAL* 1.3 61.8 + - + +
219A ALA* 3.3 2.6 + - - +
220A GLU* 3.0 65.6 + - - +
241A GLN* 3.3 38.0 + - + +
242A THR 3.0 30.7 + - - +
243A HIS* 3.8 18.8 - - + -
246A LEU* 4.1 7.0 - - + +
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Residues in contact with VAL 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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187A SER* 3.3 45.3 - - - +
188A ARG* 3.4 36.6 - - + +
191A VAL* 3.8 18.6 - - + -
213A ASN 3.6 6.5 + - - +
214A THR 3.3 5.7 + - - +
215A SER 3.3 0.4 - - - -
216A LYS* 1.3 78.3 - - + +
218A ILE* 1.3 65.9 + - - +
220A GLU* 3.5 11.6 + - - +
221A THR* 2.8 33.0 + - - +
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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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187A SER* 5.8 0.4 - - - -
190A LEU* 4.7 3.4 - - + -
191A VAL* 4.2 16.4 - - + -
198A PHE* 3.9 41.1 - - + -
204A LEU* 4.2 12.6 - - + -
214A THR* 3.1 35.4 + - + +
215A SER* 3.3 7.8 + - - +
217A VAL* 1.3 75.8 - - - +
219A ALA* 1.3 57.2 + - - +
221A THR 3.2 0.5 + - - -
222A PHE* 2.9 33.4 + - + +
225A ILE* 4.2 13.9 - - + -
227A CYS* 3.7 16.6 - - - -
265A LEU* 4.0 15.9 - - + -
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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 SER 2.8 22.1 + - - +
216A LYS* 3.7 5.2 - - - +
218A ILE* 1.3 74.7 - - - +
220A GLU* 1.3 61.7 + - - +
222A PHE 3.5 18.9 - - - +
223A PRO* 3.9 6.8 - - - +
225A ILE 4.4 5.1 - - - +
227A CYS* 4.0 15.9 - - + -
243A HIS* 3.9 32.1 + - + +
245A ASN* 4.4 12.3 - - + +
246A LEU* 4.7 2.2 - - + -
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Residues in contact with GLU 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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188A ARG* 5.2 4.7 + - - -
216A LYS* 3.0 51.2 + - - +
217A VAL* 3.9 16.6 - - - +
219A ALA* 1.3 76.7 - - - +
221A THR* 1.3 63.9 + - - +
222A PHE 3.6 0.2 + - - -
223A PRO* 4.3 9.9 - - - +
243A HIS* 4.0 15.9 - - + +
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Residues in contact with THR 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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191A VAL* 3.8 24.1 - - + +
195A ARG* 4.1 18.3 + - - +
217A VAL* 2.8 23.8 + - - +
220A GLU* 1.3 80.2 - - - +
222A PHE* 1.3 93.0 + - + +
223A PRO* 3.5 8.1 - - - +
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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