Contacts of the helix formed by residues 217 - 224 (chain A) in PDB entry 5WQA
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 SER 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A LEU* 2.6 55.0 + - - +
215A THR* 3.3 8.7 - - - -
216A ASN* 1.3 81.6 - - - +
218A GLU* 1.3 64.8 + - - +
219A LEU 4.0 2.7 - - - -
220A ALA* 3.4 9.9 + - - +
221A LEU* 3.1 23.9 + - - +
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Residues in contact with GLU 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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217A SER* 1.3 72.2 - - - +
219A LEU* 1.3 61.0 + - + +
221A LEU* 3.3 18.4 + - - +
222A MET* 2.9 45.7 + - + +
239B LYS* 3.0 29.5 + - - +
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Residues in contact with LEU 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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203A ASP 5.7 0.7 - - - +
205A PRO* 4.9 8.3 - - + -
212A LEU* 4.2 24.7 - - + -
217A SER* 3.3 6.3 + - - +
218A GLU* 1.3 80.3 - - + +
220A ALA* 1.3 61.4 + - - +
222A MET* 3.2 4.6 + - + -
223A TYR* 3.0 34.5 + - + -
228A VAL* 3.4 20.1 - - + +
229A LEU* 4.8 8.1 - - + -
232A HIS* 3.4 53.4 - - + +
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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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212A LEU 3.4 31.4 - - - +
213A ILE* 3.9 5.2 - - - +
216A ASN* 5.2 1.6 - - - -
217A SER* 3.4 10.3 + - - +
218A GLU 3.4 0.4 - - - -
219A LEU* 1.3 77.6 - - - +
221A LEU* 1.3 57.7 + - - +
224A ASN 2.8 25.6 + - - -
225A ASP* 3.1 23.8 + - - +
228A VAL* 3.6 17.6 - - + +
261B ARG* 3.3 6.1 + - - +
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Residues in contact with LEU 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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216A ASN 5.6 0.7 - - - +
217A SER 3.1 17.5 + - - +
218A GLU* 3.5 20.6 - - - +
219A LEU 3.2 0.2 - - - -
220A ALA* 1.3 76.6 - - - +
222A MET* 1.3 65.0 + - - +
223A TYR 3.4 0.2 + - - -
224A ASN* 3.7 7.8 + - - +
235B ALA* 3.5 21.8 - - + +
238B PHE* 3.6 32.1 - - + -
239B LYS* 3.7 37.5 - - + +
242B GLN* 4.3 19.7 - - - +
261B ARG* 4.0 13.9 + - - +
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Residues in contact with MET 222 (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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218A GLU* 2.9 33.3 + - + +
219A LEU* 3.2 8.9 + - + +
221A LEU* 1.3 78.8 - - - +
223A TYR* 1.3 73.4 + - + +
224A ASN* 3.8 5.2 + - - -
222B MET* 3.9 42.6 - - + -
223B TYR* 2.9 49.0 + - + +
232B HIS* 6.0 1.3 - - - -
235B ALA* 4.0 7.4 - - - +
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Residues in contact with TYR 223 (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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219A LEU* 3.0 32.9 + - + +
220A ALA 3.6 0.2 - - - -
222A MET* 1.3 84.0 - - + +
224A ASN* 1.3 72.5 + - - +
225A ASP 3.3 1.6 - - - -
226A SER* 3.2 20.3 + - - +
228A VAL* 3.6 29.8 - - + -
231A ASN* 3.5 30.1 + - + -
232A HIS* 4.0 22.9 + - + -
235A ALA* 3.6 14.7 - - - +
222B MET* 2.7 49.1 + - - -
223B TYR* 3.7 24.5 - + - -
231B ASN* 4.3 5.4 - - - +
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Residues in contact with ASN 224 (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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220A ALA 2.8 10.3 + - - -
221A LEU 3.7 6.1 + - - +
222A MET 3.5 4.8 + - - -
223A TYR* 1.3 78.4 - - - +
225A ASP* 1.3 63.6 + - - +
226A SER* 3.0 16.7 + - - +
231B ASN* 3.0 50.9 + - - +
234B LEU* 3.1 30.1 - - + +
235B ALA 3.9 4.8 + - - +
238B PHE* 4.2 6.6 - - - -
261B ARG* 3.7 7.2 + - - +
265B ILE* 3.5 31.8 - - + +
269B LEU* 5.4 1.3 - - + -
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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