Contacts of the helix formed by residues 215 - 223 (chain A) in PDB entry 2WWB
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 ALA 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A ALA 4.5 0.4 - - - +
196A PHE* 3.6 33.7 - - + +
197A SER 3.7 5.6 - - - -
201A VAL* 3.4 22.0 - - - +
214A ILE* 1.4 80.1 - - - +
216A LEU* 1.4 64.8 + - - +
217A PHE 3.3 8.3 - - - +
218A HIS* 3.4 29.2 - - - +
219A LEU* 3.7 2.8 + - - +
241A ASN* 3.8 6.5 - - - +
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Residues in contact with LEU 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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199A THR* 3.3 33.7 - - - +
200A THR* 3.4 25.4 - - - +
201A VAL* 4.1 1.5 - - - +
215A ALA* 1.4 73.3 - - - +
217A PHE* 1.4 62.2 + - + +
219A LEU* 3.3 25.7 + - + +
220A LEU 3.4 3.3 + - - -
237A GLN* 3.8 14.4 - - - +
238A ASN* 3.1 32.0 + - - +
240A PRO* 3.9 29.4 - - + -
241A ASN* 3.5 24.2 - - + +
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Residues in contact with PHE 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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195A ALA* 3.4 26.7 - - + -
196A PHE* 3.8 28.3 - + + -
205A ARG* 3.5 14.7 + - - +
215A ALA* 3.3 0.8 - - - +
216A LEU* 1.4 73.5 - - + +
218A HIS* 1.4 63.3 + - - +
220A LEU* 3.9 10.9 + - + +
221A ALA* 3.8 14.6 + - - +
238A ASN* 3.6 33.2 - - + +
241A ASN* 3.7 18.8 - - + -
242A LEU* 3.9 18.2 - - + -
245A LEU* 3.8 31.2 - - + -
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Residues in contact with HIS 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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196A PHE* 4.2 20.5 - + - -
203A THR 4.1 1.1 - - - +
204A GLY* 4.1 5.8 - - - -
205A ARG* 3.5 45.2 + - + +
207A MET* 3.2 33.5 + - + +
208A GLU* 3.8 3.4 - - - -
209A PHE* 3.7 25.3 + + + -
213A ILE 4.4 0.2 - - - -
214A ILE* 3.8 18.7 - - + -
215A ALA* 3.4 25.9 - - + +
216A LEU 3.2 0.2 - - - -
217A PHE* 1.4 77.4 - - - +
219A LEU* 1.4 61.2 + - - +
221A ALA* 3.4 13.0 + - - +
222A THR* 3.5 19.3 + - - +
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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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200A THR 4.8 12.6 - - - +
201A VAL* 5.2 1.8 - - + -
202A ASN* 3.7 24.7 - - + +
203A THR* 3.6 29.8 + - - +
215A ALA 3.7 4.8 + - - +
216A LEU* 3.3 20.8 + - + +
218A HIS* 1.4 76.7 - - - +
220A LEU* 1.4 63.6 + - - +
222A THR* 2.9 21.6 + - - +
223A ARG* 3.6 46.7 + - - +
237A GLN* 5.6 11.0 - - + +
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Residues in contact with LEU 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 LEU 3.4 2.4 + - - -
217A PHE* 4.0 14.4 - - + +
218A HIS 3.4 0.4 - - - -
219A LEU* 1.4 78.4 - - - +
221A ALA* 1.4 60.8 + - - +
223A ARG* 3.5 4.8 + - - +
224A THR 3.3 29.0 + - - +
225A ASP* 3.5 38.6 - - + +
227A VAL* 3.7 26.9 - - + -
228A ARG* 3.8 17.3 - - - +
237A GLN* 4.6 2.5 - - - +
238A ASN* 3.9 31.0 - - - +
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Residues in contact with ALA 221 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A ARG* 3.7 33.4 - - + +
217A PHE 3.8 5.3 + - - +
218A HIS 3.6 10.1 - - - +
219A LEU 3.3 0.4 - - - -
220A LEU* 1.4 78.2 - - - +
222A THR* 1.4 62.2 + - - +
223A ARG 3.2 2.0 + - - -
224A THR* 3.4 12.3 + - - +
225A ASP* 5.0 2.2 - - - +
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Residues in contact with THR 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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203A THR* 3.9 15.9 + - - +
204A GLY 3.6 22.2 - - - +
205A ARG* 3.8 15.0 - - + +
218A HIS 3.5 14.3 + - - +
219A LEU* 2.9 19.4 + - - -
221A ALA* 1.4 75.8 - - - +
223A ARG* 1.4 66.8 + - - +
224A THR 3.5 0.2 - - - -
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Residues in contact with ARG 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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202A ASN* 3.5 26.7 + - - +
203A THR* 5.2 1.0 + - - -
219A LEU* 3.6 39.2 - - - +
220A LEU* 3.5 7.5 + - - +
221A ALA 3.2 0.2 - - - -
222A THR* 1.4 85.8 + - - +
224A THR* 1.4 72.5 + - - +
227A VAL* 3.6 26.0 - - + +
237A GLN* 5.8 3.8 - - - +
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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