Contacts of the helix formed by residues 215 - 226 (chain A) in PDB entry 2WW9
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 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A ASP 3.1 9.1 + - - -
197A THR 3.4 4.7 - - - -
198A PHE 3.1 28.3 - - - -
199A GLY* 3.8 2.2 - - - -
200A VAL* 5.1 0.4 - - - -
214A GLN* 1.3 76.0 - - - +
216A ALA* 1.4 58.9 + - - +
217A LEU 3.3 3.1 - - - -
218A ILE* 3.4 6.8 + - - +
219A ASN* 3.0 30.2 + - - +
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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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196A ASP* 3.3 9.1 + - - +
197A THR* 3.2 3.3 + - - +
214A GLN* 4.6 0.6 - - - +
215A GLY* 1.4 74.3 - - - +
217A LEU* 1.4 60.3 + - - +
220A LEU* 3.0 33.4 + - - +
246A ASN* 3.6 31.4 - - - +
249A THR* 3.3 35.0 - - + -
250A THR* 4.1 1.6 - - - +
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Residues in contact with LEU 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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197A THR* 2.9 37.8 + - + +
198A PHE* 4.8 13.9 - - + -
216A ALA* 1.4 75.5 - - - +
218A ILE* 1.4 64.9 + - + +
220A LEU* 4.8 0.2 - - - -
221A ILE* 3.1 58.3 + - + +
250A THR* 3.8 25.8 + - + -
58B PHE* 5.2 11.4 - - + -
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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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198A PHE* 3.1 60.8 - - + +
199A GLY 4.5 3.4 - - - +
200A VAL* 6.0 1.1 - - - -
215A GLY* 3.4 7.5 + - - +
217A LEU* 1.4 77.8 - - + +
219A ASN* 1.4 61.9 + - - +
221A ILE* 5.4 0.2 - - - -
222A GLN* 3.1 39.1 + - + +
228A HIS* 6.2 4.0 - - + -
232A ILE* 4.9 1.4 - - + +
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Residues in contact with ASN 219 (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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215A GLY 3.0 17.5 + - - +
216A ALA 4.1 0.7 - - - +
218A ILE* 1.4 76.4 - - - +
220A LEU* 1.4 61.5 + - - +
223A GLY* 3.3 18.0 + - - -
232A ILE* 4.3 21.1 - - - +
236A ILE* 5.6 3.2 - - - +
246A ASN* 3.3 35.1 + - - +
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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 ALA 3.0 18.7 + - - +
217A LEU* 4.1 0.9 - - - +
219A ASN* 1.4 75.9 - - - +
221A ILE* 1.4 75.6 + - + +
223A GLY* 3.4 1.0 + - - -
224A LEU* 3.0 32.5 + - + +
235A ILE* 5.6 5.0 - - + +
236A ILE* 3.4 31.8 - - + +
245A PRO 4.4 1.8 - - - +
246A ASN* 3.9 8.7 - - + +
247A LEU* 3.5 51.4 - - + +
250A THR* 4.1 15.9 - - + +
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Residues in contact with ILE 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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217A LEU* 3.1 46.1 + - + +
218A ILE* 5.4 0.4 - - - -
220A LEU* 1.4 95.5 - - + +
222A GLN* 1.4 57.2 + - - +
224A LEU* 3.4 12.3 + - + +
225A ARG* 2.9 35.5 + - + +
250A THR* 5.1 2.9 - - + -
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Residues in contact with GLN 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 ILE* 3.1 27.9 + - + +
221A ILE* 1.4 75.1 - - - +
223A GLY* 1.4 59.2 + - - +
225A ARG* 3.7 29.6 + - - +
226A SER* 2.9 41.2 + - - +
227A LYS 3.6 19.8 + - - -
228A HIS* 3.7 39.4 + - + +
232A ILE* 3.9 13.5 - - + +
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Residues in contact with GLY 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 ASN 3.3 19.2 + - - -
220A LEU 3.8 0.9 - - - -
221A ILE 3.3 0.4 - - - -
222A GLN* 1.4 77.6 - - - +
224A LEU* 1.4 62.4 + - - +
225A ARG 4.7 0.2 - - - -
226A SER 3.9 2.8 + - - +
232A ILE* 3.8 11.8 - - - +
233A GLY* 3.6 11.4 - - - -
234A GLY 3.1 36.1 + - - +
235A ILE* 5.1 0.2 - - - +
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Residues in contact with LEU 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 LEU* 3.0 21.5 + - + +
221A ILE* 3.5 14.1 - - + +
223A GLY* 1.4 76.6 - - - +
225A ARG* 1.4 67.6 + - + +
234A GLY 4.0 0.6 + - - -
235A ILE* 3.6 47.8 - - + +
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Residues in contact with ARG 225 (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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221A ILE* 2.9 25.0 + - + +
222A GLN* 3.7 29.2 + - - +
223A GLY 3.3 0.9 - - - -
224A LEU* 1.4 86.7 - - + +
226A SER* 1.4 75.2 + - - +
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Residues in contact with SER 226 (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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222A GLN* 2.9 23.3 + - - +
223A GLY 3.9 8.0 - - - +
224A LEU 3.9 0.2 - - - -
225A ARG* 1.4 94.8 + - - +
227A LYS* 1.4 71.3 + - - +
232A ILE 4.2 0.3 - - - +
233A GLY* 4.0 12.2 + - - -
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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