Contacts of the helix formed by residues 210 - 224 (chain A) in PDB entry 1WDR
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 ASP 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A ASP* 3.6 22.9 - - - +
122A PHE 3.6 21.3 - - - +
123A TYR* 4.6 3.5 - - - -
124A THR* 3.6 11.7 - - - +
130A ARG* 4.2 0.2 - - - +
136A THR* 2.7 29.6 + - - +
207A GLN 4.8 0.7 - - - +
209A TYR* 1.3 79.2 - - - +
211A LYS* 1.3 58.8 + - - +
212A TYR* 2.8 20.1 + - - +
213A LEU* 2.8 39.9 + - - +
214A LYS* 2.9 26.0 + - - +
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Residues in contact with LYS 211 (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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118A ASN* 4.5 9.3 + - - +
120A ASP* 2.9 37.9 + - + +
209A TYR 3.7 1.7 + - - -
210A ASP* 1.3 73.1 - - - +
212A TYR* 1.3 95.4 + - + +
214A LYS* 4.1 5.6 - - - +
215A ALA* 3.0 29.8 + - - +
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Residues in contact with TYR 212 (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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118A ASN* 3.0 22.4 + - - -
120A ASP* 3.4 39.0 - - + -
138A GLY* 3.5 22.9 - - - +
139A VAL* 3.6 21.8 - - + -
142A GLU* 3.7 35.4 - - + -
144A ILE* 4.0 12.3 - - + +
210A ASP* 2.8 4.8 + - - +
211A LYS* 1.3 96.5 + - + +
213A LEU* 1.3 67.5 + - - +
215A ALA* 3.4 5.0 + - - +
216A ASP* 3.0 24.5 + - - +
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Residues in contact with LEU 213 (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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123A TYR* 4.3 0.7 - - + -
136A THR* 3.5 12.3 - - - +
137A VAL* 3.9 13.5 - - + -
138A GLY* 3.9 16.4 - - - +
189A TYR* 4.3 9.6 - - + +
207A GLN 4.1 6.5 - - - +
208A CYS* 3.6 31.9 - - + +
210A ASP* 2.8 32.0 + - - +
212A TYR* 1.3 72.6 - - - +
214A LYS* 1.3 67.5 + - - +
216A ASP* 3.2 4.1 + - - +
217A PHE* 2.9 21.0 + - - +
265A TRP* 3.3 18.1 - - + -
269A LYS* 3.8 35.0 - - + -
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Residues in contact with LYS 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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208A CYS 3.7 6.6 + - - +
209A TYR* 4.4 8.5 - - + +
210A ASP 2.9 17.6 + - - +
211A LYS* 4.1 6.5 - - - +
213A LEU* 1.3 78.8 - - - +
215A ALA* 1.4 58.5 + - - +
217A PHE* 3.3 3.3 + - - +
218A LYS* 2.8 46.8 + - + +
230A GLU* 4.4 16.0 + - - -
231A LEU* 4.2 26.5 - - + +
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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 3.0 18.8 + - - +
212A TYR* 3.8 4.9 - - - +
214A LYS* 1.4 74.6 - - - +
216A ASP* 1.3 62.1 + - - +
218A LYS* 3.3 6.5 + - - +
219A ALA* 3.0 30.3 + - - +
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Residues in contact with ASP 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 TYR 3.0 18.0 + - - +
213A LEU* 3.2 7.9 + - - +
215A ALA* 1.3 76.5 - - - +
217A PHE* 1.3 61.0 + - - +
219A ALA* 3.3 6.0 + - - +
220A ALA* 3.0 22.5 + - - +
223A ARG* 4.9 4.2 + - - -
265A TRP* 2.9 28.7 + - - -
269A LYS* 2.5 35.2 + - - +
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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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213A LEU 2.9 15.9 + - - +
214A LYS 3.5 2.2 - - - +
216A ASP* 1.3 74.4 - - - +
218A LYS* 1.3 71.5 + - + +
220A ALA* 3.1 3.8 + - - +
221A VAL* 2.8 52.5 + - + +
229A TRP* 3.6 17.9 - + + -
230A GLU* 3.5 18.8 - - - -
231A LEU* 3.5 44.6 - - + -
258A LYS* 5.8 2.2 - - + -
261A PHE* 4.6 3.6 - + - -
262A PHE* 3.9 29.4 - + + -
265A TRP* 3.6 39.6 - + + +
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Residues in contact with LYS 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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214A LYS* 2.8 43.7 + - + +
215A ALA* 3.8 6.7 - - - +
216A ASP 3.3 0.2 - - - -
217A PHE* 1.3 85.6 - - + +
219A ALA* 1.3 61.3 + - - +
221A VAL* 3.3 6.2 - - - +
222A ALA* 3.2 21.5 + - - +
227A PRO* 2.9 23.6 + - - +
228A GLU* 3.8 2.4 - - - +
229A TRP 2.6 31.6 + - - +
230A GLU* 3.2 31.3 + - - +
231A LEU* 5.6 0.4 - - + +
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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 ALA 3.0 17.6 + - - +
216A ASP* 3.8 5.4 - - - +
218A LYS* 1.3 76.9 - - - +
220A ALA* 1.3 58.1 + - - +
222A ALA* 3.3 6.9 + - - +
223A ARG* 3.0 48.5 + - - +
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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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216A ASP* 3.0 14.8 + - - +
217A PHE 3.1 7.2 + - - +
219A ALA* 1.3 74.2 - - - +
221A VAL* 1.3 65.5 - - - +
223A ARG* 3.1 26.5 + - - +
224A ALA* 3.0 21.5 + - - +
261A PHE* 3.7 22.7 - - + -
265A TRP* 4.0 17.3 - - + -
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Residues in contact with VAL 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 PHE* 2.8 51.1 + - + +
218A LYS* 3.3 19.1 - - - +
220A ALA* 1.3 74.0 - - - +
222A ALA* 1.3 60.5 + - - +
224A ALA* 3.1 11.9 + - - +
225A GLY 3.2 0.2 + - - -
226A HIS* 2.8 42.9 + - - +
227A PRO 4.1 7.0 - - - +
229A TRP* 3.7 36.6 - - + +
261A PHE* 3.7 16.2 - - + -
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Residues in contact with ALA 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 LYS 3.2 14.4 + - - +
219A ALA* 3.5 10.5 - - - +
220A ALA 3.2 0.4 - - - -
221A VAL* 1.3 79.2 - - - +
223A ARG* 1.3 62.3 + - + +
225A GLY* 3.0 14.7 + - - -
227A PRO* 3.7 27.3 - - + +
2002A SO4 4.3 8.1 + - - -
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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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216A ASP* 4.9 4.4 + - - -
219A ALA* 3.0 40.1 + - - +
220A ALA* 3.1 31.0 + - - +
222A ALA* 1.3 77.0 - - + +
224A ALA* 1.3 59.4 + - - +
225A GLY* 3.2 1.5 + - - -
2002A SO4 4.9 3.5 + - - -
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Residues in contact with ALA 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 3.0 12.5 + - - +
221A VAL* 3.1 10.9 + - - +
223A ARG* 1.3 74.8 - - - +
225A GLY* 1.3 57.9 + - - +
226A HIS* 3.1 23.3 + - + -
229A TRP* 4.8 1.3 - - + -
261A PHE* 3.7 29.4 - - + -
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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