Contacts of the helix formed by residues 222 - 234 (chain A) in PDB entry 2HD5
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 THR 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A ARG 4.1 0.7 + - - -
218A ASN* 3.1 7.4 + - - -
219A LEU* 2.9 35.4 + - + +
220A GLY 3.1 19.7 - - - +
221A ASN* 1.3 78.1 - - - +
223A CYS* 1.3 61.6 + - - +
224A PHE* 3.2 12.3 - - + -
225A MET* 2.9 17.0 + - + +
226A ASN* 2.9 32.1 + - - -
276A PRO* 5.5 0.2 - - - +
280A LYS* 4.0 28.9 - - + -
291A TYR* 4.5 1.3 - - + -
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Residues in contact with CYS 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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218A ASN* 3.9 5.6 - - - -
221A ASN 3.4 0.6 - - - -
222A THR* 1.3 75.1 - - - +
224A PHE* 1.3 66.4 + - - +
226A ASN* 3.9 1.3 - - - +
227A SER* 2.9 27.4 + - - -
464A HIS* 3.3 19.1 - - + +
465A TYR* 3.6 19.8 - - - +
482A ASP* 2.3 51.1 - - - -
76B GLY* 2.9 28.8 + - - +
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Residues in contact with PHE 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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221A ASN 3.2 28.7 - - - -
222A THR* 3.9 11.0 - - + -
223A CYS* 1.3 78.0 - - - +
225A MET* 1.3 92.9 + - + +
227A SER* 3.7 1.9 + - - -
228A ILE* 3.4 26.9 + - - +
280A LYS* 6.1 1.1 - - - -
288A PHE* 3.8 23.3 - + + -
292A ASN 3.9 2.7 - - - -
294A GLN* 3.4 56.8 - - + +
295A ASP 4.2 2.2 - - - -
296A ALA* 4.0 6.7 - - - +
299A PHE* 3.8 21.5 - + + -
465A TYR* 3.5 27.5 - - + -
75B GLY 3.4 11.3 + - - +
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Residues in contact with MET 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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219A LEU* 5.9 0.9 - - - -
222A THR* 2.9 18.0 + - + +
224A PHE* 1.3 107.6 - - + +
226A ASN* 1.3 61.3 + - - +
228A ILE* 3.3 4.0 + - - +
229A LEU* 2.9 39.0 + - + +
276A PRO* 5.2 6.3 - - - -
279A PHE* 3.9 20.4 - - - -
280A LYS* 4.2 36.6 - - + -
283A ILE* 4.4 6.1 - - + -
288A PHE* 5.2 4.5 - - + -
299A PHE* 3.5 34.7 - - + -
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Residues in contact with ASN 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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216A LEU* 3.5 37.0 + - + +
217A ARG 3.1 24.0 + - - -
218A ASN* 3.7 4.9 - - - +
222A THR* 2.9 21.4 + - - +
223A CYS 3.9 3.4 - - - +
225A MET* 1.3 76.2 - - - +
227A SER* 1.3 67.4 + - - +
229A LEU* 3.3 4.0 + - - +
230A GLN* 3.0 32.9 + - + +
276A PRO* 3.7 15.4 - - - +
482A ASP* 3.4 27.9 + - - +
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Residues in contact with SER 227 (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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223A CYS 2.9 18.0 + - - -
224A PHE 3.8 4.0 - - - -
226A ASN* 1.3 78.5 - - - +
228A ILE* 1.3 60.9 + - - +
230A GLN* 3.4 0.8 + - - -
231A CYS* 3.2 27.3 + - - -
454A SER* 2.7 30.6 + - - -
465A TYR* 4.0 11.0 - - - -
466A THR* 2.9 25.7 + - - -
467A ALA* 3.7 11.9 - - - +
480A PHE* 5.8 1.1 - - - -
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Residues in contact with ILE 228 (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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224A PHE 3.4 13.4 + - - +
225A MET 3.3 2.1 + - - +
226A ASN 3.3 0.4 - - - -
227A SER* 1.3 73.9 - - - +
229A LEU* 1.3 67.3 + - - +
231A CYS* 3.1 4.9 + - - +
232A LEU* 2.9 32.6 + - + +
296A ALA* 3.5 25.8 - - + +
299A PHE* 3.7 26.7 - - + -
300A LEU* 3.8 28.9 - - + -
303A LEU* 4.5 0.7 - - + -
454A SER* 4.3 7.9 - - - +
515A LEU* 3.7 30.3 - - + -
517A PHE* 4.2 12.6 - - + -
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Residues in contact with LEU 229 (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* 3.8 17.9 - - + -
225A MET* 2.9 36.6 + - + +
226A ASN* 3.3 5.8 + - - +
228A ILE* 1.3 78.0 - - - +
230A GLN* 1.3 57.1 + - - +
232A LEU* 3.3 4.6 + - - +
233A SER* 2.8 30.2 + - - -
260A PHE* 3.9 24.7 - - + -
263A LEU* 3.5 28.7 - - + -
264A ILE* 4.6 5.6 - - + +
267A ILE* 5.7 0.4 - - - -
276A PRO* 4.3 7.0 - - + -
279A PHE* 3.8 29.8 - - + -
299A PHE* 4.6 0.7 - - + -
303A LEU* 4.0 9.0 - - + -
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Residues in contact with GLN 230 (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 5.0 0.5 - - - +
214A ALA 3.1 24.6 + - - +
215A GLY* 4.0 0.6 - - - -
216A LEU* 3.8 31.2 - - + +
226A ASN* 3.0 18.8 + - + +
227A SER* 3.8 5.2 - - - +
229A LEU* 1.3 75.5 - - - +
231A CYS* 1.3 63.4 + - - +
233A SER* 3.2 13.4 + - - -
234A ASN* 2.9 30.8 + - - -
267A ILE* 4.5 8.0 - - - +
467A ALA* 4.3 3.1 - - + -
469A CYS* 3.8 15.9 - - - -
480A PHE* 3.3 42.2 - - + +
482A ASP 5.0 1.0 + - - -
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Residues in contact with CYS 231 (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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227A SER 3.2 23.4 + - - -
228A ILE* 3.1 9.7 + - - +
230A GLN* 1.3 76.2 - - - +
232A LEU* 1.3 61.1 + - - +
234A ASN* 3.4 3.7 + - - +
235A THR* 2.8 24.0 + - - -
451A TYR* 3.7 5.9 - - - -
452A ALA* 3.8 16.2 - - + -
453A VAL 3.8 23.8 - - - -
454A SER* 4.1 3.8 - - - -
467A ALA* 4.0 7.4 - - - -
469A CYS* 4.0 6.3 - - - -
517A PHE* 3.6 38.8 - - + -
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Residues in contact with LEU 232 (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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228A ILE* 2.9 28.9 + - + +
229A LEU* 3.8 4.0 - - - +
231A CYS* 1.3 72.9 - - + +
233A SER* 1.3 65.7 + - - +
234A ASN 3.1 1.6 - - - -
235A THR* 3.0 26.4 + - - +
238A LEU* 3.8 28.8 - - + +
239A ARG* 4.4 1.9 + - - -
260A PHE* 4.1 17.4 - - + -
264A ILE* 5.0 2.1 - - - +
300A LEU* 4.2 15.7 - - + -
303A LEU* 3.5 32.3 - - + -
304A LEU* 4.3 9.9 - - + -
307A LEU* 5.4 0.2 - - + -
324A PHE* 3.9 20.9 - - + -
517A PHE* 4.4 8.3 - - + -
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Residues in contact with SER 233 (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 5.2 0.3 + - - -
229A LEU 2.8 20.7 + - - -
230A GLN* 3.4 17.8 + - - -
232A LEU* 1.3 71.9 - - - +
234A ASN* 1.3 61.6 + - - +
239A ARG* 3.3 20.5 - - - +
264A ILE* 4.0 22.1 - - - +
267A ILE* 3.7 15.8 - - - +
268A TRP* 2.8 43.2 + - - +
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Residues in contact with ASN 234 (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 4.9 3.8 + - - +
230A GLN* 2.9 28.5 + - - +
231A CYS 3.6 5.2 - - - +
233A SER* 1.3 82.9 + - - +
235A THR* 1.3 59.9 + - - +
236A ARG* 3.4 5.5 + - - +
268A TRP* 3.5 12.4 - - - -
451A TYR* 3.3 19.0 - - + +
469A CYS* 3.4 28.4 - - + +
470A ARG 3.7 13.6 - - - +
471A SER* 3.8 7.3 - - - -
472A PRO* 3.3 32.2 - - - +
480A PHE* 4.1 16.7 - - - -
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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