Contacts of the helix formed by residues 210 - 224 (chain A) in PDB entry 5J1T
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 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A HIS* 4.6 1.1 - - - -
208A ASN 3.2 0.4 + - - -
209A ALA* 1.3 73.6 - - - +
211A ALA* 1.3 64.9 + - - +
212A GLU 3.3 2.5 - - - -
213A ARG* 3.1 8.8 + - - +
214A ILE* 3.0 29.0 + - - +
240A LEU* 3.8 10.4 - - - +
243A SER* 5.2 1.6 - - - -
244A VAL* 3.8 17.9 - - - +
441B ASP* 3.3 10.0 + - - -
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Residues in contact with ALA 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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102A GLY* 3.7 30.7 - - - +
103A TRP* 3.6 20.3 - - + +
104A THR 5.3 0.7 - - - +
208A ASN* 3.1 20.1 + - + +
209A ALA 3.3 1.2 + - - -
210A GLY* 1.3 77.4 - - - +
212A GLU* 1.3 62.3 + - - +
214A ILE* 3.3 4.4 + - - +
215A THR* 3.0 26.9 + - - -
441B ASP* 3.5 11.5 + - + +
444B SER* 5.4 2.5 - - - +
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Residues in contact with GLU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TRP* 3.6 13.3 - - - -
210A GLY 3.3 0.4 - - - -
211A ALA* 1.3 75.8 - - - +
213A ARG* 1.3 60.8 + - + +
215A THR* 3.2 7.2 + - - +
216A ASP* 3.0 42.0 + - - +
404A BTB 2.6 56.8 + - - -
430B ASP* 4.4 28.8 - - + +
440B SER* 4.2 6.0 + - - +
441B ASP* 3.0 20.3 + - - +
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Residues in contact with ARG 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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210A GLY* 3.1 4.2 + - - +
212A GLU* 1.3 77.8 - - + +
214A ILE* 1.3 64.2 + - - +
216A ASP* 2.8 59.7 + - - +
217A VAL* 3.3 17.4 + - - +
238A HIS* 6.3 0.2 - - - -
239A ALA* 3.1 48.9 + - - +
240A LEU* 3.6 26.5 - - + -
242A VAL* 4.4 15.0 - - + +
243A SER* 4.5 8.1 - - - +
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Residues in contact with ILE 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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101A HIS* 3.5 44.0 - - + +
102A GLY* 4.1 6.5 - - - -
210A GLY 3.0 17.9 + - - +
211A ALA 3.7 6.3 - - - +
213A ARG* 1.3 74.4 - - - +
215A THR* 1.3 63.3 + - - +
217A VAL* 3.1 6.9 + - - +
218A ALA* 3.1 18.9 + - - +
236A ILE* 4.1 30.4 - - + +
239A ALA* 5.8 0.4 - - - -
240A LEU* 4.5 5.4 - - + -
268A PRO* 4.0 9.9 - - + -
269A PHE 3.6 22.0 - - - +
270A LEU* 3.8 25.5 - - + +
271A PRO* 4.5 1.8 - - + -
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Residues in contact with THR 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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103A TRP* 3.1 29.1 - - + -
211A ALA 3.0 6.8 + - - -
212A GLU* 3.5 10.3 - - - +
214A ILE* 1.3 77.6 - - - +
216A ASP* 1.3 58.9 + - - +
218A ALA* 3.1 1.8 + - - +
219A LEU* 2.8 33.4 + - + +
271A PRO* 3.3 29.5 - - + +
306A PHE* 3.6 33.9 - - + -
313A PHE* 4.0 6.1 - - + -
404A BTB 5.5 1.1 - - - -
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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 GLU* 3.0 29.3 + - - +
213A ARG* 2.8 45.7 + - - +
214A ILE 3.2 0.4 - - - -
215A THR* 1.3 79.0 - - - +
217A VAL* 1.3 56.2 + - - +
219A LEU* 3.5 11.7 + - - +
220A ASP* 2.9 29.5 + - - +
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Residues in contact with VAL 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 ARG* 3.3 6.0 + - - +
214A ILE 3.1 7.5 + - - +
216A ASP* 1.3 75.6 - - + +
218A ALA* 1.3 67.3 + - - +
220A ASP* 3.2 6.5 + - + +
221A PHE* 3.0 46.0 + - + -
231A ILE* 4.0 20.6 - - + -
235A ASP* 3.8 17.0 - - + +
236A ILE* 4.0 13.7 - - + -
239A ALA* 3.5 32.1 - - + -
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Residues in contact with ALA 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 ILE 3.1 11.9 + - - +
215A THR 3.1 6.0 + - - +
217A VAL* 1.3 76.5 - - - +
219A LEU* 1.3 57.5 + - - +
221A PHE* 3.5 2.8 + - - +
222A TRP* 3.0 28.6 + - - +
228A ARG* 5.2 4.3 - - + +
231A ILE* 3.9 21.8 - - + +
270A LEU* 4.4 6.7 - - + -
271A PRO* 4.2 15.7 - - + -
313A PHE* 3.7 22.7 - - + -
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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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215A THR* 2.8 24.2 + - + +
216A ASP* 3.6 12.8 - - - +
218A ALA* 1.3 69.9 - - - +
220A ASP* 1.3 60.3 + - - +
222A TRP* 3.1 5.6 + - + +
223A ARG* 2.9 76.6 + - + +
306A PHE* 6.2 1.1 - - + -
307A PRO* 3.7 33.9 - - + -
310A GLU* 4.5 6.1 - - + -
312A VAL* 4.0 18.8 - - + -
313A PHE* 3.9 8.9 - - + -
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Residues in contact with ASP 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 2.9 17.6 + - - +
217A VAL* 3.2 8.3 + - - +
219A LEU* 1.3 74.9 - - - +
221A PHE* 1.3 73.1 + - + +
223A ARG* 3.4 10.5 + - - +
224A SER* 2.8 39.3 + - - -
226A LYS* 4.4 7.3 + - - -
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Residues in contact with PHE 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 VAL* 3.0 38.2 + - + +
218A ALA 3.8 4.3 - - - +
220A ASP* 1.3 85.9 - - - +
222A TRP* 1.3 63.2 + - - +
224A SER* 3.3 10.2 + - - -
226A LYS* 3.1 67.0 + - + +
227A GLN 3.9 11.4 - - - +
228A ARG* 5.4 1.1 - - - -
230A ASP* 3.7 24.5 - - + -
231A ILE* 3.5 24.5 - - + -
235A ASP* 3.6 28.9 - - - -
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Residues in contact with TRP 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 ALA 3.0 17.7 + - - +
219A LEU* 3.1 8.0 + - + +
221A PHE* 1.3 77.2 - - - +
223A ARG* 1.3 74.0 + - + +
225A GLY* 3.2 13.3 + - - -
226A LYS 4.6 5.4 - - - -
273A GLU* 4.6 17.0 + - - -
310A GLU* 3.2 47.6 - - + -
312A VAL* 3.6 36.2 - - + +
313A PHE* 4.9 3.8 - + + -
405A BTB 4.9 6.3 - - - -
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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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219A LEU* 2.9 53.6 + - + +
220A ASP* 3.8 9.1 - - - +
222A TRP* 1.3 93.0 - - + +
224A SER* 1.3 59.6 + - - +
225A GLY 3.2 1.4 + - - -
307A PRO* 4.3 4.8 - - - +
310A GLU* 2.6 35.6 + - - +
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Residues in contact with SER 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 ASP* 2.8 30.6 + - - -
221A PHE 3.7 5.4 - - - -
222A TRP 3.2 0.4 - - - -
223A ARG* 1.3 77.1 - - - +
225A GLY* 1.3 61.1 + - - +
226A LYS* 3.5 32.1 + - - +
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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