Contacts of the helix formed by residues 218 - 228 (chain A) in PDB entry 5L0T
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 ARG 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A PHE* 3.7 21.6 - - + -
212A SER 2.9 24.6 + - - -
214A THR* 3.2 12.9 + - - -
215A SER* 3.5 11.2 - - - +
216A PRO 3.0 0.8 - - - -
217A GLU* 1.3 77.2 - - - +
219A ASP* 1.3 64.4 + - - +
220A PRO 3.3 0.4 - - - -
221A LEU* 3.2 14.7 + - - +
222A ILE* 3.5 15.8 + - + +
236A TYR* 3.1 20.9 - - + +
271A PHE* 3.2 45.0 + - + +
272A ARG 2.9 26.7 + - - +
273A GLY* 4.4 0.2 - - - -
277A SER* 4.2 0.2 - - - -
279A ARG* 3.6 4.0 - - - +
404A UDP 2.8 53.7 + - - -
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Residues in contact with ASP 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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213A ARG* 2.7 41.8 + - - +
216A PRO* 2.9 22.7 + - - +
218A ARG* 1.3 77.6 - - - +
220A PRO* 1.3 65.9 - - + +
221A LEU 3.1 0.7 + - - -
222A ILE* 3.2 3.9 + - - +
223A LEU* 3.0 31.4 + - + +
236A TYR* 2.6 33.7 + - - -
249A LEU* 3.9 20.2 - - + +
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Residues in contact with PRO 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 PRO 3.8 3.8 - - - +
217A GLU* 3.3 17.9 - - - +
218A ARG 3.5 0.4 - - - -
219A ASP* 1.3 95.6 - - + +
221A LEU* 1.3 56.0 + - - +
223A LEU* 3.8 10.6 - - + +
224A LEU* 2.9 27.9 + - - +
316A THR 5.9 0.4 - - - +
317A ASP* 4.4 14.1 - - - +
318A LEU* 4.0 23.0 - - + +
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Residues in contact with LEU 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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209A PHE* 3.8 11.4 - - + -
218A ARG 3.2 4.3 + - - +
219A ASP 3.2 0.8 - - - -
220A PRO* 1.3 75.8 - - - +
222A ILE* 1.3 63.2 + - + +
224A LEU* 3.3 10.2 + - + +
225A SER* 2.9 27.7 + - - -
232A VAL* 3.8 24.2 - - + +
234A ALA* 3.6 22.2 - - + -
269A PHE* 3.7 35.9 - - + -
271A PHE* 3.6 37.7 - - + -
318A LEU* 3.6 18.4 - - + +
321A VAL* 4.7 0.7 - - + -
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Residues in contact with ILE 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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209A PHE* 4.2 16.8 - - + -
218A ARG* 3.5 14.4 - - + +
219A ASP 3.2 6.6 + - - +
221A LEU* 1.3 80.2 - - + +
223A LEU* 1.3 60.7 + - - +
225A SER* 3.2 3.8 + - - -
226A ARG* 3.1 59.0 + - - +
234A ALA* 3.7 33.8 - - + +
235A GLU* 4.5 1.1 - - - +
236A TYR* 3.9 48.7 - - + +
249A LEU* 4.3 4.9 - - + -
271A PHE* 5.9 0.2 - - + -
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Residues in contact with LEU 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 ASP* 3.0 27.7 + - + +
220A PRO* 3.9 8.3 - - + +
222A ILE* 1.3 73.7 - - - +
224A LEU* 1.3 64.3 + - - +
226A ARG* 3.2 25.1 + - + +
227A LYS* 3.0 23.1 + - - +
249A LEU* 3.8 24.5 - - + -
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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 PRO 2.9 18.8 + - - +
221A LEU* 3.6 11.0 - - + +
223A LEU* 1.3 75.8 - - - +
225A SER* 1.3 58.3 + - - +
227A LYS* 3.2 31.1 + - - +
228A ASN* 2.8 31.5 + - + +
231A LEU* 4.0 16.6 - - + -
232A VAL* 3.9 24.5 - - + -
321A VAL* 3.7 30.3 - - + -
322A GLN* 4.0 22.2 - - + +
325A LEU* 5.1 0.7 - - + -
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Residues in contact with SER 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 LEU 2.9 15.1 + - - -
222A ILE 3.5 1.3 - - - -
223A LEU 3.2 0.2 - - - -
224A LEU* 1.3 76.5 - - - +
226A ARG* 1.3 63.8 + - - +
228A ASN 4.2 1.6 - - - -
229A PRO* 3.1 29.3 - - - +
232A VAL* 2.6 30.3 + - - +
233A ASP* 3.5 2.9 + - - -
234A ALA* 2.9 39.9 + - - -
235A GLU* 5.1 1.6 - - - +
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Residues in contact with ARG 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 ILE* 3.1 37.3 + - + +
223A LEU* 3.2 26.5 + - + +
225A SER* 1.3 77.2 - - - +
227A LYS* 1.3 61.1 + - - +
229A PRO* 4.1 8.9 - - - +
234A ALA 5.6 1.1 - - - +
236A TYR* 4.8 2.8 - - - +
248A THR 3.1 26.1 + - - -
249A LEU* 2.9 26.1 + - - +
251A LYS* 3.4 39.3 - - + +
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Residues in contact with LYS 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 LEU 3.0 12.7 + - - +
224A LEU* 3.2 32.1 + - - +
226A ARG* 1.3 80.3 - - - +
228A ASN* 1.3 61.0 + - + +
229A PRO* 3.7 4.2 - - - +
322A GLN* 4.3 13.6 + - - +
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Residues in contact with ASN 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 LEU* 2.8 23.1 + - + +
225A SER 3.3 2.6 - - - +
227A LYS* 1.3 80.7 - - + +
229A PRO* 1.3 64.9 - - - +
230A LYS* 3.5 9.2 + - - +
231A LEU* 3.1 50.1 + - + +
232A VAL 3.2 11.8 + - - +
322A GLN* 5.2 5.3 - - - +
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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