Contacts of the helix formed by residues 212 - 220 (chain A) in PDB entry 1U54
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 SER 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ACP 4.0 21.5 + - - -
210A LEU 3.8 1.6 + - - -
211A GLY* 1.3 70.5 - - - -
213A LEU* 1.3 66.5 + - - +
214A LEU* 3.6 10.6 + - - +
215A ASP* 3.1 38.5 + - - +
216A ARG* 2.9 24.6 + - - +
256A ARG* 4.1 16.8 + - - +
258A LEU 4.1 5.3 + - - -
259A LEU* 4.6 1.3 - - - -
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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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211A GLY 3.4 6.3 + - - -
212A SER* 1.3 68.9 - - - +
214A LEU* 1.3 57.9 + - - +
216A ARG* 2.7 22.1 + - + +
217A LEU* 2.7 34.6 + - + +
224A PHE* 3.9 14.1 - - + -
232A TYR* 3.6 38.8 - - + -
255A ALA* 4.6 1.1 - - + +
258A LEU* 3.4 43.5 + - + +
259A LEU* 4.3 0.4 - - - +
260A LEU* 3.6 34.0 - - + +
266A VAL* 4.5 6.1 - - + -
323A MET* 4.6 8.7 - - + -
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Residues in contact with LEU 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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212A SER* 3.1 7.4 + - - +
213A LEU* 1.3 78.0 - - - +
215A ASP* 1.3 65.3 + - - +
217A LEU* 3.3 9.3 + - + +
218A ARG* 3.1 58.1 + - - +
255A ALA* 3.4 28.7 + - + +
256A ARG* 4.0 14.6 - - + +
322A GLU* 3.7 20.9 - - + +
327A GLY* 3.4 32.8 - - - -
288B GLU* 3.6 18.6 - - - +
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Residues in contact with ASP 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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101A ACP 5.1 2.9 + - - -
212A SER* 3.1 30.6 + - - +
214A LEU* 1.3 81.4 - - - +
216A ARG* 1.3 61.1 + - + +
218A ARG* 3.6 11.9 + - - +
219A LYS* 3.4 43.0 + - + +
285B VAL* 6.2 1.1 - - - +
288B GLU* 6.2 0.2 - - - +
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Residues in contact with ARG 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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210A LEU* 2.6 55.0 + - - +
212A SER 2.9 17.8 + - - +
213A LEU* 2.7 15.2 + - - +
215A ASP* 1.3 71.7 - - + +
217A LEU* 1.3 63.9 + - - +
219A LYS* 3.3 0.8 + - - -
220A HIS* 3.2 58.2 + - + +
223A HIS* 6.3 1.0 - - - -
224A PHE* 3.8 19.3 - - + -
260A LEU* 3.6 26.0 - - - -
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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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213A LEU* 2.7 43.6 + - + +
214A LEU* 3.7 17.7 - - + +
216A ARG* 1.3 74.5 - - - +
218A ARG* 1.3 59.3 + - - +
221A GLN* 3.6 13.3 + - - -
224A PHE* 3.9 19.7 - - + -
229A LEU* 3.7 30.5 - - + -
255A ALA* 4.7 3.6 - - + -
322A GLU 4.2 4.9 - - - +
323A MET* 3.7 33.7 - - + +
326A TYR* 3.3 36.5 - - + +
327A GLY 4.0 1.8 - - - +
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Residues in contact with ARG 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 LEU* 3.1 50.0 + - - +
215A ASP* 4.0 11.4 + - - +
216A ARG 3.2 0.2 - - - -
217A LEU* 1.3 77.3 - - - +
219A LYS* 1.3 58.0 + - - +
221A GLN* 2.6 19.5 - - - +
322A GLU* 4.8 2.4 + - - -
326A TYR 3.5 14.1 - - - +
327A GLY* 2.9 28.2 + - - +
328A GLN 4.7 5.1 + - - -
329A GLU* 4.8 11.3 - - - +
283B HIS* 4.0 2.4 + - - -
285B VAL* 3.5 26.9 - - + +
286B MET 5.5 0.6 + - - -
288B GLU* 3.7 26.1 + - - +
304B THR 3.6 23.9 - - - +
305B ARG* 4.1 18.4 - - - +
306B THR* 4.2 3.3 + - - -
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Residues in contact with LYS 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 ASP* 3.4 32.7 + - + +
216A ARG* 3.3 2.8 + - - -
218A ARG* 1.3 77.3 - - - +
220A HIS* 1.3 88.8 + - + +
221A GLN* 3.6 3.1 + - - +
283B HIS* 3.0 33.4 + - + +
285B VAL* 3.5 31.8 + - + +
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Residues in contact with HIS 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 ARG* 3.2 52.0 + - - +
217A LEU 3.9 3.5 - - - +
219A LYS* 1.3 102.4 - - + +
221A GLN* 1.3 70.5 + - - +
222A GLY 3.5 1.6 - - - -
223A HIS* 3.2 36.3 + + + +
224A PHE* 3.6 10.1 - - + -
283B HIS* 5.8 0.7 - + - -
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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