Contacts of the helix formed by residues 216 - 226 (chain A) in PDB entry 5YUS
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 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A LEU* 2.9 30.4 + - - +
213A LYS 4.5 1.0 + - - -
214A ARG 4.0 0.6 - - - -
215A PHE* 1.3 76.4 - - - +
217A LYS* 1.3 64.3 + - - -
219A GLY* 3.0 13.2 + - - -
220A ARG 3.6 3.3 + - - -
847B T 4.3 5.6 - - - -
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Residues in contact with LYS 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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212A LEU* 5.3 2.6 - - - +
216A GLY* 1.3 72.7 - - - -
218A PHE* 1.3 62.5 + - - +
220A ARG* 3.1 50.5 + - + +
221A ILE* 3.2 26.0 + - + +
846B C 4.3 17.7 - - - +
847B T 3.2 25.2 + - - +
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Residues in contact with PHE 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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183A GLY* 3.4 22.4 - - - -
184A VAL* 3.6 27.8 - - + -
188A SER* 3.8 30.3 - - - -
192A LEU* 4.8 1.6 - - + -
215A PHE* 3.4 36.1 + + + +
216A GLY 3.2 0.4 - - - -
217A LYS* 1.3 79.0 - - - +
219A GLY* 1.3 57.1 + - - +
221A ILE* 3.3 17.9 + - + +
222A LEU* 2.8 51.7 + - + +
846B C 5.3 1.2 + - - -
847B T 4.7 1.0 + - - -
871C C 6.0 0.2 - - - -
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Residues in contact with GLY 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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211A LEU* 3.6 25.3 - - - +
212A LEU* 4.4 2.7 - - - -
215A PHE* 3.4 22.4 - - - +
216A GLY 3.0 9.4 + - - -
218A PHE* 1.3 80.3 - - - +
220A ARG* 1.3 55.5 + - - +
222A LEU* 3.7 6.2 - - - +
223A TRP* 3.1 26.5 + - - +
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Residues in contact with ARG 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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208A LEU* 4.0 27.0 - - + +
212A LEU* 3.7 40.8 - - + +
216A GLY 3.6 3.6 + - - -
217A LYS* 3.1 39.4 + - + +
219A GLY* 1.3 75.0 - - - +
221A ILE* 1.3 67.4 + - + +
223A TRP* 3.1 9.3 + - + +
224A GLU* 2.9 46.6 + - + +
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Residues in contact with ILE 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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181A ILE* 5.9 2.2 - - + -
182A PRO 6.0 1.6 - - - +
217A LYS* 3.2 32.3 + - + +
218A PHE* 3.7 17.9 - - + +
220A ARG* 1.3 77.1 - - + +
222A LEU* 1.3 65.1 + - - +
224A GLU* 3.3 5.9 + - - +
225A ARG* 3.0 63.7 + - - +
846B C 5.5 8.7 - - - +
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Residues in contact with LEU 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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178A LEU* 4.2 22.9 - - + -
181A ILE* 4.4 7.1 - - + +
184A VAL* 3.9 27.4 - - + -
192A LEU* 3.5 37.2 - - + -
203A VAL* 4.4 9.0 - - + -
211A LEU* 4.9 9.0 - - + -
215A PHE* 4.8 9.4 - - + -
218A PHE* 2.8 33.5 + - + +
219A GLY* 3.7 5.8 - - - +
221A ILE* 1.3 77.4 - - - +
223A TRP* 1.3 60.2 + - - +
225A ARG* 4.3 2.6 - - - +
226A SER* 2.9 31.2 + - - -
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Residues in contact with TRP 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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203A VAL* 4.3 14.8 + - - -
204A GLN* 5.4 5.6 + - - +
206A CYS 4.3 13.0 + - - -
208A LEU* 3.7 50.2 - - + +
211A LEU* 3.9 15.2 - - + +
219A GLY 3.1 18.3 + - - +
220A ARG* 3.1 9.6 + - - +
222A LEU* 1.3 77.7 - - - +
224A GLU* 1.3 79.2 + - + +
226A SER* 3.7 5.2 + - - -
227A GLN* 3.0 61.8 + - - +
229A ILE* 4.6 8.7 - - + -
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Residues in contact with GLU 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 ARG* 2.9 44.2 + - + +
221A ILE* 3.8 6.0 - - - +
223A TRP* 1.3 94.8 - - + +
225A ARG* 1.3 78.2 + - - +
227A GLN* 2.8 22.9 + - - +
229A ILE* 3.0 45.8 + - + +
230A ASP* 5.2 0.9 - - - -
231A GLU 5.4 1.6 + - - -
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Residues in contact with ARG 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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147A PHE* 3.2 49.7 - - + +
173A LEU* 3.6 5.2 - - - +
181A ILE* 4.3 24.5 - - + -
182A PRO 5.7 1.1 - - - -
200A CYS* 4.6 2.0 - - - -
221A ILE* 3.0 46.9 + - - +
222A LEU* 4.5 0.9 - - - +
224A GLU* 1.3 102.7 + - - +
226A SER* 1.3 57.5 + - - +
228A GLY 2.8 17.2 + - - -
229A ILE 3.3 18.8 + - - +
230A ASP* 2.9 33.4 + - - +
231A GLU 5.0 0.4 - - - +
232A ARG* 3.1 30.1 - - - +
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Residues in contact with SER 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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173A LEU* 3.6 5.2 - - - +
178A LEU* 3.8 9.7 - - - +
181A ILE* 4.7 0.7 - - - +
200A CYS* 3.8 35.0 - - - +
203A VAL* 3.2 25.5 - - - +
204A GLN* 2.6 37.5 + - - +
222A LEU 2.9 21.9 + - - -
223A TRP 3.8 6.3 - - - -
224A GLU 3.1 1.0 - - - -
225A ARG* 1.3 75.9 - - - +
227A GLN* 1.3 53.1 + - - +
228A GLY 3.5 0.2 - - - -
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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