Contacts of the helix formed by residues 216 - 228 (chain A) in PDB entry 4CIZ
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 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A SER 3.7 7.4 + - - +
215A LEU* 1.3 74.8 - - - +
217A THR* 1.3 61.3 + - - +
218A SER* 3.9 16.0 + - - +
219A ASP* 2.9 49.3 + - - +
220A LEU* 3.2 13.8 + - - +
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Residues in contact with THR 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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215A LEU 3.8 3.6 + - - -
216A ARG* 1.3 73.4 - - - +
218A SER* 1.3 61.8 + - - +
220A LEU* 3.1 12.4 + - - +
221A ARG* 3.1 26.5 + - + +
253A VAL* 4.0 20.8 - - + +
257A PHE* 3.6 24.7 - - + -
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Residues in contact with SER 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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124A TYR* 5.0 2.4 + - - -
216A ARG* 3.9 21.3 + - - +
217A THR* 1.3 78.4 - - - +
219A ASP* 1.3 64.3 + - - +
221A ARG* 3.6 14.9 + - - +
222A LYS* 3.1 31.1 + - - +
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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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173A PHE* 3.3 52.4 - - + +
174A ASP* 4.2 7.7 - - - +
215A LEU* 6.0 0.2 - - - +
216A ARG* 2.9 46.4 + - - +
218A SER* 1.3 78.2 + - - +
220A LEU* 1.3 59.0 + - - +
222A LYS* 3.3 26.2 + - - +
223A MET 3.1 21.1 + - - -
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Residues in contact with LEU 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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173A PHE* 4.5 9.6 - - + -
215A LEU* 4.8 12.1 - - + -
216A ARG 3.2 13.1 + - - +
217A THR* 3.1 15.8 + - - +
219A ASP* 1.3 75.1 - - + +
221A ARG* 1.3 59.4 + - - +
223A MET* 3.2 4.0 + - - +
224A VAL* 2.9 33.4 + - - +
250A THR* 4.4 14.6 - - + -
253A VAL* 4.7 13.0 - - + -
254A VAL* 3.7 30.5 - - + -
257A PHE* 3.9 12.3 - - + -
1307A RET 4.1 38.1 - - + +
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Residues in contact with ARG 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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124A TYR* 4.2 9.6 + - - +
217A THR* 3.1 20.0 + - - +
218A SER* 3.7 13.9 - - - +
220A LEU* 1.3 75.8 - - - +
222A LYS* 1.3 54.2 + - - +
224A VAL* 4.5 1.6 - - - -
225A ASP* 2.8 46.3 + - - +
257A PHE* 3.2 51.7 - - + +
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Residues in contact with LYS 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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120A PHE* 3.9 4.9 - - - -
124A TYR* 3.8 35.2 + - + -
126A GLU* 3.4 26.4 + - - +
127A LEU* 4.4 10.5 - - + -
174A ASP* 2.4 38.0 + - - +
177A LEU* 3.7 19.8 - - + +
218A SER* 3.1 15.6 + - - +
219A ASP* 3.3 27.2 + - - +
220A LEU 3.1 0.2 - - - -
221A ARG* 1.3 79.0 - - - +
223A MET* 1.3 61.3 + - - +
225A ASP* 3.6 2.8 + - - +
226A MET* 3.3 18.9 + - - +
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Residues in contact with MET 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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161A PHE* 6.5 0.2 - - + -
173A PHE* 3.9 20.9 - - + -
176A ILE* 6.1 0.4 - - + -
177A LEU* 3.8 24.4 - - + +
180A TYR* 4.0 35.4 - - + +
200A ILE* 5.1 2.9 - - + -
202A GLU* 4.2 10.1 - - - +
219A ASP 3.1 13.8 + - - +
220A LEU 3.7 6.5 - - - +
222A LYS* 1.3 74.8 - - - +
224A VAL* 1.3 64.8 + - - +
226A MET* 3.1 14.7 + - - +
227A LEU* 3.1 29.0 + - + +
1307A RET 3.6 44.9 - - + -
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Residues in contact with VAL 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 LEU 2.9 20.7 + - - +
221A ARG* 3.9 3.1 - - - +
223A MET* 1.3 72.1 - - - +
225A ASP* 1.3 65.2 + - - +
227A LEU* 3.2 6.5 + - - +
228A GLN* 3.0 52.2 + - + +
254A VAL* 3.8 14.8 - - + -
257A PHE* 3.8 22.4 - - + +
258A LEU* 3.8 15.0 - - + -
262A LEU* 5.2 0.4 - - + -
1307A RET 3.8 32.1 - - + -
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Residues in contact with ASP 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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120A PHE* 3.4 18.6 - - + -
123A GLN* 5.1 6.2 - - - +
124A TYR* 3.2 24.6 + - + -
221A ARG* 2.8 32.1 + - - +
222A LYS 3.8 2.2 - - - +
223A MET 3.3 0.2 - - - -
224A VAL* 1.3 77.0 - - - +
226A MET* 1.3 52.3 + - - +
228A GLN* 3.0 13.0 - - - +
230A SER* 2.6 29.3 + - - -
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Residues in contact with MET 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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120A PHE* 3.4 19.9 - - + -
177A LEU* 3.6 41.5 - - + +
180A TYR* 3.8 20.0 - - + -
181A CYS* 3.6 26.0 - - - -
184A LEU* 4.2 16.4 - - + -
222A LYS 3.3 5.7 + - - +
223A MET* 3.1 8.4 + - - +
225A ASP* 1.3 82.2 - - - +
227A LEU* 1.3 80.2 + - + +
228A GLN* 3.1 3.4 + - - -
230A SER* 3.5 15.7 - - - -
231A PHE* 3.9 25.5 + - + +
235A PHE* 4.9 1.6 - - + -
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Residues in contact with LEU 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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180A TYR* 5.6 1.6 - - + -
200A ILE* 4.4 7.6 - - + -
223A MET* 3.1 28.9 + - + +
224A VAL* 3.2 7.8 + - - +
226A MET* 1.3 98.0 - - + +
228A GLN* 1.3 60.2 + - - +
229A ASP 4.2 1.0 + - - -
235A PHE* 3.8 46.5 - - + +
238A ILE* 4.4 18.4 - - + -
262A LEU* 4.2 26.7 - - + +
1307A RET 4.1 29.6 - - + -
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Residues in contact with GLN 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 VAL* 3.0 25.2 + - - +
225A ASP* 3.0 17.2 - - - +
227A LEU* 1.3 82.9 - - - +
229A ASP* 1.3 78.3 + - - +
230A SER* 3.3 3.0 + - - -
257A PHE 3.4 20.0 + - - -
258A LEU* 3.5 3.3 - - - -
259A LYS* 2.8 46.5 + - - +
261A LYS* 6.3 3.1 - - - +
262A LEU* 3.4 34.2 - - + +
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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