Contacts of the helix formed by residues 214 - 225 (chain A) in PDB entry 3Q72
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 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A TYR* 4.7 0.3 + - - -
211A ARG* 3.7 9.2 - - - +
212A GLU 4.4 0.2 + - - -
213A VAL* 1.3 80.9 - - - +
215A VAL* 1.3 64.7 + - - +
216A ASP* 3.9 5.1 + - - +
217A GLU* 2.8 39.2 + - - +
218A GLY* 3.0 17.0 + - - -
231A GLU* 4.2 1.8 - - - +
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Residues in contact with VAL 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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211A ARG* 3.5 12.6 - - - +
214A SER* 1.3 72.3 - - - +
216A ASP* 1.3 53.2 + - - +
218A GLY* 2.8 5.2 + - - -
219A ARG* 2.7 69.5 + - - +
229A PHE* 3.7 11.1 - - + -
231A GLU* 3.3 33.2 - - + +
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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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214A SER* 3.4 4.8 + - - +
215A VAL* 1.3 78.2 - - - +
217A GLU* 1.3 53.1 + - - +
219A ARG* 2.8 33.3 + - - +
220A ALA* 2.6 39.0 + - + +
191B ARG* 4.7 11.8 - - - +
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Residues in contact with GLU 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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174A LYS* 5.0 7.4 - - - +
177A PHE* 3.5 19.5 - - + -
212A GLU 4.3 5.2 - - - +
213A VAL* 3.6 19.1 - - + +
214A SER* 2.8 37.7 + - - +
216A ASP* 1.3 77.3 - - - +
218A GLY* 1.3 60.1 + - - +
220A ALA* 4.3 4.2 - - - +
221A CYS* 3.2 23.0 + - - +
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Residues in contact with GLY 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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169A TYR* 3.6 23.6 - - - -
177A PHE* 4.0 10.1 - - - -
200A LEU* 3.8 2.6 - - - +
214A SER 3.0 6.7 + - - -
215A VAL 2.8 8.8 + - - -
217A GLU* 1.3 78.5 - - - +
219A ARG* 1.3 59.5 + - - +
221A CYS* 3.7 3.3 + - - +
222A ALA* 3.3 15.4 + - - +
229A PHE* 3.3 18.8 - - - -
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Residues in contact with ARG 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 VAL* 2.7 46.1 + - - +
216A ASP* 2.8 32.0 + - - +
218A GLY* 1.3 72.3 - - - +
220A ALA* 1.3 61.6 + - - +
222A ALA* 3.4 3.2 + - + +
223A VAL* 3.0 26.5 + - + +
229A PHE* 3.7 28.5 - - + -
189B ARG 5.5 2.7 - - - -
190B ALA* 5.3 9.6 - - + +
191B ARG* 4.8 21.4 + - - +
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Residues in contact with ALA 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 2.6 24.1 + - - +
217A GLU* 4.3 4.9 - - - +
219A ARG* 1.3 71.8 - - - +
221A CYS* 1.3 63.3 + - - +
223A VAL* 3.0 22.1 - - - +
224A VAL* 3.3 17.7 - - + +
160B ALA* 4.3 23.8 - - + -
191B ARG* 5.2 11.7 - - + +
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Residues in contact with CYS 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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177A PHE* 3.9 19.7 - - + -
181A SER* 3.2 28.3 - - - -
200A LEU* 4.5 8.5 - - + -
217A GLU 3.2 19.7 + - - +
218A GLY 3.7 5.8 - - - +
220A ALA* 1.3 78.5 - - - +
222A ALA* 1.3 62.2 + - - +
224A VAL* 4.1 1.5 - - - -
225A PHE* 3.1 44.3 + - - +
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Residues in contact with ALA 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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200A LEU* 4.4 5.3 - - + +
218A GLY 3.3 7.3 + - - +
219A ARG* 3.6 7.2 - - + +
220A ALA 3.2 0.4 - - - -
221A CYS* 1.3 75.9 - - - +
223A VAL* 1.3 66.3 + - - +
225A PHE 3.5 0.3 - - - -
226A ASP 2.9 4.9 + - - -
227A CYS* 2.8 54.2 + - + +
229A PHE* 3.4 34.3 - - + -
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Residues in contact with VAL 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 ARG* 3.0 19.9 + - + +
220A ALA* 3.0 21.3 - - - +
222A ALA* 1.3 73.9 - - - +
224A VAL* 1.3 65.3 + - + +
226A ASP* 3.0 14.0 + - - +
97B LEU* 5.4 1.7 - - - +
183B LEU* 5.5 5.9 - - - +
186B GLN* 3.4 44.8 + - + +
187B LEU* 3.5 30.9 - - + +
190B ALA* 3.6 16.8 - - + -
191B ARG* 5.0 5.2 - - - +
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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 ALA* 3.3 20.5 + - + +
221A CYS* 4.2 4.0 - - - +
223A VAL* 1.3 79.0 - - + +
225A PHE* 1.3 68.8 + - + +
226A ASP 3.6 0.5 + - - -
95B LEU* 4.9 8.3 - - + -
97B LEU* 4.2 21.1 - - + +
145B ILE* 3.1 51.7 - - + +
146B TRP* 4.0 6.1 + - - -
160B ALA* 5.6 7.0 - - + +
165B TYR* 4.5 22.7 - - + +
187B LEU* 5.7 0.7 - - + -
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Residues in contact with PHE 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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181A SER* 5.4 8.7 - - - -
184A ARG* 2.9 30.8 + - + +
185A VAL* 3.8 24.9 - - + -
221A CYS* 3.1 37.9 + - - +
222A ALA 3.5 0.9 - - - -
224A VAL* 1.3 85.1 - - + +
226A ASP* 1.3 67.3 + - - +
227A CYS* 3.5 4.9 + - - -
145B ILE* 3.9 38.1 - - + -
146B TRP* 3.1 35.0 - + + -
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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