Contacts of the helix formed by residues 207 - 219 (chain A) in PDB entry 3F78
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 ASN 207 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A PHE* 4.1 4.8 - - - -
174A SER 2.8 16.2 + - - +
175A THR* 3.0 37.9 + - - +
177A TYR* 2.7 39.5 + - - +
205A LEU* 4.5 6.8 - - - +
206A THR* 1.3 68.9 - - - +
208A THR* 1.3 63.1 + - - +
211A ALA* 3.1 6.1 + - - +
243A THR* 2.7 25.9 + - - +
244A ASP* 3.3 30.6 + - - +
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Residues in contact with THR 208 (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* 3.4 29.3 - - + -
206A THR* 2.9 20.3 + - - +
207A ASN* 1.3 69.3 - - - +
209A PHE* 1.3 65.3 + - - +
211A ALA* 3.2 3.4 + - + +
212A ILE* 3.1 41.6 + - + +
236A ILE* 4.6 9.9 - - + -
238A THR* 4.8 4.9 + - + +
240A GLY 5.1 0.9 + - - -
242A ALA* 3.7 18.3 + - - +
244A ASP* 3.1 2.2 + - - -
258A ILE* 5.1 2.0 - - + -
277A PHE* 4.1 18.3 - - + -
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Residues in contact with PHE 209 (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 THR* 1.3 77.2 - - - +
210A GLY* 1.3 64.3 + - - +
212A ILE* 3.3 3.1 + - - +
213A ASN* 3.2 28.6 + - - +
242A ALA* 4.1 4.7 - - + -
244A ASP* 3.0 37.1 + - - +
245A SER* 3.4 30.3 - - - +
246A GLY 3.5 30.7 - - - -
247A ASN* 3.8 15.9 - - - +
248A ILE* 3.8 12.7 - - + +
276A LYS* 3.5 31.2 - - + -
277A PHE* 3.7 26.9 - + - -
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Residues in contact with GLY 210 (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 TYR* 3.1 23.2 - - - -
209A PHE* 1.3 75.8 - - - +
211A ALA* 1.3 51.7 + - - +
213A ASN* 3.3 9.7 + - - +
214A TYR* 2.8 35.0 + - - +
244A ASP* 2.9 13.1 + - - -
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Residues in contact with ALA 211 (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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135A LEU* 3.8 15.3 - - + +
173A PHE* 3.5 39.7 - - + -
177A TYR* 3.2 12.5 - - + -
207A ASN 3.1 13.4 + - - +
208A THR* 3.4 9.6 - - - +
209A PHE 3.2 0.4 - - - -
210A GLY* 1.3 75.5 - - - +
212A ILE* 1.3 62.1 + - - +
214A TYR* 3.3 4.7 + - - +
215A VAL* 3.1 26.5 + - - +
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Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 3.8 20.0 - - + -
208A THR* 3.1 21.2 + - + +
209A PHE 3.8 3.8 - - - +
211A ALA* 1.3 74.1 - - - +
213A ASN* 1.3 64.7 + - - +
215A VAL* 3.2 7.3 + - - +
216A ALA* 3.1 19.6 + - - +
234A LEU* 4.2 12.0 - - + +
236A ILE* 3.8 16.8 - - + -
248A ILE* 3.8 18.8 - - + -
251A ALA* 3.5 24.9 - - + +
256A ARG* 4.6 2.7 - - - -
277A PHE* 3.4 45.3 - - + +
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Residues in contact with ASN 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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209A PHE* 3.2 19.7 + - - +
210A GLY* 3.6 9.8 - - - +
212A ILE* 1.3 77.8 - - - +
214A TYR* 1.3 61.5 + - - +
216A ALA* 3.2 6.0 + - - +
217A THR* 3.0 31.7 + - + +
247A ASN* 2.9 24.1 + - - +
248A ILE* 3.5 17.7 - - - +
249A ASP 4.4 0.2 + - - -
250A ALA* 3.5 24.4 + - + +
251A ALA 4.4 0.9 + - - -
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Residues in contact with TYR 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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171A VAL* 3.9 23.8 - - + -
177A TYR* 3.7 43.5 + + + -
178A LYS* 4.4 0.2 - - - -
179A THR* 2.8 38.3 + - - -
210A GLY 2.8 18.2 + - - +
211A ALA 3.3 8.3 - - - +
212A ILE 3.2 0.2 - - - -
213A ASN* 1.3 71.4 - - - +
215A VAL* 1.3 60.3 + - - +
217A THR* 4.0 4.9 - - - -
218A GLU* 2.7 63.6 + - + +
219A VAL* 3.7 9.1 + - + -
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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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133A VAL* 3.9 22.2 - - + -
135A LEU* 3.9 26.5 - - + -
171A VAL* 4.1 18.8 - - + -
211A ALA 3.1 14.9 + - - +
212A ILE 3.6 7.4 - - - +
214A TYR* 1.3 77.0 - - - +
216A ALA* 1.3 63.2 + - - +
219A VAL* 3.1 24.4 + - + -
220A PHE* 3.2 36.2 + - + -
234A LEU* 4.0 16.8 - - + -
254A ILE* 4.7 0.2 - - + -
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Residues in contact with ALA 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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212A ILE 3.1 13.0 + - - +
213A ASN* 3.2 10.3 + - - +
215A VAL* 1.3 78.5 - - - +
217A THR* 1.3 59.3 + - - +
220A PHE* 4.1 18.0 - - - +
232A LYS* 5.3 2.3 + - - -
250A ALA* 3.5 36.3 - - + +
251A ALA* 3.9 10.8 - - + -
254A ILE* 3.9 13.4 - - + +
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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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213A ASN* 3.0 18.8 + - + +
214A TYR* 3.7 2.3 + - - -
216A ALA* 1.3 80.2 - - + +
218A GLU* 1.3 86.4 + - - +
219A VAL 3.8 0.4 - - - -
221A ARG* 3.5 19.5 - - - +
250A ALA* 4.4 18.4 - - + -
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Residues in contact with GLU 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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179A THR* 5.0 1.9 + - - -
182A ASP* 4.7 0.7 - - - +
214A TYR* 2.7 55.3 + - + +
217A THR* 1.3 98.1 + - - +
219A VAL* 1.3 57.4 - - - +
221A ARG* 3.7 17.8 + - - +
224A LEU* 3.2 22.5 - - - +
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Residues in contact with VAL 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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133A VAL* 3.8 18.6 - - + -
169A ALA* 3.7 29.4 - - + -
171A VAL* 3.6 28.5 - - + -
179A THR* 3.8 15.0 - - + +
182A ASP* 4.6 7.1 - - - +
183A PHE* 3.7 15.2 - - + -
214A TYR* 3.9 9.4 - - + -
215A VAL* 3.1 18.8 + - + +
218A GLU* 1.3 81.9 - - - +
220A PHE* 1.3 62.1 + - - +
221A ARG* 2.9 12.1 + - - +
224A LEU* 4.4 9.4 - - - +
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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