Contacts of the helix formed by residues 205 - 216 (chain A) in PDB entry 1H13
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 ILE 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A ASP* 5.6 0.9 - - + -
147A GLU* 4.8 4.9 - - - +
148A TYR* 3.5 38.6 - - + +
202A SER 4.8 3.4 - - - +
203A TYR* 3.4 12.2 + - - +
204A HIS* 1.3 78.8 - - - +
206A PRO* 1.3 69.4 - - + +
208A PHE* 3.0 57.1 + - + +
209A TYR* 3.6 14.5 + - + +
288A ASN* 3.7 23.1 - - + +
291A LEU* 3.9 24.0 - - + -
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Residues in contact with PRO 206 (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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204A HIS 3.5 7.2 - - - +
205A ILE* 1.3 87.9 - - - +
207A ALA* 1.3 61.3 - - - +
209A TYR* 2.9 26.9 + - + +
210A ASP* 3.2 8.8 + - - +
229A ALA* 3.7 10.8 - - - +
232A SER* 3.4 15.7 - - - +
233A ARG* 3.5 39.5 - - + +
236A LEU* 4.0 15.3 - - + -
288A ASN 5.0 3.1 - - - +
292A ASP* 3.4 24.0 - - + +
301A TRP* 5.2 1.1 - - + -
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Residues in contact with ALA 207 (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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205A ILE 3.2 1.0 - - - -
206A PRO* 1.3 75.0 - - - +
208A PHE* 1.3 62.2 + - - +
210A ASP* 3.3 3.3 + - - +
211A TYR 3.0 17.8 + - - -
233A ARG* 4.0 4.9 - - - +
291A LEU* 3.9 18.2 - - + -
292A ASP* 2.9 20.9 + - - +
295A LEU* 4.1 4.9 - - + -
296A MET* 3.7 19.1 - - + -
399A PHE* 3.4 27.9 - - + -
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Residues in contact with PHE 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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147A GLU* 4.3 13.0 - - + -
148A TYR* 3.7 39.3 - + - -
151A PHE* 3.6 54.1 - + + -
205A ILE* 3.0 48.8 + - + +
207A ALA* 1.3 77.9 - - - +
209A TYR* 1.3 59.9 + - + +
211A TYR* 3.2 6.9 + - - +
212A PHE* 2.8 45.9 + + + -
291A LEU* 4.1 5.4 - - + -
397A PHE* 4.1 13.7 - + - -
399A PHE* 4.1 6.3 - + - -
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Residues in contact with TYR 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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147A GLU* 2.7 32.4 + - + -
184A MET* 4.6 4.5 - - + -
189A ILE* 4.1 8.9 - - - +
203A TYR 3.2 14.4 + - - -
204A HIS* 3.7 4.3 + - - -
205A ILE* 3.6 17.4 + - + -
206A PRO* 2.9 19.6 + - + +
208A PHE* 1.3 78.1 - - + +
210A ASP* 1.3 58.9 + - - +
212A PHE* 3.2 19.8 + + - +
213A ALA* 2.9 23.9 + - - +
225A TRP* 3.5 40.2 - + + +
228A VAL* 3.5 25.4 - - + -
229A ALA* 3.7 12.6 - - - +
232A SER* 3.5 24.4 + - - -
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Residues in contact with ASP 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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12A TYR* 4.5 2.7 - - + -
206A PRO 3.2 2.7 + - - +
207A ALA 3.6 7.2 - - - +
209A TYR* 1.3 79.3 - - - +
211A TYR* 1.3 60.9 + - - +
213A ALA* 3.3 8.1 + - - +
214A ASN* 3.2 28.3 + - - +
225A TRP 5.1 0.2 - - - -
226A ARG* 4.4 10.2 - - - +
229A ALA* 3.5 15.1 - - - +
233A ARG* 2.8 39.5 + - - -
296A MET* 3.5 27.5 - - + +
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Residues in contact with TYR 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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12A TYR* 3.5 22.1 - - - -
151A PHE* 3.6 18.6 - + - -
154A LEU* 3.4 29.6 + - + +
155A ASN* 3.2 39.4 + - - -
207A ALA 3.0 13.2 + - - +
208A PHE* 3.4 8.1 - - - +
210A ASP* 1.3 73.0 - - - +
212A PHE* 1.3 70.1 + + - +
214A ASN 3.1 5.9 + - - -
215A ASN* 2.9 40.5 + - - -
399A PHE* 3.7 31.9 - + + -
400A TYR 2.7 32.2 + - - -
401A ASN* 3.6 5.2 - - - -
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Residues in contact with PHE 212 (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 GLU* 3.6 25.4 - - + -
150A ALA* 4.0 2.7 - - + -
151A PHE* 3.7 27.6 - - + -
154A LEU* 3.6 21.1 - - + -
176A LEU* 3.4 31.0 - - + -
179A ILE* 4.9 5.8 - - + -
208A PHE* 2.8 32.5 + + + -
209A TYR* 3.4 25.1 - + - +
211A TYR* 1.3 80.4 - + - +
213A ALA* 1.3 63.2 + - - +
215A ASN* 2.9 11.6 + - - -
216A VAL* 3.2 18.0 + - - +
225A TRP* 3.8 33.7 - + + -
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Residues in contact with ALA 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 TYR 2.9 12.8 + - - +
210A ASP* 3.5 12.6 - - - +
211A TYR 3.2 0.2 - - - -
212A PHE* 1.3 78.0 - - - +
214A ASN* 1.3 64.2 + - - +
215A ASN 3.3 0.3 + - - -
216A VAL* 3.5 5.8 - - - +
222A LYS* 2.8 56.1 + - + +
225A TRP* 3.7 11.4 - - + +
226A ARG* 3.8 11.2 - - + +
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Residues in contact with ASN 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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12A TYR* 3.1 43.8 + - - +
210A ASP* 3.2 9.0 + - - +
211A TYR 3.1 4.4 + - - +
213A ALA* 1.3 80.1 - - - +
215A ASN* 1.3 63.2 + - - +
222A LYS* 3.5 14.1 + - - +
401A ASN* 4.4 8.6 - - - +
402A ASN 5.3 0.2 - - - +
404A PHE* 3.8 12.1 - - - -
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Residues in contact with ASN 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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12A TYR* 3.9 0.2 + - - -
154A LEU* 4.0 21.0 - - + +
169A TYR* 2.6 34.0 + - - -
173A ILE* 4.2 1.4 - - - +
211A TYR* 2.9 40.6 + - - +
212A PHE 2.9 6.2 + - - +
214A ASN* 1.3 81.9 - - - +
216A VAL* 1.3 55.5 + - - +
401A ASN* 3.0 24.8 + - - -
402A ASN* 2.9 43.7 + - - +
404A PHE* 3.5 7.0 - - - -
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Residues in contact with VAL 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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169A TYR* 3.8 3.4 - - - -
173A ILE* 4.0 11.2 - - + -
176A LEU* 3.7 27.6 - - + -
212A PHE 3.5 12.1 - - - +
213A ALA* 3.5 15.7 - - - +
214A ASN 4.6 0.2 - - - +
215A ASN* 1.3 81.1 - - - +
217A THR* 1.3 62.3 + - - +
218A ASN* 4.3 1.3 - - - +
221A ASP* 3.7 20.0 - - + +
222A LYS* 2.6 56.2 + - + +
225A TRP* 4.4 8.1 - - + +
404A PHE* 4.9 3.0 - - - -
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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