Contacts of the helix formed by residues 213 - 224 (chain A) in PDB entry 3HS3
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 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A PRO* 4.3 18.1 - - + +
212A ASN* 1.3 80.8 + - - +
214A PRO* 1.3 66.6 - - - +
215A TYR* 3.3 12.2 + - - +
216A ILE* 2.9 54.7 + - + +
217A SER* 3.2 18.9 + - - -
238A TYR* 3.5 8.6 + - - -
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Residues in contact with PRO 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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212A ASN* 3.8 5.6 - - - +
213A ASN* 1.3 88.5 - - - +
215A TYR* 1.3 57.3 + - - +
217A SER* 3.4 2.3 + - - -
218A ALA* 2.9 30.1 + - - +
237A LEU* 4.0 21.1 - - + +
238A TYR* 3.3 49.3 - - + +
241A GLU* 3.6 24.1 - - + +
270B TYR* 5.4 0.2 - - - +
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Residues in contact with TYR 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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213A ASN* 3.1 8.9 + - - +
214A PRO* 1.3 79.9 - - - +
216A ILE* 1.3 75.9 + - + +
218A ALA* 3.1 13.7 + - - +
219A GLN* 3.1 53.7 + - + +
241A GLU* 3.9 24.9 - - - +
245A GLU* 4.4 1.6 + - - -
248A ARG* 4.4 17.7 - - - -
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Residues in contact with ILE 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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210A PRO* 4.9 15.9 - - + -
213A ASN* 2.9 46.9 + - + +
215A TYR* 1.3 84.2 - - + +
217A SER* 1.3 63.2 + - - +
219A GLN* 3.1 9.5 + - + +
220A SER* 3.1 23.0 + - - -
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Residues in contact with SER 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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177A GLN* 2.9 40.0 + - - +
209A THR* 2.7 32.9 + - - +
210A PRO* 5.3 0.8 - - - +
213A ASN 3.2 5.5 + - - -
214A PRO 3.6 8.1 - - - -
215A TYR 3.2 0.2 - - - -
216A ILE* 1.3 79.2 - - - +
218A ALA* 1.3 58.6 + - - +
220A SER* 3.4 4.6 + - - -
221A ALA* 3.0 13.3 + - - +
233A THR* 4.5 0.3 + - - -
238A TYR* 3.6 26.8 - - - -
242A ILE* 5.3 0.2 - - - -
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Residues in contact with ALA 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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214A PRO 2.9 17.7 + - - +
215A TYR* 3.1 6.0 + - - +
217A SER* 1.3 75.4 - - - +
219A GLN* 1.3 72.8 + - - +
221A ALA* 3.4 0.5 + - - +
222A LEU* 3.0 29.8 + - - +
238A TYR 5.0 0.2 - - - +
241A GLU* 3.7 35.4 - - + +
242A ILE* 3.9 17.9 - - + +
245A GLU* 4.4 2.0 - - + -
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Residues in contact with GLN 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 TYR* 3.1 60.2 + - + +
216A ILE* 3.1 9.2 + - + +
218A ALA* 1.3 78.6 - - - +
220A SER* 1.3 57.7 + - - +
222A LEU 3.4 0.2 + - - -
223A ASN* 2.9 43.0 + - - +
241A GLU* 5.7 0.2 + - - -
245A GLU* 2.9 47.5 + - - +
248A ARG* 4.5 0.2 - - - +
249A ARG* 3.1 16.5 + - - +
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Residues in contact with SER 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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177A GLN* 4.1 0.2 - - - -
207A GLU* 2.6 29.9 + - - -
216A ILE* 3.1 13.1 + - - -
217A SER* 3.6 9.4 - - - -
219A GLN* 1.3 79.0 - - - +
221A ALA* 1.3 61.7 + - - +
223A ASN* 3.5 12.5 + - - +
224A LYS* 2.9 40.2 + - - +
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Residues in contact with ALA 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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175A LEU* 3.9 8.9 - - + +
177A GLN* 3.5 23.5 - - - +
217A SER 3.0 16.6 + - - +
218A ALA 3.6 4.7 - - - +
219A GLN 3.2 0.2 - - - -
220A SER* 1.3 77.5 - - - +
222A LEU* 1.3 59.8 + - + +
224A LYS* 3.3 5.5 + - - +
225A SER* 3.0 26.7 + - - -
231A ILE* 4.0 16.7 - - + +
242A ILE* 3.9 19.1 - - + -
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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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218A ALA 3.0 21.4 + - - +
221A ALA* 1.3 76.8 - - + +
223A ASN* 1.3 66.6 + - - +
225A SER* 3.0 24.2 + - - +
226A ASN* 4.8 1.2 + - - -
242A ILE* 3.7 38.6 - - + +
245A GLU* 3.7 17.5 - - + -
246A ALA* 3.9 15.5 - - - +
249A ARG* 3.5 29.4 + - - +
251A LEU* 3.7 31.4 - - + +
257A PHE* 4.0 13.2 - - + -
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Residues in contact with ASN 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 GLN* 2.9 31.4 + - - +
220A SER* 3.7 10.3 - - - +
221A ALA 3.3 0.4 - - - -
222A LEU* 1.3 77.0 - - - +
224A LYS* 1.3 60.3 + - + +
226A ASN* 4.6 10.2 + - - +
227A GLN* 5.1 1.0 + - - -
249A ARG* 2.9 29.5 + - - +
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Residues in contact with LYS 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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175A LEU* 3.9 28.5 - - + -
205A LEU* 4.3 10.1 - - + -
207A GLU* 2.8 27.8 + - - +
220A SER* 2.9 35.2 + - - +
221A ALA 3.7 4.7 - - - +
223A ASN* 1.3 80.5 - - + +
225A SER* 1.3 65.4 + - - +
226A ASN* 3.2 4.5 - - - -
227A GLN* 3.0 36.0 + - - +
228A PHE* 3.2 21.4 - - + -
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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