Contacts of the helix formed by residues 208 - 221 (chain A) in PDB entry 5FHH
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 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A GLN 3.8 1.6 + - - -
207A LEU* 1.3 76.8 - - - +
209A GLU* 1.3 64.6 + - - +
210A GLU* 3.6 11.1 + - - +
211A GLN* 3.1 30.7 + - - +
212A ALA* 2.9 22.1 + - - +
376A LEU* 4.7 1.0 - - - +
377A THR 5.6 1.2 + - - -
378A LYS* 6.1 4.3 - - - -
380A TRP* 4.5 20.7 + - - -
701A ADP 4.4 1.4 + - - -
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Residues in contact with GLU 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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207A LEU 3.9 0.4 + - - -
208A SER* 1.3 73.1 - - - +
210A GLU* 1.3 63.9 + - - +
212A ALA* 3.3 6.1 + - - +
213A ALA* 3.0 23.9 + - - +
216A ARG* 5.3 1.6 + - - -
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Residues in contact with GLU 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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208A SER* 3.6 9.2 + - - +
209A GLU* 1.3 80.9 - - - +
211A GLN* 1.3 63.8 + - - +
213A ALA* 3.4 16.2 - - - +
214A VAL* 3.6 10.6 - - - +
374A LEU* 5.6 0.2 - - - +
375A GLU* 4.0 15.1 - - - +
376A LEU* 3.6 15.7 - - + +
377A THR* 2.3 56.3 + - - +
378A LYS* 4.7 4.2 - - - +
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Residues in contact with GLN 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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207A LEU* 3.4 20.0 - - + +
208A SER* 3.1 20.6 + - - +
210A GLU* 1.3 78.6 - - - +
212A ALA* 1.3 57.0 + - - +
213A ALA 3.0 0.2 - - - -
214A VAL* 2.8 26.0 + - - +
215A LEU 3.2 7.6 + - - -
232A THR 4.4 2.6 + - - -
233A GLY* 3.4 23.2 + - - -
236A TYR* 4.5 2.9 - - - -
237A LEU* 3.7 23.9 - - + +
376A LEU* 3.6 19.1 - - + -
380A TRP* 5.1 2.3 - - - +
701A ADP 2.4 52.9 + - - -
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Residues in contact with ALA 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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207A LEU* 4.5 15.0 - - + +
208A SER 2.9 16.2 + - - +
209A GLU* 3.3 6.3 + - - +
211A GLN* 1.3 75.3 - - - +
213A ALA* 1.3 60.5 + - - +
215A LEU* 3.7 16.0 - - + +
216A ARG* 3.2 38.7 + - + +
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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 GLU 3.0 11.7 + - - +
210A GLU* 3.4 13.7 - - - +
211A GLN 3.0 0.4 + - - -
212A ALA* 1.3 78.5 - - - +
214A VAL* 1.3 61.8 + - - +
216A ARG* 3.6 19.6 + - - +
217A ALA* 3.3 22.3 + - - +
374A LEU* 4.6 13.3 - - + +
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Residues in contact with VAL 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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210A GLU 3.6 11.7 - - - +
211A GLN* 2.8 18.7 + - - +
213A ALA* 1.3 69.1 - - - +
215A LEU* 1.3 65.5 + - - +
217A ALA* 3.2 2.6 + - - +
218A VAL* 3.1 25.3 + - + +
224A ILE* 3.5 25.5 - - + +
226A PHE* 3.5 45.1 - - + -
237A LEU* 3.5 17.5 - - + -
241A ILE* 4.6 5.6 - - + -
339A ILE* 6.2 0.2 - - + -
374A LEU* 4.1 15.5 - - + -
375A GLU 5.6 1.1 - - - +
376A LEU* 5.0 4.7 - - + -
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Residues in contact with LEU 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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207A LEU* 4.6 23.1 - - + -
211A GLN 3.2 3.9 + - - +
212A ALA* 3.7 17.9 - - + +
213A ALA 3.3 0.2 - - - -
214A VAL* 1.3 78.9 - - - +
216A ARG* 1.3 74.0 + - + +
218A VAL* 3.0 13.5 - - - +
219A LEU* 2.9 50.5 - - + +
237A LEU* 4.7 7.7 - - + +
240A ARG* 4.6 15.3 - - + -
241A ILE* 4.7 7.6 - - + -
244A SER* 4.3 14.6 - - - +
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Residues in contact with ARG 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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209A GLU 5.3 1.6 + - - -
212A ALA* 3.2 28.0 + - - +
213A ALA* 3.6 17.2 + - - +
215A LEU* 1.3 90.0 - - + +
217A ALA* 1.3 58.3 + - - +
219A LEU* 3.3 10.6 + - + +
220A LYS* 2.8 27.8 + - - +
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Residues in contact with ALA 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 ALA 3.3 10.5 + - - +
214A VAL 3.2 1.8 + - - -
216A ARG* 1.3 78.6 - - - +
218A VAL* 1.3 61.2 + - - +
220A LYS* 3.3 20.5 + - - +
222A GLN* 3.3 23.4 + - + +
224A ILE* 3.6 28.7 - - + -
372A VAL* 6.0 2.2 - - + -
374A LEU* 5.3 2.5 - - + -
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Residues in contact with VAL 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 VAL 3.1 13.5 + - - +
215A LEU* 3.0 25.6 - - - +
217A ALA* 1.3 73.9 - - - +
219A LEU* 1.3 65.8 + - + +
220A LYS 3.1 1.1 - - - -
221A GLY 2.9 8.1 + - - -
222A GLN 4.2 2.5 - - - -
224A ILE* 4.0 12.9 - - + +
241A ILE* 3.8 20.4 - - + -
245A LEU* 3.8 12.7 - - + +
337A GLN* 2.5 42.4 + - - +
339A ILE* 3.3 35.2 - - + -
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Residues in contact with LEU 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 LEU* 2.9 52.1 + - + +
216A ARG* 3.4 12.8 - - + +
218A VAL* 1.3 86.1 - - + +
220A LYS* 1.3 61.1 + - - +
221A GLY* 3.3 0.7 + - - -
241A ILE* 5.3 1.1 - - + -
244A SER* 4.1 25.4 - - - +
245A LEU* 4.2 15.7 - - + -
337A GLN* 5.2 0.2 - - - +
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Residues in contact with LYS 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 ARG 2.8 13.7 + - - +
217A ALA* 3.3 17.0 - - - +
218A VAL 3.1 0.6 - - - -
219A LEU* 1.3 78.0 - - - +
221A GLY* 1.3 55.7 + - - +
222A GLN* 4.5 5.2 - - + +
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Residues in contact with GLY 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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218A VAL 2.9 7.2 + - - -
219A LEU 3.1 1.0 - - - -
220A LYS* 1.3 78.1 - - - +
222A GLN* 1.3 58.9 + - - +
223A SER 3.8 1.4 + - - -
337A GLN* 3.1 34.6 + - - +
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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