Contacts of the helix formed by residues 217 - 227 (chain A) in PDB entry 1BFD
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 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A VAL* 3.4 5.6 - - - +
212A ASP* 3.1 42.5 + - - +
215A ASN* 3.2 8.7 - - - +
216A ALA* 1.3 79.1 + - - +
218A ALA* 1.3 64.8 + - - +
220A CYS* 3.0 6.3 + - - +
221A VAL* 3.0 26.8 + - - +
240A CYS 3.5 2.8 + - - -
241A PRO* 3.4 40.5 - - - +
242A PHE* 4.0 3.6 - - - +
243A PRO* 5.5 4.5 - - + +
391A ASN 5.2 0.6 + - - -
392A PRO* 3.8 28.3 - - + +
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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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215A ASN* 4.9 3.8 + - - +
216A ALA 3.4 0.4 - - - -
217A ASN* 1.3 77.4 - - - +
219A ASP* 1.3 66.5 + - - +
221A VAL* 3.2 11.4 + - - +
222A MET* 3.1 22.0 + - - +
392A PRO* 5.6 1.0 - - - +
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Residues in contact with ASP 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 ASN 5.2 1.4 - - - +
216A ALA* 3.1 17.7 + - - +
218A ALA* 1.3 79.1 - - - +
220A CYS* 1.3 58.5 + - - +
222A MET* 3.4 7.6 + - - +
223A LEU* 3.0 23.4 + - - +
319A GLY 4.7 2.3 - - - +
322A ALA* 3.8 22.2 - - + +
323A SER* 3.8 29.5 + - - -
326A ALA* 3.2 19.6 - - + +
327A ASN* 5.5 2.3 + - - -
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Residues in contact with CYS 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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205A ILE* 5.1 2.6 - - + +
207A LEU* 3.9 36.1 - - + -
211A VAL* 3.8 23.1 - - + -
216A ALA 3.0 17.4 + - - +
217A ASN 3.5 8.3 - - - +
219A ASP* 1.3 73.9 - - - +
221A VAL* 1.3 60.8 + - - +
223A LEU* 3.5 9.3 - - + +
224A ALA* 2.9 30.3 + - - +
242A PHE* 3.8 4.5 - - + -
273A ILE* 4.5 9.9 - - - -
322A ALA* 4.2 17.5 - - - -
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Residues in contact with VAL 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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217A ASN 3.0 20.1 + - - +
218A ALA* 3.4 11.4 - - - +
220A CYS* 1.3 76.3 - - - +
222A MET* 1.3 57.6 + - - +
224A ALA* 3.2 3.8 + - - +
225A GLU* 2.9 52.7 + - - +
242A PHE* 3.5 14.8 - - + -
243A PRO* 3.7 33.4 - - + -
246A HIS* 3.7 15.7 - - + +
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Residues in contact with MET 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 3.1 10.1 + - - +
219A ASP* 3.6 13.9 - - - +
220A CYS 3.3 0.2 - - - -
221A VAL* 1.3 78.9 - - - +
223A LEU* 1.3 56.6 + - - +
225A GLU* 3.3 12.2 + - - +
226A ARG* 2.8 63.8 + - + +
326A ALA* 3.0 31.9 - - + +
327A ASN* 3.5 19.7 - - - +
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Residues in contact with LEU 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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197A LEU* 5.1 2.2 - - + -
205A ILE* 4.2 13.9 - - + -
219A ASP 3.0 17.0 + - - +
220A CYS* 3.5 11.0 - - + +
221A VAL 3.3 0.2 - - - -
222A MET* 1.3 75.0 - - - +
224A ALA* 1.3 58.0 + - - +
226A ARG* 3.3 4.1 + - - +
227A LEU* 2.9 42.6 + - + +
271A LEU* 4.0 13.2 - - + -
273A ILE* 3.9 28.7 - - + -
322A ALA* 5.4 3.1 - - - +
325A LEU* 3.9 28.7 - - + +
326A ALA* 4.1 8.7 - - + +
329A VAL* 3.8 31.4 - - + -
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Residues in contact with ALA 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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205A ILE* 3.8 13.6 - - + +
220A CYS 2.9 17.5 + - - +
221A VAL 3.5 4.0 - - - +
223A LEU* 1.3 76.2 - - - +
225A GLU* 1.3 58.5 + - + +
228A LYS* 2.8 24.4 + - - -
229A ALA 3.1 15.1 + - - +
231A VAL* 3.6 31.6 - - + -
242A PHE* 4.0 9.2 - - + -
248A CYS* 4.0 8.8 - - - -
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Residues in contact with GLU 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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221A VAL* 2.9 31.2 + - - +
222A MET* 3.7 9.6 - - - +
224A ALA* 1.3 73.8 - - - +
226A ARG* 1.3 64.1 + - + +
228A LYS* 2.8 33.2 + - - +
246A HIS* 2.8 36.6 + - + +
331A GLU* 5.7 0.4 - - - -
336A LEU* 4.2 15.6 - - + +
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Residues in contact with ARG 226 (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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222A MET* 2.8 48.2 + - + +
223A LEU 3.7 3.6 - - - +
225A GLU* 1.3 79.7 - - + +
227A LEU* 1.3 58.5 + - - +
228A LYS* 3.4 4.8 + - - +
326A ALA 2.9 23.3 + - - -
327A ASN* 3.1 21.2 + - - +
329A VAL* 3.1 38.5 + - + -
330A GLU 3.7 9.3 - - - +
331A GLU* 3.5 17.6 + - - +
332A SER* 2.8 31.4 + - - -
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Residues in contact with LEU 227 (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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197A LEU* 3.9 45.1 - - + +
198A ASN* 4.8 3.1 - - - +
203A PRO* 4.6 10.3 - - + -
205A ILE* 4.3 15.0 - - + -
223A LEU* 2.9 41.9 + - + +
224A ALA* 4.3 0.7 - - - +
226A ARG* 1.3 76.4 - - - +
228A LYS* 1.3 67.9 + - - +
229A ALA* 3.3 12.7 + - + +
271A LEU* 5.2 2.2 - - + -
329A VAL* 4.3 18.8 - - + -
330A GLU 4.7 4.9 - - - +
332A SER* 4.1 2.5 - - - -
334A ARG* 2.7 34.4 + - - +
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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