Contacts of the helix formed by residues 211 - 216 (chain A) in PDB entry 1EBF
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 PRO 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A VAL* 4.1 20.9 - - + -
202A LYS* 3.8 32.1 - - + -
207A THR* 3.1 28.7 - - + +
208A GLU 3.4 0.6 - - - +
209A PRO 3.7 8.5 - - - +
210A ASP* 1.3 86.9 - - - +
212A ARG* 1.3 55.6 + - - +
213A ASP 3.1 0.4 - - - -
214A ASP* 2.9 21.8 + - - +
215A LEU* 3.1 20.5 + - + +
260A PHE* 4.8 6.1 - - + -
261A LEU* 4.5 14.4 - - + -
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Residues in contact with ARG 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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210A ASP* 2.8 35.3 + - - +
211A PRO* 1.3 77.0 - - - +
213A ASP* 1.3 60.6 + - - +
214A ASP 3.1 1.9 + - - -
215A LEU* 3.9 5.4 - - - +
216A ASN* 3.0 30.6 + - - +
247A ILE* 3.7 21.5 - - + +
252A GLU 4.6 9.1 + - - -
253A SER* 5.9 0.8 - - - +
255A LYS* 3.7 23.8 + - - +
256A SER* 3.7 2.4 - - - +
257A ALA* 2.6 36.7 - - - +
260A PHE* 3.3 49.1 - - + +
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Residues in contact with ASP 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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208A GLU* 4.1 21.2 - - + +
209A PRO* 5.7 0.7 - - - +
210A ASP* 3.0 28.7 + - - +
212A ARG* 1.3 80.7 - - - +
214A ASP* 1.3 62.1 + - - +
216A ASN* 3.7 20.6 + - - +
218A LEU* 5.8 0.2 - - - +
219A ASP* 4.8 11.1 + - - +
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Residues in contact with ASP 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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174A SER* 5.1 2.6 + - - +
176A THR* 3.5 34.1 + - + -
177A LEU* 3.5 27.1 - - + +
180A ILE* 5.9 0.2 - - + -
207A THR* 3.1 15.6 - - - +
208A GLU* 2.9 44.1 + - - +
211A PRO* 2.9 5.9 + - + +
213A ASP* 1.3 82.8 - - - +
215A LEU* 1.3 66.0 + - + +
216A ASN 3.3 2.7 + - - -
217A GLY* 3.5 7.5 + - - -
219A ASP* 5.4 9.3 - - - +
220A VAL* 5.8 0.2 - - - +
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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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177A LEU* 3.8 23.1 - - + -
180A ILE* 4.1 17.7 - - + -
194A PHE* 4.2 12.6 - - + -
198A VAL* 4.4 21.1 - - + -
211A PRO* 3.1 14.7 + - + +
212A ARG* 3.7 1.1 + - - +
214A ASP* 1.3 77.2 - - + +
216A ASN* 1.3 60.5 + - - +
217A GLY* 3.2 1.7 + - - -
244A GLN 4.9 0.3 - - - +
245A SER* 4.0 0.2 - - - -
246A LEU* 2.8 53.3 + - + +
247A ILE* 4.2 12.3 - - + -
260A PHE* 3.9 32.1 - - + -
264A LEU* 4.6 3.8 - - + -
287A PHE* 5.1 0.9 - - - -
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Residues in contact with ASN 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 ARG 3.0 22.7 + - - +
213A ASP* 3.7 23.7 + - - +
215A LEU* 1.3 75.6 - - - +
217A GLY* 1.3 57.7 + - - +
218A LEU* 2.7 47.4 + - - +
219A ASP 4.2 0.7 + - - -
243A VAL* 4.3 6.9 - - - +
245A SER* 3.5 28.7 - - - +
247A ILE* 3.9 15.1 - - + +
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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