Contacts of the helix formed by residues 210 - 222 (chain A) in PDB entry 5E67
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 ASP 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A ILE 4.4 2.8 - - - +
101A THR* 3.2 20.7 - - - -
102A GLU* 3.0 43.6 + - - +
164A LYS* 5.9 0.5 + - - -
206A GLN* 3.9 21.0 + - + +
207A HIS* 3.1 15.4 + - - +
208A ALA 3.1 1.2 - - - -
209A ARG* 1.3 82.8 + - - +
211A VAL* 1.3 64.7 + - - +
212A LYS* 3.1 4.3 + - - +
213A LEU* 3.3 15.4 + - + +
214A MET* 3.1 21.9 + - - +
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Residues in contact with VAL 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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208A ALA 2.9 18.7 + - - +
209A ARG* 3.2 5.6 - - - +
210A ASP* 1.3 76.7 - - - +
212A LYS* 1.3 75.8 + - + +
214A MET* 3.2 2.5 + - + +
215A GLU* 2.7 53.1 + - + +
226A ILE* 6.1 2.5 - - + -
235A LEU* 3.8 21.1 - - + -
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Residues in contact with LYS 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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163A ASN* 3.1 35.7 - - - +
209A ARG 5.0 0.6 + - - +
210A ASP 3.1 1.4 + - - -
211A VAL* 1.3 90.7 - - + +
213A LEU* 1.3 60.5 + - - +
215A GLU* 3.2 24.5 + - - +
216A SER* 2.9 29.9 + - - -
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Residues in contact with LEU 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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100A ILE* 3.9 26.9 - - + +
101A THR* 3.7 34.1 - - + -
164A LYS 5.1 11.8 + - - +
166A ILE* 4.0 22.7 - - + -
171A TRP* 4.1 15.5 - - + -
175A PHE* 4.7 7.9 - - + -
206A GLN* 5.4 1.6 - - + -
210A ASP* 3.3 20.1 + - + +
212A LYS* 1.3 78.8 - - - +
214A MET* 1.3 69.2 + - - +
216A SER* 2.9 26.1 + - - +
217A LEU* 3.2 9.9 + - + +
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Residues in contact with MET 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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175A PHE* 5.0 1.6 - - - -
204A ILE* 3.3 33.2 - - + +
206A GLN* 3.7 42.4 - - + +
210A ASP 3.1 13.7 + - - +
211A VAL 3.5 7.9 - - - +
213A LEU* 1.3 79.9 - - + +
215A GLU* 1.3 65.0 + - - +
217A LEU* 3.2 34.9 + - - +
226A ILE* 3.4 22.0 - - + +
235A LEU* 3.9 26.5 - - + +
237A TYR* 3.8 18.6 - - + +
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Residues in contact with GLU 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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211A VAL* 2.7 34.8 + - + +
212A LYS* 3.5 29.2 + - - +
213A LEU 3.2 0.2 - - - -
214A MET* 1.3 74.6 - - - +
216A SER* 1.3 57.0 + - - +
218A ILE* 3.0 33.9 + - + +
219A SER* 4.2 1.2 + - - -
226A ILE* 4.2 15.9 - - + -
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Residues in contact with SER 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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164A LYS 5.4 2.8 + - - -
165A ASN* 5.8 2.9 - - - -
166A ILE* 4.1 13.2 + - - +
212A LYS 2.9 13.0 + - - -
213A LEU* 2.9 25.8 + - - +
215A GLU* 1.3 73.3 - - - +
217A LEU* 1.3 64.8 + - - +
218A ILE 3.1 0.4 + - - -
219A SER* 3.3 12.0 + - - -
220A TYR* 2.9 23.4 + - - +
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Residues in contact with LEU 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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166A ILE* 3.8 17.3 - - + -
171A TRP* 5.4 0.4 - - + -
172A LEU* 3.7 34.3 - - + -
175A PHE* 5.5 2.9 - - + -
204A ILE* 3.9 23.1 - - + -
213A LEU* 3.7 11.7 - - + +
214A MET* 3.4 41.7 - - - +
215A GLU 3.1 1.0 - - - -
216A SER* 1.3 79.5 + - - +
218A ILE* 1.3 57.1 + - - +
220A TYR* 3.7 4.4 - - - +
221A LEU* 2.8 36.2 + - + +
237A TYR* 3.8 25.6 + - + -
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Residues in contact with ILE 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 GLU* 3.0 19.7 + - + +
217A LEU* 1.3 76.3 - - - +
219A SER* 1.3 54.8 + - - +
222A GLY* 2.8 30.0 + - - -
223A CYS* 3.1 27.0 + - - +
224A GLY 3.6 27.4 - - - +
225A PHE* 4.2 5.6 - - - -
226A ILE* 3.6 26.5 - - + +
237A TYR* 4.0 7.0 - - + -
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Residues in contact with SER 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 GLU 4.2 1.0 + - - -
216A SER* 3.3 14.5 + - - -
218A ILE* 1.3 79.0 - - - +
220A TYR* 1.3 70.0 + - - +
221A LEU 3.3 0.5 + - - -
222A GLY* 3.3 10.0 + - - +
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Residues in contact with TYR 220 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A ILE* 3.8 38.5 - - + +
168A ASP* 3.8 3.1 - - - -
169A PRO* 3.3 35.4 - - + +
172A LEU* 3.8 24.9 - - + -
216A SER* 2.9 19.8 + - - +
217A LEU* 3.7 7.6 - - - +
219A SER* 1.3 80.0 + - - +
221A LEU* 1.3 65.1 + - + +
252A PHE* 3.9 24.5 - + - -
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Residues in contact with LEU 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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172A LEU* 3.9 31.9 - - + -
202A PHE* 4.3 9.0 - - + -
204A ILE* 5.0 1.6 - - + -
217A LEU* 2.8 20.7 + - + +
220A TYR* 1.3 79.4 - - + +
222A GLY* 1.3 64.3 + - - +
223A CYS* 3.2 14.8 + - - -
237A TYR* 3.5 37.7 - - + +
248A LYS* 3.5 18.0 - - - +
249A ILE* 4.2 15.9 - - + -
252A PHE* 4.1 31.2 - - + -
253A PHE* 4.9 2.2 - - + -
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Residues in contact with GLY 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 ILE* 2.8 11.5 + - - -
219A SER* 3.3 10.7 + - - -
220A TYR 3.7 0.2 + - - -
221A LEU* 1.3 79.5 - - - +
223A CYS* 1.3 57.1 + - - +
248A LYS* 2.9 30.9 + - - -
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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