Contacts of the helix formed by residues 217 - 228 (chain A) in PDB entry 1EUB
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 PHE 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A LYS* 3.3 48.7 - - + -
137A ALA* 3.4 6.5 - - - -
140A LYS* 3.4 38.1 - - + -
141A ALA* 3.5 12.7 - - - +
144A VAL* 5.4 3.4 - - + +
209A SER* 3.0 48.0 - - - -
215A ASN* 2.6 21.5 + - + -
216A LEU* 1.3 70.2 - - - +
218A LEU* 1.3 50.5 + - - +
221A ALA* 2.5 38.6 - - - +
247A THR* 4.9 3.1 - - + -
248A GLY* 4.5 15.2 - - - +
249A LYS 5.7 0.9 - - - +
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Residues in contact with LEU 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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3A MSB 3.1 23.3 - - - +
214A TYR* 4.9 2.2 - - + -
215A ASN* 2.4 26.4 + - - +
217A PHE* 1.3 73.0 - - - +
219A VAL* 1.3 70.1 + - - +
221A ALA* 3.1 2.3 + - - +
222A HIS* 2.8 23.6 + - - +
239A LEU* 3.6 15.6 - - + +
244A TYR* 3.2 43.5 - - + +
245A THR 4.7 1.1 - - - +
246A TYR* 3.1 24.5 - - + +
247A THR* 3.7 17.7 - - + +
248A GLY* 3.5 15.0 - - - +
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Residues in contact with VAL 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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3A MSB 4.0 13.8 - - + -
185A LEU* 3.4 27.4 - - + -
186A ALA* 4.4 2.5 - - + -
201A PHE* 3.1 34.1 - - + -
207A TRP* 5.0 2.2 - - + -
214A TYR* 4.0 17.9 - - + -
215A ASN 2.9 21.8 - - - +
216A LEU* 3.1 21.5 - - + +
218A LEU* 1.3 75.9 - - - +
220A ALA* 1.3 56.9 + - - +
222A HIS* 2.8 5.1 + - - +
223A GLU* 2.7 33.1 + - - +
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Residues in contact with ALA 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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141A ALA* 3.9 9.2 - - + -
165A ILE* 3.2 35.9 - - + -
201A PHE* 3.8 13.7 - - + -
216A LEU* 2.5 29.0 + - - +
219A VAL* 1.3 76.2 - - - +
221A ALA* 1.3 61.3 + - - +
222A HIS 2.9 0.3 + - - -
223A GLU* 3.0 0.6 + - - -
224A PHE* 2.7 31.4 + - + +
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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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141A ALA* 3.9 22.0 - - - +
144A VAL* 4.9 12.3 - - + -
145A TRP* 4.5 13.1 - - + -
217A PHE 2.5 26.0 + - - +
218A LEU* 3.6 2.7 - - - +
220A ALA* 1.3 80.2 - - - +
222A HIS* 1.3 57.6 + - - +
224A PHE* 4.2 4.8 - - - +
225A GLY* 3.0 20.8 + - - -
239A LEU* 3.1 19.5 - - + +
248A GLY* 5.6 0.9 - - - -
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Residues in contact with HIS 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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1A HAV 2.6 23.6 + - - -
3A MSB 2.4 47.2 + + + -
218A LEU 2.8 12.8 + - - +
219A VAL 2.8 11.8 + - - +
221A ALA* 1.3 77.6 - - - +
223A GLU* 1.3 64.1 + - - -
225A GLY* 3.1 2.9 + - - -
226A HIS* 3.0 19.3 + + - +
239A LEU* 2.9 25.0 + - + +
240A MET* 2.9 33.6 - - - -
241A PHE* 3.1 4.5 + + - -
276A ZN 2.2 26.5 - - - -
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Residues in contact with GLU 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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1A HAV 3.2 8.6 + - - -
186A ALA* 2.5 38.9 - - + +
187A HIS 2.6 2.3 - - - -
188A ALA* 2.4 42.6 + - - +
199A ALA* 3.5 27.4 - - + -
201A PHE* 3.5 29.2 - - + -
219A VAL 2.7 11.6 + - - +
220A ALA 3.7 2.9 - - - +
222A HIS* 1.3 72.5 - - - +
224A PHE* 1.3 50.4 + - - +
226A HIS* 2.7 23.0 + - - +
227A SER* 2.4 25.2 + - - -
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Residues in contact with PHE 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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120A TYR* 4.0 8.5 - + + -
138A PHE* 6.2 0.2 - - + -
142A PHE* 2.9 48.9 - + - -
145A TRP* 5.4 11.7 - + + -
163A ILE* 3.6 19.7 - - + -
164A MET* 3.3 16.6 - - - -
165A ILE* 3.2 54.7 - - + -
199A ALA* 3.7 9.0 - - + -
220A ALA* 2.7 24.2 + - + +
221A ALA* 4.2 5.6 - - - +
223A GLU* 1.3 72.7 - - + +
225A GLY* 1.3 64.3 + - - +
226A HIS 2.8 1.6 + - - -
227A SER* 3.0 7.0 - - - -
228A LEU* 2.9 31.1 + - + +
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Residues in contact with GLY 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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145A TRP* 3.8 27.9 - - - -
221A ALA 3.0 19.1 + - - -
222A HIS* 3.1 6.2 + - - -
224A PHE* 1.3 76.8 - - - +
226A HIS* 1.3 60.7 + - - +
229A GLY* 2.8 26.2 + - - -
230A LEU 3.7 1.2 + - - -
239A LEU* 5.4 0.4 - - - -
240A MET* 4.3 12.7 - - - +
262A ILE* 5.6 0.5 - - - +
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Residues in contact with HIS 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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1A HAV 2.9 25.8 - - + -
188A ALA* 3.8 11.4 - - + -
189A PHE 5.7 0.2 - - - -
191A PRO* 5.5 0.3 - - - +
222A HIS 3.0 5.3 + - - +
223A GLU* 2.7 17.2 + - - +
225A GLY* 1.3 71.5 - - - +
227A SER* 1.3 69.7 + - - +
228A LEU 2.7 3.1 + - - -
229A GLY 2.8 9.5 + - - -
230A LEU* 3.1 24.5 + - - +
231A ASP 3.3 9.9 - - - -
232A HIS* 2.5 31.1 + + - -
240A MET* 3.2 38.5 - - + +
276A ZN 2.2 26.4 - - - -
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Residues in contact with SER 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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163A ILE* 3.1 14.4 - - - +
188A ALA* 2.9 23.0 - - - +
189A PHE 3.0 21.1 - - - +
190A PRO* 4.4 0.2 - - - +
191A PRO* 3.2 14.4 - - - +
197A GLY* 3.2 26.8 - - - -
199A ALA* 4.1 5.5 - - - +
223A GLU 2.4 31.6 + - - -
224A PHE* 3.0 13.7 - - - -
226A HIS* 1.3 74.3 - - - +
228A LEU* 1.3 54.2 + - - -
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Residues in contact with LEU 228 (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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111A LEU 4.5 0.9 - - - +
115A LYS 5.5 0.2 - - - +
118A LEU* 3.4 42.6 - - + -
142A PHE* 6.2 1.6 - - + -
145A TRP* 3.7 31.9 - - + +
151A LEU* 4.1 14.6 - - + -
163A ILE* 3.5 22.4 - - + -
191A PRO* 4.3 9.0 - - + +
197A GLY* 5.0 0.4 - - - -
224A PHE* 2.9 15.2 + - + +
226A HIS 2.7 2.8 + - - -
227A SER* 1.3 77.1 - - - +
229A GLY* 1.3 63.8 + - - +
266A TYR* 2.3 54.9 + - + +
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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