Contacts of the helix formed by residues 217 - 231 (chain B) 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 GLY 217 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B LEU* 4.7 1.3 - - - -
214B ASP 3.3 11.7 + - - -
215B LEU 2.8 8.2 - - - -
216B ASN* 1.3 77.8 + - - +
218B LEU* 1.3 62.9 + - - +
219B ASP 3.3 2.5 - - - -
220B VAL* 3.3 11.2 - - - +
221B ALA* 3.3 20.3 + - - +
243B VAL* 3.7 8.2 - - - +
287B PHE* 4.1 25.4 - - - -
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ASP 5.2 2.0 - - - +
216B ASN* 2.7 34.1 + - - +
217B GLY* 1.3 71.7 - - - +
219B ASP* 1.3 58.2 + - - +
221B ALA* 3.2 7.4 + - + +
222B ARG* 2.9 60.2 + - + +
238B PRO* 4.5 17.5 - - + +
239B THR* 4.6 14.4 - - + -
243B VAL* 5.1 1.8 - - - -
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Residues in contact with ASP 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LYS* 3.3 24.6 + - - -
174B SER* 5.5 7.2 - - - +
213B ASP 4.9 11.7 + - - +
214B ASP* 5.5 9.2 + - - +
216B ASN* 4.4 0.8 + - - -
217B GLY* 3.3 1.0 - - - -
218B LEU* 1.3 76.7 - - - +
220B VAL* 1.3 68.7 + - + +
222B ARG* 3.0 28.3 + - - +
223B LYS* 3.1 40.8 + - - +
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Residues in contact with VAL 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B PHE* 4.4 13.4 - - + +
174B SER* 3.4 38.8 - - - +
177B LEU* 4.2 4.5 - - + -
217B GLY* 3.3 8.9 + - - +
219B ASP* 1.3 76.2 - - + +
221B ALA* 1.3 57.9 + - - +
223B LYS* 3.2 8.0 + - - +
224B VAL* 2.7 40.4 + - + +
287B PHE* 3.6 23.8 - - + +
288B ILE 4.8 3.1 - - - +
289B GLY* 5.5 0.9 - - - -
300B VAL* 3.3 36.3 - - + -
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Residues in contact with ALA 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLY 3.3 9.6 + - - +
218B LEU* 3.2 14.3 + - + +
220B VAL* 1.3 82.0 - - - +
222B ARG* 1.3 60.8 + - - +
224B VAL* 4.2 0.7 - - - -
225B THR* 3.0 30.1 + - - -
238B PRO* 3.5 26.0 - - + +
241B PHE* 3.6 10.3 - - + -
243B VAL* 3.7 19.3 - - + -
300B VAL* 4.0 7.0 - - + -
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Residues in contact with ARG 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LYS* 4.2 22.0 - - + +
118B LYS* 4.2 33.6 - - - +
121B SER* 2.8 44.8 + - - +
218B LEU* 2.9 41.3 + - + +
219B ASP* 3.0 25.2 + - - +
221B ALA* 1.3 79.1 - - - +
223B LYS* 1.3 58.7 + - - +
225B THR* 3.4 4.5 + - - -
226B ILE* 3.2 26.3 + - - +
238B PRO* 4.1 13.6 - - - +
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Residues in contact with LYS 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LYS* 3.6 17.4 - - + +
145B THR 3.4 28.3 - - - +
146B VAL* 3.9 14.8 - - + +
147B GLY 4.9 3.8 - - - +
173B PHE* 2.9 47.8 + - + +
174B SER* 4.6 3.4 - - - +
175B GLY 5.2 2.0 - - - +
219B ASP* 3.1 33.2 + - - +
220B VAL 3.2 5.6 + - - +
222B ARG* 1.3 74.1 - - - +
224B VAL* 1.3 60.8 + - - +
226B ILE* 3.3 10.2 + - - +
227B VAL* 3.0 32.6 + - - +
338B GLY 5.1 7.5 + - - -
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Residues in contact with VAL 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B PHE* 4.2 12.3 - - + -
220B VAL 2.7 30.7 + - - +
221B ALA* 3.8 7.2 - - - +
222B ARG 3.3 0.2 - - - -
223B LYS* 1.3 75.3 - - - +
225B THR* 1.3 57.0 + - - +
227B VAL* 4.0 5.1 - - - +
228B GLY* 2.8 32.2 + - - -
235B VAL* 4.9 0.2 - - - +
241B PHE* 4.4 2.0 - - + -
289B GLY* 3.7 26.2 - - - -
290B LYS 4.0 7.6 - - - +
291B VAL* 3.8 13.7 - - + -
298B VAL* 3.3 33.1 - - + +
299B SER 4.5 1.8 - - - +
300B VAL* 4.0 7.4 - - + -
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Residues in contact with THR 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B SER* 4.3 11.2 - - - -
221B ALA 3.0 17.2 + - - -
222B ARG 3.5 10.5 - - - -
224B VAL* 1.3 77.1 - - - +
226B ILE* 1.3 61.0 + - - +
228B GLY 4.1 0.2 - - - -
229B ARG* 3.0 72.6 + - - +
235B VAL* 3.8 15.1 - - + +
237B SER 3.7 4.3 + - - -
238B PRO* 3.3 23.1 - - + +
241B PHE* 3.5 8.2 - - - -
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Residues in contact with ILE 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LYS* 4.3 11.7 - - + -
120B PHE* 3.8 28.0 - - + +
121B SER* 4.4 2.0 - - - -
127B TRP* 3.9 12.2 - - + -
142B HIS* 3.7 26.2 - - + +
145B THR* 3.2 29.8 - - + +
146B VAL* 3.8 18.6 - - + -
153B ILE* 4.3 0.4 - - + -
222B ARG 3.2 17.3 - - - +
223B LYS* 3.3 9.4 + - - +
224B VAL 3.2 0.4 - - - -
225B THR* 1.3 75.1 - - - +
227B VAL* 1.3 66.1 + - - +
229B ARG* 3.3 3.8 + - - +
230B ILE* 3.0 32.6 + - + +
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B VAL* 3.7 27.8 - - + -
152B ILE* 5.3 1.1 - - + -
153B ILE* 5.7 0.7 - - + -
156B LEU* 4.3 10.5 - - + -
169B ILE* 3.4 45.3 - - + -
173B PHE* 4.2 13.5 - - + -
223B LYS 3.0 20.3 + - - +
224B VAL* 4.0 4.7 - - - +
226B ILE* 1.3 74.0 - - - +
228B GLY* 1.3 59.5 + - - +
230B ILE* 3.1 12.7 + - + +
231B SER* 2.8 32.2 + - - +
291B VAL* 4.9 4.0 - - + -
321B ILE* 4.4 5.2 - - + -
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Residues in contact with GLY 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B VAL 2.8 21.6 + - - -
225B THR 4.2 0.2 - - - -
227B VAL* 1.3 74.0 - - - +
229B ARG* 1.3 60.6 + - - +
231B SER* 3.1 8.5 + - - -
232B GLY 3.2 0.3 + - - -
233B VAL* 2.9 33.0 + - - +
235B VAL* 4.6 5.4 - - - -
291B VAL* 3.9 26.4 - - - +
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Residues in contact with ARG 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PHE 3.0 24.7 + - - -
122B SER 2.9 27.5 + - - -
123B ASP 3.7 7.7 + - - -
124B LEU* 3.4 16.0 - - + +
127B TRP* 3.7 50.5 + - + +
225B THR* 3.0 37.0 + - - +
226B ILE 3.6 4.0 - - - +
227B VAL 3.2 0.2 - - - -
228B GLY* 1.3 72.3 - - - +
230B ILE* 1.3 68.2 + - - +
232B GLY* 2.8 15.9 + - - -
233B VAL 3.3 15.9 + - - +
234B GLU* 4.7 7.4 - - - +
235B VAL* 2.7 31.9 + - - +
236B GLU 3.1 13.3 + - - -
237B SER 3.9 0.2 - - - +
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Residues in contact with ILE 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B TRP* 4.0 7.0 - - + -
142B HIS* 4.2 4.0 - - - +
153B ILE* 3.7 40.8 - - + -
156B LEU* 3.7 31.9 - - + -
157B ARG* 3.9 31.9 - - + +
160B ILE* 3.2 24.3 - - + +
226B ILE* 3.0 26.6 + - + +
227B VAL* 3.4 11.2 - - - +
229B ARG* 1.3 76.2 - - - +
231B SER* 1.3 57.8 + - - +
232B GLY 3.3 3.8 + - - -
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Residues in contact with SER 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B LEU* 4.7 3.6 - - - +
160B ILE* 4.9 0.7 - - - -
166B VAL* 3.2 37.9 - - - +
169B ILE* 3.3 22.8 - - - +
227B VAL* 2.8 17.8 + - - +
228B GLY* 3.5 10.1 - - - -
229B ARG 3.0 0.8 - - - -
230B ILE* 1.3 76.5 - - - +
232B GLY* 1.3 58.0 + - - +
233B VAL 3.4 0.7 - - - -
291B VAL* 4.7 4.5 - - - -
293B VAL* 3.6 22.0 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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