Contacts of the helix formed by residues 174 - 185 (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 SER 174 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ILE* 4.2 2.6 - - - +
173B PHE* 1.3 77.9 - - - +
175B GLY* 1.3 58.8 + - - +
176B THR* 3.5 6.9 + - - -
177B LEU* 3.0 35.6 + - - +
178B SER* 2.8 31.9 + - - -
214B ASP* 4.9 4.0 + - - -
219B ASP* 5.5 7.7 - - - +
220B VAL* 3.4 26.9 - - - +
223B LYS* 4.6 3.6 - - - +
287B PHE* 5.7 0.2 - - - -
319B ASN* 4.8 2.0 - - - -
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Residues in contact with GLY 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B PHE 4.0 2.0 + - - -
174B SER* 1.3 71.2 + - - +
176B THR* 1.3 57.7 + - - +
178B SER* 3.3 3.0 + - - -
179B TYR* 2.9 28.6 + - - +
223B LYS* 5.2 2.6 - - - +
317B SER* 3.3 38.2 + - - -
319B ASN* 4.7 4.6 + - - -
338B GLY 5.0 2.6 + - - -
339B ALA* 4.4 11.1 - - - +
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Residues in contact with THR 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B SER* 3.5 6.0 + - - -
175B GLY* 1.3 77.1 - - - +
177B LEU* 1.3 59.4 + - - +
179B TYR* 3.1 8.5 + - + +
180B ILE* 2.9 44.8 + - + +
201B ALA* 5.5 1.8 - - + -
206B TYR* 2.6 30.4 + - + +
207B THR* 3.5 24.2 - - - +
214B ASP* 3.7 26.3 + - + -
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ILE* 5.3 1.6 - - + -
174B SER* 3.0 25.8 + - - +
176B THR* 1.3 76.3 - - - +
178B SER* 1.3 65.6 + - - +
180B ILE* 4.2 19.1 - - + -
181B PHE* 3.0 33.7 + - + +
214B ASP* 3.3 31.4 - - + +
215B LEU* 4.2 18.6 - - + -
217B GLY* 4.7 1.6 - - - -
220B VAL* 4.2 4.0 - - + -
246B LEU* 4.6 9.2 - - + -
287B PHE* 3.6 48.1 - - + +
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Residues in contact with SER 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ILE* 3.6 21.0 - - - +
174B SER 2.8 20.1 + - - -
175B GLY 3.5 4.5 - - - -
177B LEU* 1.3 73.8 - - - +
179B TYR* 1.3 66.7 + - - +
181B PHE* 3.5 2.2 + - - +
182B ASN* 2.9 44.0 + - - -
286B ARG* 6.0 1.5 - - - +
314B LEU* 3.9 5.4 - - - +
316B GLY 4.1 1.6 - - - -
318B ASP 2.3 30.7 + - - -
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Residues in contact with TYR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B GLY 2.9 14.4 + - - +
176B THR* 3.3 11.0 - - - +
178B SER* 1.3 77.3 - - - +
180B ILE* 1.3 65.7 + - + +
182B ASN* 3.1 12.9 + - + +
183B GLU* 2.6 57.4 + - + +
197B VAL* 4.9 5.2 - - + -
200B VAL* 5.2 4.8 - - + +
201B ALA* 4.0 26.7 - - + -
204B LEU* 4.4 8.1 - - + +
206B TYR* 3.9 40.9 - + + -
316B GLY* 3.1 35.8 + - - +
317B SER* 4.4 4.3 - - - +
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Residues in contact with ILE 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B THR* 2.9 38.1 + - + +
177B LEU* 4.0 17.9 - - + +
178B SER 3.3 0.2 - - - -
179B TYR* 1.3 76.9 - - - +
181B PHE* 1.3 64.2 + - + +
183B GLU 3.1 1.6 + - - -
184B PHE* 2.8 26.4 + - + +
194B PHE* 3.7 31.2 - - + -
197B VAL* 3.4 29.9 - - + +
198B VAL* 4.0 22.0 - - + -
201B ALA* 4.4 15.7 - - + -
207B THR* 5.2 2.7 - - - +
211B PRO* 6.2 1.6 - - + -
214B ASP* 5.8 0.4 - - + -
215B LEU* 4.8 5.4 - - + -
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Residues in contact with PHE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LEU* 3.0 32.5 + - + +
178B SER* 4.3 2.0 - - - +
180B ILE* 1.3 82.6 - - + +
182B ASN* 1.3 57.7 + - - +
184B PHE* 4.2 20.0 - + - -
185B SER* 3.0 23.0 + - - +
194B PHE* 4.6 12.8 - + - -
246B LEU* 3.6 28.0 - - + -
271B LEU* 5.1 1.8 - - + -
285B LEU* 3.6 40.6 - - + +
286B ARG* 3.1 24.6 + - - +
287B PHE* 3.9 20.9 - + + +
302B ILE* 3.5 38.8 - - + -
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Residues in contact with ASN 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ILE* 6.1 0.2 - - - +
178B SER* 2.9 35.4 + - - +
179B TYR* 3.1 6.9 + - + +
181B PHE* 1.3 77.7 - - - +
183B GLU* 1.3 62.6 + - + +
186B THR* 3.0 23.9 - - - +
286B ARG* 3.5 30.5 + - - +
314B LEU* 3.6 31.0 + - - +
315B LYS 3.8 2.0 - - - -
316B GLY* 3.0 29.4 + - - +
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Residues in contact with GLU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B TYR* 2.6 57.2 + - + +
182B ASN* 1.3 83.5 - - + +
184B PHE* 1.3 63.6 - - - +
186B THR* 3.8 5.4 - - - +
190B ASN* 3.2 21.7 + - - +
192B VAL* 4.9 3.8 - - + +
197B VAL* 3.6 22.9 - - + -
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Residues in contact with PHE 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ILE 2.8 17.2 + - - +
181B PHE* 4.2 17.3 - + - -
183B GLU* 1.3 78.3 - - - +
185B SER* 1.3 64.7 + - - +
190B ASN* 2.6 25.7 + - - +
192B VAL 3.6 19.5 - - - -
193B LYS 4.4 0.7 - - - -
194B PHE* 3.7 39.5 - + + -
197B VAL* 4.0 11.6 - - + +
271B LEU* 3.5 49.8 - - + -
272B THR* 4.2 5.4 - - - -
275B LYS* 3.2 38.2 - - + -
285B LEU* 4.2 9.6 - - + -
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Residues in contact with SER 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B PHE* 3.0 13.2 + - - +
182B ASN 4.2 0.2 - - - +
184B PHE* 1.3 79.4 - - - +
186B THR* 1.3 64.4 + - - +
275B LYS* 4.8 10.1 + - - +
278B ALA* 5.4 1.0 - - - +
283B LYS 4.8 0.2 + - - -
284B VAL* 2.9 21.5 - - - +
285B LEU* 2.6 55.4 + - - +
286B ARG* 3.0 12.8 + - - -
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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