Contacts of the helix formed by residues 174 - 185 (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 SER 174 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ILE* 3.4 4.1 - - - +
173A PHE* 1.3 80.5 - - - +
175A GLY* 1.3 58.2 + - - +
176A THR* 3.5 6.2 + - - -
177A LEU* 3.1 33.8 + - - +
178A SER* 2.9 32.2 + - - -
214A ASP* 5.1 3.5 + - - +
219A ASP* 4.6 11.8 + - - +
220A VAL* 3.5 24.6 - - - +
223A LYS* 5.1 0.2 - - - +
287A PHE* 5.6 0.7 - - - -
319A ASN* 3.6 2.9 - - - -
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Residues in contact with GLY 175 (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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173A PHE 4.2 0.4 + - - -
174A SER* 1.3 72.5 + - - +
176A THR* 1.3 56.6 + - - +
179A TYR* 3.1 21.8 + - - +
206A TYR* 5.8 0.3 - - - +
223A LYS* 5.8 0.4 - - - +
317A SER* 3.2 34.2 - - - +
319A ASN* 3.5 8.8 + - - +
338A GLY 5.5 1.5 + - - -
339A ALA* 5.1 15.8 - - - +
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Residues in contact with THR 176 (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* 3.2 5.0 + - - -
175A GLY* 1.3 77.5 - - - +
177A LEU* 1.3 57.6 + - - +
179A TYR* 3.5 5.6 + - - +
180A ILE* 3.1 45.7 + - + +
201A ALA* 5.2 0.9 - - + -
206A TYR* 2.5 31.0 + - + +
207A THR* 3.7 13.4 - - + +
208A GLU* 5.6 0.9 + - - -
214A ASP* 3.5 42.6 + - + +
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Residues in contact with LEU 177 (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 ILE* 5.9 0.4 - - + -
174A SER* 3.1 26.6 + - - +
176A THR* 1.3 75.2 - - - +
178A SER* 1.3 65.3 + - - +
180A ILE* 4.4 8.1 - - + -
181A PHE* 3.0 34.8 + - + +
214A ASP* 3.5 26.2 - - + +
215A LEU* 3.8 30.1 - - + -
217A GLY* 5.1 0.9 - - - -
220A VAL* 4.0 4.9 - - + -
246A LEU* 4.0 13.0 - - + -
287A PHE* 3.3 50.2 + - + +
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Residues in contact with SER 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ILE* 3.4 19.6 - - - +
174A SER 2.9 19.8 + - - -
175A GLY 3.9 3.6 - - - -
177A LEU* 1.3 74.2 - - - +
179A TYR* 1.3 62.8 + - - +
181A PHE* 3.8 2.3 - - - +
182A ASN* 2.8 52.6 + - - +
286A ARG* 6.1 0.7 - - - +
287A PHE 6.4 0.2 - - - +
314A LEU* 3.9 5.2 - - - +
317A SER 3.7 3.8 - - - -
318A ASP 2.8 27.4 + - - -
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Residues in contact with TYR 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A GLY 3.1 16.5 + - - +
176A THR* 3.6 5.4 - - - +
177A LEU 3.3 0.2 - - - -
178A SER* 1.3 80.6 + - - +
180A ILE* 1.3 67.9 + - + +
182A ASN* 3.2 2.0 + - + +
183A GLU* 3.1 60.8 + - + +
197A VAL* 4.7 5.4 - - + -
200A VAL* 4.0 8.4 - - + +
201A ALA* 3.5 36.8 - - + -
204A LEU* 3.3 21.1 - - - +
206A TYR* 3.7 38.4 - + + -
316A GLY* 4.0 16.6 - - - -
317A SER* 3.6 15.0 - - - -
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Residues in contact with ILE 180 (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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176A THR* 3.1 32.4 + - + +
177A LEU* 3.9 7.9 - - + +
178A SER 3.4 0.2 - - - -
179A TYR* 1.3 79.0 - - - +
181A PHE* 1.3 56.3 + - + +
183A GLU 3.2 1.2 + - - -
184A PHE* 2.7 37.1 + - - +
194A PHE* 3.6 33.7 - - + -
197A VAL* 3.4 24.6 - - + +
198A VAL* 4.1 25.6 - - + -
201A ALA* 4.1 19.3 - - + -
207A THR* 5.2 1.6 - - - +
215A LEU* 4.1 16.8 - - + -
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Residues in contact with PHE 181 (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* 3.0 34.0 + - + +
178A SER* 4.2 2.2 - - - +
180A ILE* 1.3 78.2 - - + +
182A ASN* 1.3 60.9 + - - +
183A GLU 3.0 2.2 - - - -
184A PHE* 4.1 19.3 - + - -
185A SER 2.7 26.0 + - - -
194A PHE* 4.0 17.7 - + - -
246A LEU* 3.7 27.6 - - + -
271A LEU* 5.9 0.4 - - + -
285A LEU* 3.3 38.1 - - + +
286A ARG* 3.1 24.2 + - - +
287A PHE* 4.0 17.3 - + + +
302A ILE* 3.9 37.2 - - + -
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Residues in contact with ASN 182 (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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178A SER* 2.8 39.6 + - - +
179A TYR 3.7 4.0 - - - +
181A PHE* 1.3 77.5 - - - +
183A GLU* 1.3 66.9 + - + +
185A SER 3.9 1.4 - - - +
186A THR* 3.5 19.2 - - - +
286A ARG* 3.3 33.9 + - - +
314A LEU* 3.7 33.2 + - - +
316A GLY 3.0 25.8 + - - +
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Residues in contact with GLU 183 (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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179A TYR* 3.1 50.2 + - + +
180A ILE 3.5 6.7 - - - +
181A PHE 3.0 0.4 - - - -
182A ASN* 1.3 85.9 - - + +
184A PHE* 1.3 63.9 + - - +
185A SER 3.4 0.7 + - - -
186A THR* 3.9 12.1 - - - +
190A ASN* 4.5 7.6 + - - -
192A VAL* 4.6 7.0 - - + +
197A VAL* 3.8 16.8 - - + -
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Residues in contact with PHE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ILE 2.7 24.7 + - - +
181A PHE* 4.1 15.0 - + - -
183A GLU* 1.3 74.9 - - - +
185A SER* 1.3 62.8 + - - +
186A THR 4.2 0.4 - - - -
190A ASN* 4.1 1.5 + - - -
192A VAL* 3.6 18.8 - - - -
193A LYS* 3.9 2.5 - - - -
194A PHE* 3.4 53.8 - + + -
197A VAL* 4.0 11.6 - - + +
271A LEU* 3.6 44.4 - - + -
272A THR* 4.3 5.2 - - - -
275A LYS* 2.9 45.5 + - + +
285A LEU* 4.3 10.5 - - + -
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Residues in contact with SER 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A PHE 2.7 15.8 + - - +
182A ASN 3.9 0.7 - - - +
183A GLU 3.4 0.2 - - - -
184A PHE* 1.3 87.4 - - - +
186A THR* 1.3 62.5 + - - +
275A LYS* 4.0 18.3 + - - +
278A ALA* 5.8 0.2 - - - +
284A VAL* 2.8 37.3 - - - +
285A LEU* 3.1 26.8 + - - +
286A ARG* 3.0 18.2 + - - -
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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