Contacts of the helix formed by residues 184 - 198 (chain A) in PDB entry 1L7R
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 GLU 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A ARG* 3.6 27.5 + - + -
183A PRO* 1.3 90.9 - - - +
185A ASP* 1.3 69.9 + - - +
186A ALA 3.2 2.9 - - - -
187A ALA* 3.0 12.3 + - + +
188A ASP* 2.9 40.0 + - - +
216A ARG* 4.8 9.1 + - - +
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Residues in contact with ASP 185 (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 ILE* 3.5 27.6 - - + +
178A ARG* 3.2 28.0 + - - -
181A ALA* 3.4 12.3 - - + +
182A ARG* 2.6 41.2 + - - +
184A GLU* 1.3 78.3 - - - +
186A ALA* 1.3 64.1 + - - +
188A ASP* 3.3 8.0 + - - +
189A PHE* 2.9 35.6 + - + -
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Residues in contact with ALA 186 (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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182A ARG 4.5 0.8 + - - -
183A PRO 4.1 10.4 + - - +
184A GLU 3.2 0.4 - - - -
185A ASP* 1.3 80.7 - - - +
187A ALA* 1.3 61.9 + - - +
189A PHE* 3.4 11.1 + - - +
190A VAL* 3.3 24.2 + - - +
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Residues in contact with ALA 187 (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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183A PRO 4.9 0.8 + - - +
184A GLU* 3.0 14.1 + - + +
186A ALA* 1.3 78.3 - - - +
188A ASP* 1.3 67.2 + - - +
190A VAL* 3.1 12.3 + - - +
191A GLN* 2.9 31.1 + - - +
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Residues in contact with ASP 188 (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 ILE* 3.6 20.5 - - + +
178A ARG* 5.7 0.5 + - - -
184A GLU* 2.9 34.2 + - - +
185A ASP* 3.7 3.3 + - - +
187A ALA* 1.3 78.7 - - - +
189A PHE* 1.3 57.3 + - - +
191A GLN* 3.0 13.6 + - - +
192A LEU* 2.8 35.5 + - - +
213A LEU* 3.6 11.9 - - + +
216A ARG* 3.0 41.5 + - - -
217A LEU* 4.1 7.8 - - + +
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Residues in contact with PHE 189 (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 THR* 3.7 39.3 - - + -
175A ILE* 3.2 37.0 - - + +
176A THR* 3.8 15.7 - - - -
185A ASP* 2.9 29.6 + - + +
186A ALA* 3.6 8.3 - - - +
188A ASP* 1.3 76.2 - - - +
190A VAL* 1.3 64.0 + - + +
192A LEU* 3.4 7.2 + - + +
193A ALA* 3.1 23.6 + - - +
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Residues in contact with VAL 190 (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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186A ALA 3.3 17.0 - - - +
187A ALA* 3.1 10.9 + - - +
189A PHE* 1.3 78.1 - - + +
191A GLN* 1.3 58.5 + - + +
193A ALA* 3.3 7.7 + - - +
194A ALA* 3.0 27.2 + - + +
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Residues in contact with GLN 191 (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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187A ALA* 2.9 18.3 + - - +
188A ASP* 3.0 21.1 + - - +
190A VAL* 1.3 76.3 - - + +
192A LEU* 1.3 65.1 + - - +
194A ALA* 3.2 9.5 + - - +
195A ILE* 3.2 24.8 + - - +
212A PRO* 6.1 0.7 - - - +
213A LEU* 3.4 34.6 - - + +
216A ARG* 4.9 3.2 - - - +
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Residues in contact with LEU 192 (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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168A ALA* 4.0 14.8 - - + +
171A GLY* 3.9 5.2 - - - -
172A THR* 3.5 43.3 - - - +
175A ILE* 3.9 17.5 - - + -
188A ASP 2.8 24.4 + - - +
189A PHE* 3.8 8.5 - - - +
191A GLN* 1.3 72.4 - - - +
193A ALA* 1.3 62.3 + - - +
195A ILE* 3.2 7.5 + - - +
196A LEU* 3.1 28.2 + - + +
213A LEU* 3.5 20.4 - - + -
214A LEU* 3.9 18.2 - - + -
217A LEU* 3.9 15.0 - - + -
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Residues in contact with ALA 193 (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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189A PHE 3.1 14.3 + - - +
190A VAL* 3.5 11.7 - - - +
192A LEU* 1.3 73.2 - - - +
194A ALA* 1.3 60.6 + - - +
196A LEU* 3.2 10.8 + - - +
197A ASN* 2.9 42.6 + - - +
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Residues in contact with ALA 194 (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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190A VAL* 3.0 14.3 + - + +
191A GLN* 3.4 13.9 - - + +
193A ALA* 1.3 78.7 - - - +
195A ILE* 1.3 60.7 + - + +
197A ASN* 3.5 7.9 + - - +
198A ASP* 3.3 22.2 + - - +
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Residues in contact with ILE 195 (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 LEU* 4.2 27.1 - - + +
168A ALA* 4.3 4.5 - - + -
191A GLN 3.2 9.4 + - - +
192A LEU* 3.2 10.7 + - + +
193A ALA 3.2 0.6 - - - -
194A ALA* 1.3 79.5 - - + +
196A LEU* 1.3 64.9 + - + +
198A ASP 3.1 3.0 + - - -
199A VAL* 3.0 28.9 + - + -
202A ALA* 3.9 26.9 - - + -
211A GLN* 5.3 2.9 - - - +
213A LEU* 4.0 18.8 - - + -
214A LEU* 3.9 35.2 - - + -
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Residues in contact with LEU 196 (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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165A GLY* 3.8 32.5 - - - +
168A ALA* 3.9 14.4 - - + +
169A LEU* 3.7 29.2 - - + +
172A THR* 5.0 5.2 - - - +
192A LEU 3.1 16.4 + - - +
193A ALA* 3.2 10.5 + - - +
195A ILE* 1.3 80.0 - - - +
197A ASN* 1.3 63.1 + - - +
198A ASP 3.5 0.3 + - - -
199A VAL* 3.8 15.9 - - + +
408A PHE* 5.1 9.9 - - + +
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Residues in contact with ASN 197 (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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193A ALA* 2.9 28.7 + - - +
194A ALA* 4.0 7.9 - - - +
195A ILE 3.2 0.4 - - - -
196A LEU* 1.3 78.9 - - - +
198A ASP* 1.3 62.1 + - + +
199A VAL 4.0 0.2 - - - -
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Residues in contact with ASP 198 (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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194A ALA 3.3 11.0 + - - +
195A ILE 3.1 7.6 + - - +
197A ASN* 1.3 81.9 - - + +
199A VAL* 1.3 62.9 + - - +
200A ALA* 3.8 6.6 + - - +
201A GLY* 2.9 30.1 + - - -
202A ALA* 3.1 15.1 + - - +
409A HIS* 5.7 1.5 - - - -
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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