Contacts of the helix formed by residues 223 - 235 (chain A) in PDB entry 3LRA
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 PRO 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A GLU* 2.8 30.1 - - - +
216A GLN* 4.9 4.0 + - - +
221A VAL* 3.0 22.7 - - + +
222A PRO* 1.3 106.4 - - + +
224A GLN* 1.3 71.3 - - - +
225A LYS* 3.0 23.1 - - + +
226A LEU* 3.6 22.2 + - + +
227A GLN* 4.2 6.2 + - - +
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Residues in contact with GLN 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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222A PRO 4.2 1.6 - - - +
223A PRO* 1.3 82.4 - - - +
225A LYS* 1.3 57.1 + - + +
226A LEU 3.3 1.1 - - - -
227A GLN* 3.3 13.1 + - + +
228A ALA* 2.6 36.9 + - + +
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Residues in contact with LYS 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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140A LEU* 4.0 17.1 - - + +
143A ASP* 3.9 25.0 + - + +
144A LEU* 4.0 29.6 - - + +
147A GLU* 3.1 34.3 - - - +
223A PRO* 3.0 13.9 - - + -
224A GLN* 1.3 80.2 - - + +
226A LEU* 1.3 59.7 + - - +
228A ALA* 3.6 6.4 - - - +
229A LEU* 2.8 32.1 + - - +
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Residues in contact with LEU 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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144A LEU* 3.1 30.5 - - + -
148A LEU* 5.1 0.2 - - + -
160A LEU* 5.6 0.2 - - + -
212A LEU* 3.5 27.2 - - + +
215A LEU* 3.5 40.6 - - + -
216A GLN* 3.8 23.3 - - + -
221A VAL* 4.0 17.3 - - + -
222A PRO 5.4 0.9 - - - -
223A PRO* 3.6 31.6 - - + +
224A GLN 3.3 0.4 - - - -
225A LYS* 1.3 74.7 - - - +
227A GLN* 1.3 53.5 + - - +
229A LEU 3.7 0.2 - - - -
230A GLN* 2.8 36.2 + - - +
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Residues in contact with GLN 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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216A GLN* 2.7 42.6 + - - +
223A PRO 4.2 1.5 + - - +
224A GLN* 3.3 20.1 + - + +
226A LEU* 1.3 78.5 - - - +
228A ALA* 1.3 52.2 + - - +
230A GLN* 3.0 16.1 + - - +
231A ARG* 2.8 62.9 + - - +
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Residues in contact with ALA 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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133A ILE* 4.7 4.6 - - + +
134A LEU* 4.7 8.9 - - + +
140A LEU* 4.0 17.3 - - + +
224A GLN 2.6 22.4 + - - +
225A LYS* 3.6 7.2 - - - +
227A GLN* 1.3 76.7 - - - +
229A LEU* 1.3 57.1 + - - +
231A ARG* 3.1 9.8 + - - +
232A VAL* 2.9 27.5 + - - +
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Residues in contact with LEU 229 (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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137A ALA 4.8 1.6 - - - +
140A LEU* 3.7 17.2 - - + +
141A ALA* 4.4 15.5 - - + -
144A LEU* 3.6 26.0 - - + -
164A LEU* 3.9 25.1 - - + -
173A LEU* 4.4 15.5 - - + -
212A LEU* 3.8 15.9 - - + -
225A LYS 2.8 19.2 + - - +
226A LEU 3.8 3.1 - - - +
228A ALA* 1.3 69.5 - - - +
230A GLN* 1.3 61.6 + - - +
232A VAL* 2.7 42.3 - - + +
233A LEU* 2.9 24.7 + - + +
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Residues in contact with GLN 230 (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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209A ILE* 3.8 20.2 - - + -
212A LEU* 3.4 17.9 - - + +
213A GLU* 3.2 26.5 + - + +
216A GLN* 3.1 18.5 - - - +
226A LEU 2.8 19.4 + - - +
227A GLN* 3.3 17.1 + - - +
229A LEU* 1.3 79.0 - - - +
231A ARG* 1.3 59.0 - - - +
233A LEU* 3.6 3.2 + - - +
234A GLN* 2.5 64.2 + - - +
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Residues in contact with ARG 231 (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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133A ILE* 3.5 42.4 - - + +
227A GLN* 2.8 46.0 + - - +
228A ALA* 3.5 8.0 - - - +
229A LEU 3.1 0.2 - - - -
230A GLN* 1.3 82.9 - - - +
232A VAL* 1.3 59.5 + - - +
234A GLN* 3.8 5.7 - - - +
235A SER* 2.9 26.5 + - - -
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Residues in contact with VAL 232 (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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133A ILE* 4.1 15.9 - - + +
134A LEU* 4.8 7.6 - - + -
137A ALA* 3.9 15.3 - - + -
140A LEU* 4.6 3.1 - - + -
173A LEU* 5.5 1.6 - - + -
176A HIS* 3.6 33.9 - - + +
228A ALA 2.9 10.8 + - - +
229A LEU* 2.7 52.9 - - + +
231A ARG* 1.3 76.6 - - - +
233A LEU* 1.3 62.3 + - + +
235A SER* 2.7 25.5 - - - -
238A CYS* 3.0 15.8 - - + +
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Residues in contact with LEU 233 (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* 6.0 2.2 - - + -
169A VAL* 5.9 4.0 - - + -
172A LEU* 4.6 2.9 - - + -
173A LEU* 4.4 20.6 - - + -
205A ILE* 4.0 32.2 - - + +
208A ALA* 4.1 20.4 - - + -
209A ILE* 3.8 34.1 - - + +
212A LEU* 4.3 11.4 - - + -
229A LEU* 2.9 25.2 + - + +
230A GLN 4.0 1.3 - - - +
232A VAL* 1.3 86.4 - - + +
234A GLN* 1.3 58.9 + - - +
235A SER 3.7 0.2 + - - -
238A CYS* 4.2 20.4 - - - -
239A ASN* 4.0 14.7 + - - -
242A ARG* 5.5 0.2 + - - -
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Residues in contact with GLN 234 (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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209A ILE* 3.6 34.0 - - + +
213A GLU* 3.8 8.1 + - - -
230A GLN* 2.5 47.5 + - - +
231A ARG* 4.2 6.9 - - - +
233A LEU* 1.3 76.1 - - - +
235A SER* 1.3 68.4 + - - +
236A GLU* 3.3 2.6 + - - +
239A ASN* 3.7 11.8 - - - +
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Residues in contact with SER 235 (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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131A VAL 4.4 1.6 + - - -
133A ILE* 3.6 26.9 + - - +
176A HIS* 5.0 0.6 - - - -
231A ARG 2.9 15.3 + - - -
232A VAL* 2.7 24.0 + - - -
234A GLN* 1.3 78.6 - - - +
236A GLU* 1.3 58.6 + - - +
237A PHE* 3.0 19.7 + - - +
238A CYS* 3.5 10.0 + - - +
239A ASN* 2.9 25.8 + - - +
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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