Contacts of the helix formed by residues 222 - 235 (chain A) in PDB entry 1LTQ
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 THR 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A SER* 3.2 12.6 - - - -
220A ASP* 3.2 1.9 + - - -
221A PRO* 1.3 88.1 - - + +
223A LYS* 1.3 66.8 + - - +
225A TYR* 4.1 18.6 - - + -
226A ARG* 2.7 55.9 + - - +
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Residues in contact with LYS 223 (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 GLU* 6.0 0.9 - - + -
215A SER 3.4 1.2 + - - -
216A GLY* 4.3 4.3 - - - -
217A THR* 4.4 11.8 + - + +
220A ASP* 2.6 68.4 + - - +
222A THR* 1.3 78.8 - - - +
224A TYR* 1.3 91.5 + - + +
226A ARG* 3.4 14.0 + - - +
227A MSE 3.1 43.3 + - + +
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Residues in contact with TYR 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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181A LEU* 3.4 61.7 - - + -
182A GLU* 3.8 14.9 + - - +
184A CYS* 4.9 2.9 - - - -
213A ARG* 5.1 0.9 - - + -
214A GLU* 3.2 25.6 - - + +
215A SER 2.8 7.5 + - - -
216A GLY* 3.5 16.6 - - - -
217A THR* 3.8 26.7 - - + +
223A LYS* 1.3 96.7 - - + +
225A TYR* 1.3 57.5 + - - -
226A ARG 3.2 1.1 - - - -
227A MSE 3.9 8.9 - - - +
228A THR* 2.9 37.8 + - - +
245A GLN* 3.8 4.7 - - - +
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Residues in contact with TYR 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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215A SER* 2.7 28.2 + - - +
222A THR* 3.6 23.8 - - + +
224A TYR* 1.3 72.0 - - - +
226A ARG* 1.3 62.1 + - + +
228A THR* 3.7 0.2 - - - -
229A ARG* 2.9 59.0 + - - +
243A GLN* 3.2 58.0 + - + +
244A CYS* 5.0 0.2 - - - -
245A GLN* 3.3 42.3 + - + +
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Residues in contact with ARG 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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220A ASP* 2.7 39.2 + - - -
222A THR* 2.7 58.8 + - - +
223A LYS* 3.5 16.4 + - - +
225A TYR* 1.3 79.5 - - + +
227A MSE 1.3 60.4 + - + +
229A ARG* 3.2 26.2 + - - +
230A LYS* 2.9 29.5 + - - +
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Residues in contact with MSE 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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181A LEU 3.9 21.3 - - - +
182A GLU* 4.3 16.8 - - - +
184A CYS* 4.1 13.5 - - - -
185A ASP* 4.7 22.3 - - + +
223A LYS* 3.1 34.4 + - + +
224A TYR* 3.4 13.9 + - - +
226A ARG* 1.3 74.2 - - + +
228A THR* 1.3 61.1 + - - +
230A LYS* 3.2 6.3 + - - +
231A TRP* 2.8 31.8 + - - +
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Residues in contact with THR 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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166A VAL* 4.0 28.3 - - + -
184A CYS* 4.4 0.7 - - - -
209A VAL* 5.5 0.2 - - + -
211A SER* 5.0 2.7 - - - -
213A ARG* 2.8 39.6 + - - +
224A TYR 2.9 22.5 + - - -
225A TYR 3.7 3.6 - - - -
227A MSE 1.3 77.3 - - - +
229A ARG* 1.3 57.8 + - - +
231A TRP* 3.2 5.3 + - + +
232A VAL* 2.9 34.6 + - + +
243A GLN* 3.8 13.7 - - + +
245A GLN* 4.0 10.6 + - - +
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Residues in contact with ARG 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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225A TYR* 2.9 46.7 + - + +
226A ARG* 3.2 26.8 + - - +
228A THR* 1.3 76.2 - - - +
230A LYS* 1.3 62.5 + - - +
232A VAL* 3.4 3.8 + - - +
233A GLU* 3.1 55.9 + - + +
240A LEU* 6.1 1.1 - - + -
243A GLN* 3.1 29.9 + - - +
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Residues in contact with LYS 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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226A ARG 2.9 16.8 + - - +
227A MSE 3.7 6.5 - - - +
229A ARG* 1.3 76.5 - - - +
231A TRP* 1.3 60.8 + - - +
233A GLU* 4.1 10.1 - - - +
234A ASP* 2.8 59.5 + - + +
235A ILE* 5.4 0.2 - - - -
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Residues in contact with TRP 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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166A VAL* 4.5 9.9 - - + -
170A LEU* 3.4 28.0 - - + -
171A ALA* 3.4 31.9 - - + -
184A CYS 4.1 13.7 - - - +
185A ASP* 3.9 13.2 - - - -
187A ASP* 2.7 31.4 + - + +
188A VAL 3.8 11.9 - - - -
189A ILE* 4.0 9.4 - - + -
213A ARG* 5.6 3.8 - - - +
227A MSE 2.8 22.0 + - - +
228A THR* 3.5 7.4 - - - +
230A LYS* 1.3 73.5 - - - +
232A VAL* 1.3 72.2 + - + +
235A ILE* 2.9 64.6 + - + +
236A ALA* 3.1 30.7 + - + -
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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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166A VAL* 4.5 11.9 - - + -
170A LEU* 4.9 3.6 - - + -
209A VAL* 4.6 10.1 - - + -
228A THR* 2.9 32.2 + - + +
229A ARG* 3.9 6.5 - - - +
231A TRP* 1.3 94.2 - - + +
233A GLU* 1.3 57.9 + - - +
236A ALA* 3.6 2.7 - - - +
237A GLY 2.8 23.9 + - - -
238A VAL* 3.0 39.5 + - + +
240A LEU* 4.1 21.8 - - + -
243A GLN* 5.5 0.7 - - - +
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Residues in contact with GLU 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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229A ARG* 3.1 46.2 + - + +
230A LYS* 3.7 8.5 - - - +
232A VAL* 1.3 76.1 - - - +
234A ASP* 1.3 74.8 + - - +
237A GLY* 3.3 21.0 - - - -
238A VAL 4.9 3.8 - - - +
240A LEU* 4.8 16.0 - - + +
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Residues in contact with ASP 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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230A LYS* 2.8 48.9 + - + +
233A GLU* 1.3 90.0 - - - +
235A ILE* 1.3 66.3 + - + +
237A GLY* 4.6 0.9 + - - -
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Residues in contact with ILE 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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185A ASP* 3.9 13.2 - - + +
187A ASP 4.5 5.2 - - - +
188A VAL* 5.7 0.9 - - - -
189A ILE* 4.0 21.0 - - + +
231A TRP* 2.9 58.3 + - + +
234A ASP* 1.3 81.6 - - + +
236A ALA* 1.3 63.8 + - - +
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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