Contacts of the helix formed by residues 224 - 242 (chain A) in PDB entry 3TJJ
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 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A PHE* 4.7 2.0 - - - -
223A ARG* 1.3 76.1 - - - +
225A VAL* 1.3 62.9 + - - +
226A ASP* 3.3 9.9 + - - +
227A GLU* 3.0 21.8 + - - +
228A THR* 2.8 27.1 + - - -
227B GLU* 3.8 21.9 + - - -
230B ARG* 3.8 16.5 - - - +
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Residues in contact with VAL 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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130A ALA* 4.0 15.9 - - + +
131A PHE* 3.8 52.7 - - + +
134A ARG* 3.5 38.6 - - + +
138A PHE* 3.9 15.8 - - + -
223A ARG 4.2 1.2 + - - +
224A SER* 1.3 70.3 + - - +
226A ASP* 1.3 57.1 + - - +
228A THR* 3.1 3.5 + - - -
229A LEU* 2.9 39.4 + - + +
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Residues in contact with ASP 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ARG* 2.8 38.0 + - - -
224A SER* 3.3 7.4 + - - +
225A VAL* 1.3 77.7 - - - +
227A GLU* 1.3 61.9 + - - +
229A LEU* 3.4 8.4 + - - +
230A ARG* 3.0 22.9 + - - +
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Residues in contact with GLU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A SER* 3.0 14.9 + - - +
226A ASP* 1.3 77.3 - - - +
228A THR* 1.3 62.1 + - - +
230A ARG* 2.8 48.6 + - - +
231A LEU* 3.1 36.7 + - + +
215B THR* 6.0 1.7 - - - +
223B ARG* 5.5 0.3 - - - -
224B SER* 3.9 5.2 + - - -
227B GLU* 3.7 55.6 - - + +
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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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112A VAL* 3.6 42.2 - - + -
131A PHE* 3.7 17.0 - - + -
138A PHE* 4.0 7.4 - - + -
202A LEU* 3.7 19.8 - - + +
204A ILE* 4.5 2.9 - - + -
223A ARG* 5.2 0.3 - - - +
224A SER 2.8 15.3 + - - -
225A VAL 3.1 8.1 + - - -
227A GLU* 1.3 78.0 - - - +
229A LEU* 1.3 57.7 + - - +
231A LEU* 3.2 10.2 + - - +
232A VAL* 3.0 29.3 + - + +
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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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134A ARG* 3.6 7.9 - - - +
137A GLU* 3.5 43.1 - - + +
138A PHE* 3.1 41.7 - - + -
141A ILE* 4.5 6.7 - - + -
225A VAL* 2.9 34.8 + - + +
226A ASP* 3.5 7.2 - - - +
228A THR* 1.3 75.2 - - - +
230A ARG* 1.3 59.1 + - - +
232A VAL* 4.0 3.0 - - - +
233A GLN* 2.9 50.3 + - - +
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Residues in contact with ARG 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 ASP 3.0 13.8 + - - +
227A GLU* 2.8 47.2 + - - +
229A LEU* 1.3 75.3 - - - +
231A LEU* 1.3 78.9 + - - +
233A GLN* 3.9 9.8 + - - +
234A ALA* 3.0 27.6 + - + +
217B ASN* 4.8 0.4 - - - +
221B VAL* 4.5 9.9 - - - +
222B GLY 3.0 31.7 + - - +
223B ARG* 4.0 3.4 + - - +
224B SER* 3.8 25.3 - - - +
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Residues in contact with LEU 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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202A LEU* 5.7 2.2 - - + -
204A ILE* 3.5 27.4 - - + -
213A GLN* 4.0 25.8 - - + +
215A THR* 5.0 3.1 - - - +
227A GLU* 3.1 36.3 + - + +
228A THR* 3.6 4.9 - - - +
229A LEU 3.2 0.2 - - - -
230A ARG* 1.3 101.8 - - - +
232A VAL* 1.3 56.7 + - - +
234A ALA* 3.2 5.8 + - - +
235A PHE* 2.9 37.8 + - + -
215B THR* 6.4 0.2 - - + -
217B ASN* 3.8 14.8 - - - +
221B VAL* 3.7 19.7 - - + -
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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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110A TYR* 4.2 11.0 - - + -
112A VAL* 3.9 27.6 - - + -
138A PHE* 4.8 2.9 - - + -
141A ILE* 4.0 11.2 - - + -
143A THR* 3.3 29.2 - - + +
204A ILE* 4.1 20.2 - - + -
228A THR 3.0 20.8 + - - +
229A LEU* 4.0 4.0 - - - +
231A LEU* 1.3 74.6 - - - +
233A GLN* 1.3 63.4 + - - +
235A PHE* 3.2 8.9 + - - +
236A GLN* 3.0 36.2 + - - +
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Residues in contact with GLN 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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137A GLU 5.4 1.2 + - - -
141A ILE* 3.8 33.3 - - + +
229A LEU* 2.9 38.2 + - - +
230A ARG* 3.9 7.9 - - - +
232A VAL* 1.3 77.2 - - - +
234A ALA* 1.3 55.4 + - - +
236A GLN* 3.4 9.6 + - - +
237A TYR* 2.9 30.5 + - - +
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Residues in contact with ALA 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 ARG* 3.0 24.3 + - + +
231A LEU 3.6 3.6 - - - +
233A GLN* 1.3 72.9 - - - +
235A PHE* 1.3 64.7 + - - +
237A TYR* 3.8 5.5 - - - +
238A THR* 2.8 34.6 + - + +
220B PRO 5.6 0.2 - - - +
221B VAL* 3.6 27.6 - - + -
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Residues in contact with PHE 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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110A TYR* 3.4 21.3 - - + +
204A ILE* 4.3 10.8 - - + -
212A ARG* 3.2 56.8 - - + -
213A GLN* 3.8 27.6 - - + -
231A LEU* 2.9 37.9 + - + +
232A VAL 3.8 3.1 - - - +
234A ALA* 1.3 76.3 - - - +
236A GLN* 1.3 58.0 + - - +
238A THR* 3.2 3.6 + - - -
239A ASP* 2.9 34.1 + - - +
217B ASN* 4.9 1.1 - - + -
218B ASP* 3.9 19.7 - - + -
220B PRO* 5.0 0.7 - - + -
221B VAL* 3.4 31.9 - - + -
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Residues in contact with GLN 236 (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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110A TYR* 3.7 30.0 - - + +
141A ILE* 2.7 47.6 + - - +
142A ASN* 4.4 8.5 + - - +
143A THR* 3.6 10.1 + - - -
232A VAL* 3.0 23.1 + - - +
233A GLN* 3.8 7.2 - - - +
235A PHE* 1.3 79.0 - - - +
237A TYR* 1.3 60.7 + - - +
239A ASP* 3.6 8.7 - - - +
240A LYS* 3.2 24.3 + - - +
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Residues in contact with TYR 237 (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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233A GLN 2.9 18.6 + - - +
234A ALA* 3.8 7.0 - - - +
235A PHE 3.3 0.2 - - - -
236A GLN* 1.3 77.6 - - - +
238A THR* 1.3 61.4 + - + +
240A LYS* 3.3 2.0 + - - -
241A HIS* 2.7 82.6 + + + +
242A GLY 5.4 2.7 - - - -
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Residues in contact with THR 238 (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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212A ARG* 5.2 0.3 + - - -
234A ALA* 2.8 26.2 + - + +
235A PHE* 3.2 12.0 + - - -
237A TYR* 1.3 83.2 - - + +
239A ASP* 1.3 61.0 + - - +
242A GLY* 2.9 45.8 + - - +
220B PRO* 3.5 46.9 - - + +
221B VAL* 4.1 0.7 - - + +
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Residues in contact with ASP 239 (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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110A TYR* 2.4 33.6 + - - -
206A ASP* 4.7 1.4 - - - +
207A ASP* 4.4 5.9 - - - +
212A ARG* 2.9 27.2 + - - -
235A PHE 2.9 22.4 + - - +
236A GLN* 3.6 7.0 - - - +
238A THR* 1.3 77.2 + - - +
240A LYS* 1.3 60.6 + - + +
242A GLY 4.8 0.3 + - - -
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Residues in contact with LYS 240 (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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236A GLN 3.2 15.1 + - - +
237A TYR* 3.8 3.4 - - - +
238A THR 3.2 0.4 - - - -
239A ASP* 1.3 80.6 - - - +
241A HIS* 1.3 95.0 + - + +
242A GLY 3.7 0.7 - - - -
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Residues in contact with HIS 241 (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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237A TYR* 2.7 75.5 + + + +
240A LYS* 1.3 115.3 + - + +
242A GLY* 1.3 63.0 + - - +
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Residues in contact with GLY 242 (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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237A TYR* 5.3 3.1 - - - -
238A THR* 2.9 40.7 + - - +
239A ASP 4.6 0.6 + - - -
240A LYS 3.7 1.6 - - - -
241A HIS* 1.3 84.0 - - - +
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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