Contacts of the helix formed by residues 223 - 235 (chain A) in PDB entry 1TJY
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 ASN 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A LEU* 4.9 0.2 - - - +
39A VAL* 3.7 32.9 - - - +
195A ASN* 3.1 51.2 + - - +
196A ASP 4.6 1.3 - - - +
197A ALA* 4.7 13.7 + - - +
200A SER* 4.2 11.7 - - - +
221A ASP* 3.0 7.8 + - - +
222A ALA* 1.3 78.3 - - - +
224A ALA* 1.3 64.1 + - - +
225A LEU 3.3 2.0 - - - -
226A PRO* 3.4 6.4 - - - +
227A ALA* 3.2 23.2 + - - +
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Residues in contact with ALA 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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158A PHE* 3.3 57.3 - - + +
159A TYR* 4.0 6.3 - - - -
193A GLY* 5.9 0.4 - - - +
200A SER* 4.5 4.0 + - - +
219A ALA* 4.1 2.7 - - + -
221A ASP* 2.9 24.3 + - + +
223A ASN* 1.3 76.9 - - - +
225A LEU* 1.3 58.2 + - - +
227A ALA 3.3 0.7 + - - -
228A ALA* 2.9 27.2 + - - +
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Residues in contact with LEU 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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219A ALA* 3.8 13.8 - - + +
221A ASP 3.1 14.5 + - - +
224A ALA* 1.3 76.1 - - - +
226A PRO* 1.3 68.8 - - + +
228A ALA* 3.2 2.9 + - - +
229A ALA* 3.1 19.9 + - - +
242A ILE* 3.7 20.9 - - + +
243A VAL* 3.7 29.2 - - - +
244A GLY 3.7 13.0 - - - -
245A PHE 3.9 4.3 - - - +
246A SER* 3.9 8.1 - - - -
251A MET* 3.7 25.6 - - + -
260A VAL* 4.7 1.3 - - + -
263A PHE* 3.6 29.8 - - + -
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Residues in contact with PRO 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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222A ALA 3.0 28.7 - - - +
223A ASN* 3.4 11.2 - - - +
225A LEU* 1.3 92.6 - - + +
227A ALA* 1.3 54.1 + - - -
229A ALA* 3.3 3.8 + - + +
230A GLN* 2.9 30.1 + - - +
250A VAL* 3.7 20.9 - - + -
251A MET* 3.8 14.4 - - - -
254A TYR* 3.8 26.8 - - + +
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Residues in contact with ALA 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PHE* 4.3 1.1 - - + -
197A ALA* 4.9 2.5 - - - +
200A SER* 3.5 38.4 - - - +
201A LEU* 3.7 11.3 - - + +
204A ALA* 3.7 2.2 - - - +
223A ASN 3.2 20.6 + - - +
224A ALA 3.6 3.6 - - - +
226A PRO* 1.3 76.2 - - - +
228A ALA* 1.3 59.4 + - - +
230A GLN* 3.4 4.7 + - - -
231A ALA* 2.8 31.4 + - - +
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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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158A PHE* 4.2 6.7 - - + -
204A ALA* 3.8 11.6 - - + +
208A ILE* 4.2 2.6 - - - +
217A ILE* 4.2 28.0 - - + -
219A ALA* 5.0 0.7 - - + -
224A ALA 2.9 18.0 + - - +
225A LEU* 3.2 6.7 + - - +
227A ALA* 1.3 76.2 - - - +
229A ALA* 1.3 63.3 + - - +
231A ALA* 3.4 2.6 + - - +
232A ALA* 3.0 23.2 + - - +
242A ILE* 3.8 19.0 - - + +
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Residues in contact with ALA 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 LEU 3.1 10.3 + - - +
226A PRO* 3.6 6.3 - - + +
228A ALA* 1.3 77.2 - - - +
230A GLN* 1.3 62.0 + - - +
232A ALA 3.3 1.4 + - - -
233A GLU* 3.1 26.2 + - - +
242A ILE* 4.0 5.5 - - - +
251A MET* 4.7 0.2 - - + -
254A TYR* 3.5 30.5 - - + -
259A THR* 3.5 14.9 - - + +
260A VAL* 3.7 23.1 - - + -
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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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201A LEU* 3.9 20.0 - - + -
226A PRO 2.9 17.6 + - - +
227A ALA* 3.8 5.2 - - - +
229A ALA* 1.3 75.4 - - - +
231A ALA* 1.3 59.2 + - - +
233A GLU* 3.2 16.1 + - - +
234A ASN* 2.8 63.2 + - - +
254A TYR* 2.7 35.0 + - - +
257A ARG* 4.2 4.0 + - - -
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Residues in contact with ALA 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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201A LEU* 3.7 8.0 - - + +
204A ALA* 3.5 24.7 - - + -
205A GLU* 3.6 27.6 - - + +
208A ILE* 3.9 6.1 - - + -
227A ALA 2.8 19.1 + - - +
228A ALA 3.6 3.4 - - - +
229A ALA 3.3 0.2 - - - -
230A GLN* 1.3 76.8 - - - +
232A ALA* 1.3 61.1 + - - +
234A ASN* 3.6 2.0 - - - +
235A LEU* 3.0 30.1 + - - +
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Residues in contact with ALA 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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208A ILE* 3.6 14.7 - - + +
228A ALA 3.0 12.8 + - - +
229A ALA 3.3 8.0 + - - +
231A ALA* 1.3 76.4 - - - +
233A GLU* 1.3 58.7 + - - +
235A LEU 3.5 0.3 + - - -
236A LYS* 3.0 7.8 + - - -
237A ARG* 2.9 47.5 + - + +
240A LEU* 4.5 3.4 - - + -
242A ILE* 3.7 20.6 - - + -
259A THR* 4.3 5.8 - - + -
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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 ALA 3.1 12.5 + - - +
230A GLN* 3.6 18.5 + - - +
232A ALA* 1.3 74.3 - - - +
234A ASN* 1.3 64.9 + - - +
236A LYS* 3.1 18.7 + - - +
254A TYR* 3.5 14.8 - - - -
257A ARG* 3.0 44.2 + - - +
259A THR* 2.5 35.7 + - + +
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Residues in contact with ASN 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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201A LEU* 4.0 15.1 - - - +
205A GLU* 3.0 29.1 - - - +
230A GLN* 2.8 48.1 + - - +
231A ALA 3.6 3.1 - - - +
233A GLU* 1.3 77.4 - - - +
235A LEU* 1.3 62.3 + - + +
236A LYS* 3.4 11.3 + - - +
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Residues in contact with LEU 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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205A GLU* 3.7 43.3 - - + +
208A ILE* 3.7 29.4 - - + -
209A LYS* 3.6 31.0 - - + -
231A ALA 3.0 17.8 + - - +
232A ALA 4.3 1.8 - - - +
234A ASN* 1.3 79.5 - - + +
236A LYS* 1.3 71.1 - - - +
237A ARG* 3.2 3.3 + - + +
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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