Contacts of the helix formed by residues 221 - 232 (chain A) in PDB entry 1PT6
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 MET 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A TYR* 3.3 11.2 - - + -
187A GLY 2.9 23.0 + - - +
188A GLU* 3.5 23.3 - - + +
189A ASN 5.5 0.2 - - - +
219A GLN* 5.1 3.6 - - + -
220A THR* 1.3 71.7 - - - +
222A THR* 1.3 59.3 + - - +
223A ALA 3.3 2.7 - - - -
224A LEU* 3.1 24.0 + - + -
225A GLY 2.9 24.3 + - - -
257A HIS* 4.2 24.2 - - - -
258A ASP* 3.4 31.4 - - + +
261A ARG* 5.6 3.4 - - - +
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Residues in contact with THR 222 (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 TYR* 2.7 32.8 + - + +
220A THR* 3.3 17.7 + - - +
221A MET* 1.3 73.1 - - - +
223A ALA* 1.3 61.2 + - - +
226A THR* 2.9 44.0 + - - +
250A ILE* 4.2 9.4 - - + -
252A THR* 3.8 7.6 + - + +
254A GLY 4.5 2.3 + - - -
256A SER* 3.7 15.4 - - - -
258A ASP* 3.6 1.6 + - - -
262A LEU* 4.7 2.7 - - + -
298A GLU* 5.0 2.1 + - - +
299A ILE* 5.7 0.2 - - - +
302A ILE* 3.7 29.6 - - + -
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Residues in contact with ALA 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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222A THR* 1.3 79.8 - - - +
224A LEU* 1.3 55.3 + - - +
226A THR* 3.9 1.1 - - - -
227A ASP* 2.9 33.6 + - - +
258A ASP* 3.2 39.3 + - + +
261A ARG* 4.1 13.2 - - + +
262A LEU* 3.9 30.1 - - + +
265A VAL* 3.7 8.1 - - + +
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Residues in contact with LEU 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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188A GLU 4.1 7.9 - - - +
189A ASN* 3.9 22.7 - - - +
190A VAL* 3.5 26.2 - - + +
221A MET* 3.1 27.9 + - + +
223A ALA* 1.3 76.7 - - - +
225A GLY* 1.3 58.1 + - - +
227A ASP* 4.5 2.7 - - + +
228A THR* 2.7 45.6 + - - +
258A ASP* 3.3 7.6 + - - +
261A ARG* 4.3 17.0 - - - +
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Residues in contact with GLY 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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148A VAL* 3.7 12.4 - - - +
184A VAL* 4.3 4.7 - - - +
186A TYR* 3.9 15.3 - - - -
190A VAL* 3.7 16.5 - - - +
221A MET 2.9 14.7 + - - -
222A THR 3.3 1.7 + - - -
224A LEU* 1.3 76.1 - - - +
226A THR* 1.3 57.3 + - - +
228A THR* 3.4 2.6 + - - -
229A ALA* 3.0 27.2 + - - +
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Residues in contact with THR 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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148A VAL* 3.9 6.4 - - - +
222A THR* 2.9 28.9 + - - +
223A ALA* 3.9 1.3 - - - -
225A GLY* 1.3 76.0 - - - +
227A ASP* 1.3 56.1 + - - +
229A ALA* 3.2 7.0 + - - +
230A ARG* 3.0 24.1 + - - +
248A MET* 3.5 25.7 - - + +
250A ILE* 4.1 18.4 - - + +
262A LEU* 5.1 1.8 - - - +
265A VAL* 3.6 20.6 - - + -
266A ILE* 4.4 13.9 - - + -
269A CYS* 4.1 8.1 - - - -
276A ARG* 5.2 0.4 - - - -
302A ILE* 5.1 1.2 - - - +
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Residues in contact with ASP 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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223A ALA 2.9 21.4 + - - +
224A LEU* 4.0 3.8 - - + +
226A THR* 1.3 75.6 - - - +
228A THR* 1.3 57.0 + - - +
230A ARG* 2.8 37.5 + - - +
231A LYS* 2.9 54.8 + - - +
261A ARG* 3.3 22.2 + - - +
265A VAL* 3.7 21.8 - - + +
268A ASP* 4.7 0.7 - - - +
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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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184A VAL* 4.7 6.3 - - + -
190A VAL* 3.6 33.6 - - + +
192A HIS* 3.8 13.2 - - + +
224A LEU* 2.7 29.1 + - - +
225A GLY 3.6 3.6 - - - -
227A ASP* 1.3 75.1 - - - +
229A ALA* 1.3 59.8 + - - +
231A LYS* 4.5 13.3 + - - +
232A GLU* 3.0 47.7 + - - +
233A ALA* 3.2 6.4 + - - +
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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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146A VAL* 3.9 13.0 - - + -
148A VAL* 3.6 31.0 - - + -
184A VAL* 4.6 4.2 - - + +
225A GLY 3.0 8.2 + - - +
226A THR 3.4 9.2 - - - +
228A THR* 1.3 75.6 - - - +
230A ARG* 1.3 64.0 + - - +
233A ALA* 3.3 10.2 + - - +
234A PHE* 3.0 31.2 + - - -
248A MET* 3.6 10.5 - - + -
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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 THR 3.0 13.6 + - - +
227A ASP* 2.8 36.4 + - - +
229A ALA* 1.3 79.9 - - - +
231A LYS* 1.3 83.1 + - - +
234A PHE* 3.6 23.7 - - - +
235A THR* 5.0 0.2 - - - +
246A LYS* 5.3 0.5 + - - -
248A MET* 3.9 5.3 - - - +
265A VAL 4.7 1.2 + - - -
268A ASP* 3.5 44.4 + - - +
269A CYS* 4.0 11.4 - - - +
272A GLU* 2.8 52.5 + - - +
274A ILE* 3.8 14.5 - - + +
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Residues in contact with LYS 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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227A ASP* 2.9 33.3 + - - +
228A THR* 4.6 9.3 + - - +
230A ARG* 1.3 106.9 - - - +
232A GLU* 1.3 85.9 + - + +
235A THR* 3.0 19.0 - - - +
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Residues in contact with GLU 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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190A VAL* 5.7 0.9 - - - +
192A HIS* 2.7 37.0 + - + +
228A THR* 3.0 24.2 + - - +
230A ARG 3.5 0.2 - - - -
231A LYS* 1.3 104.0 + - - +
233A ALA* 1.3 64.2 + - - +
234A PHE 3.3 1.1 - - - -
235A THR* 2.6 28.3 + - - -
238A ARG* 3.4 18.9 + - - +
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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