Contacts of the helix formed by residues 223 - 237 (chain A) in PDB entry 1GPU
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 ASP 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A VAL* 4.7 6.4 - - + +
218A GLU 5.9 0.3 + - - -
219A ASN* 2.9 30.1 + - + +
220A GLY 4.7 0.6 - - - -
222A GLU* 1.3 74.2 - - - +
224A LEU* 1.3 63.9 + - - +
225A ALA* 3.8 7.8 + - - +
226A GLY* 3.2 26.5 + - - -
227A ILE* 3.0 27.7 + - - +
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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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4A PHE* 3.3 43.6 - - + -
8A ASP* 4.2 17.5 - - + -
9A LYS* 4.7 14.4 - - + -
12A VAL* 4.4 15.7 - - + -
39A PRO* 3.8 32.3 - - + +
42A HIS* 4.8 2.2 - - + -
43A VAL* 3.8 18.6 - - + +
222A GLU* 2.8 21.3 + - - +
223A ASP* 1.3 71.5 - - - +
225A ALA* 1.3 57.9 + - - +
227A ILE* 3.3 5.3 + - + +
228A ALA* 2.9 24.3 + - - +
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Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN* 6.2 2.0 - - - +
4A PHE* 3.7 16.2 - - + -
223A ASP* 3.3 7.3 + - - +
224A LEU* 1.3 77.2 - - - +
226A GLY* 1.3 53.8 + - - +
228A ALA* 3.2 3.2 + - - +
229A LYS* 2.7 35.4 + - - +
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Residues in contact with GLY 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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217A VAL* 3.8 10.6 - - - +
223A ASP* 3.2 28.6 + - - -
225A ALA* 1.3 76.8 - - - +
227A ILE* 1.3 63.0 + - - +
229A LYS* 3.3 8.4 + - - +
230A ALA* 3.0 24.1 + - - +
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Residues in contact with ILE 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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39A PRO* 4.1 8.7 - - + +
40A ALA* 3.9 37.0 - - + +
43A VAL* 3.9 19.3 - - + -
183A ILE* 4.9 5.4 - - + -
217A VAL* 3.9 23.3 - - + +
220A GLY* 4.1 13.0 - - - +
223A ASP 3.0 19.2 + - - +
224A LEU* 3.6 9.2 - - - +
226A GLY* 1.3 74.1 - - - +
228A ALA* 1.3 64.3 + - - +
230A ALA* 3.2 4.3 + - - +
231A ILE* 3.1 37.6 + - + +
244A ILE* 6.4 1.6 - - + -
246A MET* 4.0 16.4 - - - -
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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
----------------------------------------------------------
4A PHE* 3.6 25.8 - - + -
43A VAL* 3.6 11.2 - - + +
47A GLN* 6.3 1.3 - - + -
224A LEU 2.9 16.8 + - - +
225A ALA* 3.5 5.4 - - - +
227A ILE* 1.3 78.0 - - - +
229A LYS* 1.3 56.3 + - - +
231A ILE* 3.4 6.4 + - - +
232A ALA* 3.0 28.7 + - - +
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Residues in contact with LYS 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 ALA 2.7 19.9 + - - +
226A GLY* 3.6 8.3 - - - +
227A ILE 3.2 0.2 - - - -
228A ALA* 1.3 73.5 - - - +
230A ALA* 1.3 57.4 + - - +
232A ALA* 3.3 8.4 + - + +
233A GLN* 2.9 39.3 + - + +
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Residues in contact with ALA 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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215A LEU* 3.3 23.7 - - + +
216A TYR 4.8 2.7 - - - +
217A VAL* 3.9 8.5 - - + -
226A GLY 3.0 13.4 + - - +
227A ILE 3.2 8.5 + - - +
229A LYS* 1.3 76.7 - - - +
231A ILE* 1.3 58.3 + - - +
233A GLN* 3.3 1.6 + - - -
234A ALA* 2.9 26.0 + - - +
244A ILE* 3.7 33.9 - - + -
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Residues in contact with ILE 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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43A VAL* 4.1 8.7 - - + -
44A LEU* 4.0 33.0 - - + -
47A GLN* 3.5 31.9 - - + +
152A TYR* 4.2 17.5 - - + +
181A ILE* 4.3 2.4 - - + +
183A ILE* 4.3 9.6 - - + -
227A ILE* 3.1 30.9 + - + +
228A ALA* 3.6 7.0 - - - +
229A LYS 3.3 0.2 - - - -
230A ALA* 1.3 74.8 - - - +
232A ALA* 1.3 63.2 + - - +
234A ALA* 3.2 13.9 + - - +
235A LYS* 3.2 16.7 + - - +
244A ILE* 4.1 17.3 - - + -
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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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228A ALA 3.0 14.3 + - - +
229A LYS* 3.3 12.3 + - + +
231A ILE* 1.3 78.0 - - - +
233A GLN* 1.3 61.3 + - - +
235A LYS* 3.2 24.8 + - - +
236A LEU* 3.5 13.0 + - - +
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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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213A GLU* 4.0 9.2 + - - +
215A LEU* 3.7 24.5 - - + -
229A LYS* 2.9 29.0 + - + +
230A ALA* 3.6 5.6 - - - +
232A ALA* 1.3 75.8 - - - +
234A ALA* 1.3 65.1 + - - +
236A LEU* 3.0 46.1 + - - +
237A SER* 3.6 6.8 + - - -
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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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178A GLY 4.2 6.8 - - - +
181A ILE* 3.6 27.0 - - + +
213A GLU* 3.8 4.9 - - - -
215A LEU* 3.9 0.4 - - - +
230A ALA 2.9 14.6 + - - +
231A ILE* 3.2 10.7 + - - +
233A GLN* 1.3 76.9 - - - +
235A LYS* 1.3 60.6 + - - +
237A SER* 2.9 22.7 + - - +
242A THR* 3.7 35.3 + - + -
244A ILE* 4.7 0.7 - - + -
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Residues in contact with LYS 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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47A GLN* 3.0 30.0 + - - +
61A ASP* 5.5 1.6 + - - -
150A TYR* 3.5 52.7 + - + +
152A TYR* 3.0 25.5 + - - -
178A GLY 5.2 2.0 - - - +
179A ASN* 5.6 0.5 - - - +
181A ILE* 4.0 5.4 - - + -
231A ILE* 3.4 14.8 - - - +
232A ALA* 3.2 13.6 + - - +
233A GLN 3.1 0.6 - - - -
234A ALA* 1.3 76.0 - - - +
236A LEU* 1.3 65.4 + - + +
237A SER 3.4 1.0 + - - -
238A LYS* 3.8 15.8 + - - +
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Residues in contact with LEU 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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232A ALA 3.6 15.3 - - - +
233A GLN* 3.0 36.3 + - - +
235A LYS* 1.3 80.9 - - + +
237A SER* 1.3 57.7 + - - +
238A LYS* 3.1 17.1 + - - +
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Residues in contact with SER 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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178A GLY* 3.7 7.6 - - - +
213A GLU* 2.5 41.9 + - - -
233A GLN* 3.6 1.8 + - - -
234A ALA 2.9 15.9 + - - +
235A LYS 4.5 0.7 - - - -
236A LEU* 1.3 74.0 - - - +
238A LYS* 1.3 57.3 + - - +
239A ASP* 3.1 17.2 + - - -
240A LYS* 3.1 26.3 - - - +
242A THR* 3.2 3.8 + - - -
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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