Contacts of the helix formed by residues 226 - 242 (chain A) in PDB entry 1GQC
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 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ARG* 4.1 11.4 - - - +
16A LEU* 4.4 1.8 - - - -
225A ASP* 1.3 83.3 - - + +
227A PRO* 1.3 64.6 - - - +
228A ALA* 2.9 16.9 + - + +
229A CYS* 2.9 38.6 + - + +
230A LEU* 2.8 35.5 + - - +
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Residues in contact with PRO 227 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ARG* 4.8 12.3 - - + +
16A LEU* 3.7 24.2 - - + -
225A ASP 4.4 1.1 - - - +
226A THR* 1.3 89.0 - - - +
228A ALA* 1.3 61.6 + - - +
230A LEU* 3.8 15.5 + - + +
231A GLU* 3.7 21.0 + - - +
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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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226A THR* 2.9 15.6 + - + +
227A PRO* 1.3 82.6 - - - +
229A CYS* 1.3 64.1 + - - +
231A GLU* 3.5 13.9 + - - +
232A LYS* 3.8 7.3 + - - +
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Residues in contact with CYS 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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222A PRO* 5.0 8.1 - - + -
223A GLY 3.3 21.1 - - - +
226A THR* 2.9 25.9 + - + +
228A ALA* 1.3 76.0 - - - +
230A LEU* 1.3 65.8 + - - +
231A GLU 3.0 2.7 - - - -
232A LYS* 2.9 31.4 + - - +
233A VAL* 2.9 26.7 + - - +
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Residues in contact with LEU 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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16A LEU* 4.7 6.5 - - + -
22A LEU* 4.3 22.0 - - + -
24A ILE* 4.6 9.0 - - + -
223A GLY 4.6 0.6 + - - -
224A VAL* 3.5 39.2 - - + +
226A THR 2.8 20.2 + - - +
227A PRO* 3.9 15.5 - - + +
228A ALA 3.3 0.2 - - - -
229A CYS* 1.3 71.8 - - - +
231A GLU* 1.3 64.0 + - - +
233A VAL* 3.6 2.0 + - - +
234A ARG* 3.1 61.3 + - + +
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Residues in contact with GLU 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 PRO 3.7 12.1 + - - +
228A ALA* 3.5 10.6 + - - +
229A CYS 3.0 0.4 - - - -
230A LEU* 1.3 82.3 - - - +
232A LYS* 1.3 65.2 + - - +
233A VAL 3.1 1.3 - - - -
234A ARG* 3.2 35.6 + - - +
235A ALA* 3.0 24.8 + - - +
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Residues in contact with LYS 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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222A PRO* 4.1 26.5 - - + -
228A ALA 3.8 4.5 + - - +
229A CYS* 2.9 41.7 + - - +
231A GLU* 1.3 78.3 - - - +
233A VAL* 1.3 58.0 + - - +
235A ALA* 3.5 5.8 + - + +
236A LEU* 3.0 45.9 + - + +
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Residues in contact with VAL 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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24A ILE* 4.2 10.1 - - + -
100A PRO* 3.8 27.8 - - + -
101A MET* 4.3 12.7 - - + +
222A PRO* 3.7 30.3 - - + +
223A GLY 4.1 7.2 - - - +
224A VAL* 3.8 20.6 - - + -
229A CYS 2.9 16.7 + - - +
230A LEU 3.6 8.5 - - - +
231A GLU 3.1 0.2 - - - -
232A LYS* 1.3 75.6 - - - +
234A ARG* 1.3 60.3 + - - +
236A LEU* 4.0 4.7 - - - +
237A MET* 2.8 35.4 + - + +
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Residues in contact with ARG 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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22A LEU* 4.6 7.9 - - - +
23A ASP* 2.9 42.7 + - - +
24A ILE* 4.3 19.3 - - + +
25A VAL* 4.2 7.3 - - + +
230A LEU* 3.1 43.6 + - + +
231A GLU* 3.2 32.0 + - - +
233A VAL* 1.3 74.3 - - - +
235A ALA* 1.3 60.0 + - - +
237A MET* 3.8 4.7 - - - +
238A ALA* 2.9 34.0 + - - +
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Residues in contact with ALA 235 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A GLU 3.0 17.0 + - - +
232A LYS* 3.6 7.4 - - + +
234A ARG* 1.3 78.0 - - - +
236A LEU* 1.3 63.1 + - + +
238A ALA* 3.4 4.1 + - - +
239A GLN* 2.8 30.9 + - - +
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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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101A MET* 3.3 28.9 - - + -
221A GLY* 5.5 0.4 - - - -
222A PRO* 4.1 21.5 - - + -
232A LYS* 3.0 29.5 + - + +
233A VAL 4.0 0.4 - - - +
235A ALA* 1.3 80.9 - - + +
237A MET* 1.3 67.1 + - - +
239A GLN* 2.8 12.8 + - + +
240A GLU* 2.8 28.0 + - + +
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Residues in contact with MET 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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24A ILE* 3.8 23.6 - - + -
25A VAL* 4.4 7.0 - - + -
32A HIS* 4.1 28.0 - - + -
36A ARG* 3.4 26.2 - - - -
100A PRO* 3.5 47.6 - - + +
101A MET* 3.9 16.0 - - - +
233A VAL* 2.8 25.5 + - + +
234A ARG 3.8 2.5 - - - +
236A LEU* 1.3 74.1 - - - +
238A ALA* 1.3 60.8 + - - +
240A GLU* 3.3 18.9 - - - +
241A LEU* 3.4 13.5 + - + +
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Residues in contact with ALA 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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25A VAL* 3.8 19.0 - - + +
234A ARG 2.9 19.4 + - - +
235A ALA* 3.8 3.8 - - - +
237A MET* 1.3 75.1 - - - +
239A GLN* 1.3 65.8 + - - +
241A LEU* 3.2 25.3 + - + +
242A ALA* 3.4 6.1 + - - +
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Residues in contact with GLN 239 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A ALA 2.8 18.8 + - - +
236A LEU* 3.3 13.9 - - + +
238A ALA* 1.3 76.9 - - - +
240A GLU* 1.3 62.5 + - - +
242A ALA* 3.1 32.5 + - + +
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Residues in contact with GLU 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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36A ARG* 3.3 30.4 + - - +
101A MET* 3.7 30.6 - - + +
236A LEU* 2.8 13.1 + - + +
237A MET* 3.3 12.1 - - - +
238A ALA 3.1 0.2 - - - -
239A GLN* 1.3 74.0 - - - +
241A LEU* 1.3 67.4 + - + +
242A ALA 3.0 7.9 + - - -
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Residues in contact with LEU 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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25A VAL* 4.2 27.1 - - + +
32A HIS* 6.4 0.9 - - + -
237A MET* 3.6 14.8 - - + +
238A ALA* 3.2 20.3 + - + +
240A GLU* 1.3 78.8 - - + +
242A ALA* 1.3 62.9 + - - +
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Residues in contact with ALA 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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238A ALA 3.4 4.9 + - - +
239A GLN* 3.1 29.1 + - + +
240A GLU 3.0 8.4 - - - -
241A LEU* 1.3 84.1 - - - +
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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