Contacts of the helix formed by residues 221 - 235 (chain A) in PDB entry 2GDZ
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 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 VAL* 4.2 0.4 - - - -
187A ASN* 5.2 5.7 + - - +
219A ILE* 4.8 4.8 - - - +
220A LEU* 1.3 75.2 - - - +
222A PRO* 1.4 72.8 - - + +
223A PRO* 3.9 11.7 - - + -
224A LEU* 3.0 41.2 + - + +
225A ILE* 3.9 3.5 + - - +
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Residues in contact with PRO 222 (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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16A GLY* 4.3 11.2 - - - +
17A ILE* 4.4 5.7 - - - +
20A ALA* 3.7 22.6 - - + +
186A VAL* 3.8 21.5 - - + -
187A ASN* 3.8 25.8 - - + +
188A THR* 4.4 7.0 - - + -
220A LEU 4.1 1.1 - - - +
221A ASP* 1.4 81.4 - - + +
223A PRO* 1.4 72.0 - - + +
225A ILE* 2.9 18.7 + - + +
226A ALA 3.2 8.5 + - - -
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Residues in contact with PRO 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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20A ALA* 4.1 7.6 - - + -
23A GLU* 6.0 2.2 - - - +
221A ASP* 3.3 13.2 - - + -
222A PRO* 1.4 97.4 - - + +
224A LEU* 1.3 59.6 + - + +
226A ALA* 3.1 11.7 + - + +
227A ASN* 2.9 35.7 + - - +
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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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220A LEU* 4.0 22.2 - - + -
221A ASP* 3.2 44.9 - - + +
223A PRO* 1.3 79.3 - - + +
225A ILE* 1.3 69.3 + - + +
227A ASN* 3.3 28.9 + - - +
228A GLY 3.4 8.1 + - - -
245A ILE* 4.1 11.5 - - + +
251A ILE* 4.4 4.0 - - - +
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Residues in contact with ILE 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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17A ILE* 4.0 11.4 - - + -
21A PHE* 3.6 25.1 - - + -
136A MET* 4.4 0.9 - - + -
181A ILE* 4.2 12.6 - - + +
183A PRO* 3.9 29.4 - - + -
186A VAL* 3.8 39.5 - - + -
220A LEU* 4.0 12.8 - - + -
221A ASP 4.2 1.8 - - - +
222A PRO* 2.9 10.9 + - + +
224A LEU* 1.3 75.6 - - - +
226A ALA* 1.3 64.4 + - - +
228A GLY* 3.0 13.2 + - - -
229A LEU 3.1 9.5 + - - -
245A ILE* 3.9 23.4 - - + +
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Residues in contact with ALA 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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20A ALA 3.6 15.9 - - - +
21A PHE* 3.6 20.0 - - + -
24A ALA* 3.6 28.0 - - + -
222A PRO 3.2 6.2 + - - +
223A PRO* 3.1 14.3 + - + +
225A ILE* 1.3 75.7 - - - +
227A ASN* 1.3 62.8 + - - +
229A LEU* 3.0 4.0 + - - +
230A ILE* 3.0 27.3 + - - +
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Residues in contact with ASN 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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24A ALA* 6.0 0.9 - - - +
223A PRO* 2.9 22.8 + - - +
224A LEU* 3.4 28.8 - - - +
225A ILE 3.2 0.4 - - - -
226A ALA* 1.3 74.6 - - - +
228A GLY* 1.3 61.4 + - - +
230A ILE* 3.3 8.2 + - - +
231A THR* 2.9 27.4 + - - +
251A ILE* 3.9 12.1 - - + -
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Residues in contact with GLY 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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181A ILE* 4.4 1.6 - - - -
224A LEU 3.4 4.2 + - - -
225A ILE 3.0 8.9 + - - -
227A ASN* 1.3 77.7 - - - +
229A LEU* 1.3 65.0 + - - +
231A THR* 3.2 3.9 + - - -
232A LEU* 3.0 19.6 + - - +
243A MET* 3.4 31.4 - - - +
245A ILE* 4.0 4.5 - - - -
251A ILE* 3.5 12.5 - - - +
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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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21A PHE* 3.6 48.9 - - + +
24A ALA* 5.9 0.2 - - + -
25A LEU* 4.0 26.0 - - + -
89A VAL* 3.9 15.9 - - + -
134A ILE* 3.7 43.7 - - + -
181A ILE* 4.0 9.5 - - + +
225A ILE 3.1 4.9 + - - -
226A ALA* 3.0 9.8 + - + +
228A GLY* 1.3 74.5 - - - +
230A ILE* 1.3 66.9 + - + +
232A LEU* 3.1 6.4 + - - +
233A ILE* 3.0 33.0 + - + +
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Residues in contact with ILE 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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3A VAL* 4.5 6.1 - - + -
24A ALA* 4.3 18.6 - - + +
25A LEU* 3.8 31.2 - - + -
28A LYS* 3.5 33.0 - - + +
226A ALA 3.0 17.9 + - - +
227A ASN* 3.8 9.4 - - - +
228A GLY 3.3 0.2 - - - -
229A LEU* 1.3 77.3 - - + +
231A THR* 1.3 63.6 + - - +
233A ILE* 3.2 7.9 + - + +
234A GLU* 2.9 52.1 + - + +
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Residues in contact with THR 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 ASN 2.9 15.7 + - - -
228A GLY* 3.3 11.2 - - - -
230A ILE* 1.3 76.5 - - - +
232A LEU* 1.3 63.1 + - - +
234A GLU* 4.0 5.2 - - - +
235A ASP* 3.1 27.4 + - + +
238A LEU* 4.7 8.5 - - + -
243A MET* 3.8 18.2 - - + -
251A ILE* 4.2 12.7 - - + +
253A PHE* 5.0 4.3 - - + -
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Residues in contact with LEU 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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132A ILE* 3.3 13.2 - - + +
134A ILE* 3.9 18.4 - - + -
177A ARG* 2.9 27.0 + - - -
179A ASN* 4.0 28.0 - - + +
180A ALA 4.6 2.9 - - - +
181A ILE* 3.6 34.5 - - + -
228A GLY 3.0 14.0 + - - +
229A LEU* 3.1 6.9 + - - +
231A THR* 1.3 77.5 - - - +
233A ILE* 1.3 59.5 + - - +
235A ASP 3.5 4.3 - - - +
238A LEU* 3.8 20.8 - - + +
241A ALA* 4.6 1.6 - - + -
243A MET* 3.6 22.7 - - + -
253A PHE* 4.3 7.4 - - + -
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Residues in contact with ILE 233 (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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1A HIS* 3.5 10.8 - - + +
3A VAL* 3.9 20.9 - - + -
6A LYS* 4.8 12.2 + - + +
25A LEU* 3.7 24.9 - - + -
87A ILE* 4.0 28.7 - - + -
132A ILE* 3.8 15.0 - - + -
134A ILE* 4.1 15.9 - - + -
177A ARG* 2.9 20.2 + - - +
229A LEU* 3.0 37.7 + - + +
230A ILE* 3.2 10.3 + - + +
232A LEU* 1.3 75.0 - - - +
234A GLU* 1.3 60.3 + - - +
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Residues in contact with GLU 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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0A ALA* 3.2 17.6 - - + +
1A HIS* 2.9 44.6 + - - +
2A MET* 5.6 0.3 - - - -
3A VAL* 3.7 16.3 + - + +
28A LYS* 2.8 34.9 + - - -
230A ILE* 2.9 30.7 + - - +
231A THR* 4.1 4.4 - - - +
233A ILE* 1.3 76.3 - - - +
235A ASP* 1.3 59.4 + - + +
236A ASP 3.4 2.0 + - - -
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Residues in contact with ASP 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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0A ALA* 5.3 1.3 - - - +
177A ARG* 3.0 21.5 + - - -
231A THR* 3.1 20.3 + - + +
232A LEU 3.5 1.6 - - - +
233A ILE 3.4 0.4 - - - -
234A GLU* 1.3 74.7 - - - +
236A ASP* 1.3 62.2 + - - +
237A ALA* 2.9 26.8 + - - +
238A LEU* 3.2 33.9 + - + +
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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