Contacts of the helix formed by residues 217 - 232 (chain A) in PDB entry 2G1X
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 PHE 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A ILE* 5.3 4.7 - - + +
212A SER 3.3 2.2 + - - -
213A THR* 3.1 15.0 + - - +
215A GLY 3.2 2.0 - - - -
216A ALA* 1.4 82.8 - - + +
218A TYR* 1.4 82.3 + + + +
219A PHE 3.3 1.5 + - - -
220A PRO* 3.5 4.1 - - - +
221A THR* 2.6 46.6 + - + -
323A PHE* 5.3 14.1 - + - -
327A TRP* 5.5 4.0 - - + -
328A LEU* 3.8 29.8 - - + -
331A PHE* 3.6 58.1 - + + -
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Residues in contact with TYR 218 (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 THR* 3.1 13.7 + - - +
214A VAL* 4.6 11.7 - - + -
217A PHE* 1.4 90.2 - + + +
219A PHE* 1.3 54.8 + - - +
221A THR* 3.0 11.5 + - + -
222A LEU* 2.6 74.0 + - + +
225A ILE* 5.8 4.7 - - + +
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Residues in contact with PHE 219 (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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214A VAL 4.5 3.7 - - - +
215A GLY* 3.9 20.2 - - - +
218A TYR* 1.3 83.2 - + - +
220A PRO* 1.3 81.1 - - + +
222A LEU* 3.0 23.0 + - + +
223A LEU* 3.0 33.8 + - + +
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Residues in contact with PRO 220 (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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137A ILE* 4.2 24.9 - - + +
138A LEU* 5.7 2.5 - - - -
141A CYS* 4.9 19.2 - - + +
215A GLY 3.1 25.1 - - - +
216A ALA 4.4 6.1 - - - +
217A PHE 3.6 9.9 - - - +
219A PHE* 1.3 108.1 - - + +
221A THR* 1.3 56.1 + - - +
223A LEU* 3.3 5.4 + - + +
224A LEU* 2.8 31.2 + - - +
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Residues in contact with THR 221 (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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137A ILE* 5.0 9.2 - - - +
217A PHE* 2.6 37.7 + - + -
218A TYR* 3.0 18.5 + - + -
220A PRO* 1.3 75.5 - - - +
222A LEU* 1.3 60.1 + - - +
224A LEU* 3.9 5.3 - - + +
225A ILE* 2.7 59.7 + - + +
320A LEU* 5.9 6.5 - - + -
324A ILE* 6.4 1.6 - - + -
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Residues in contact with LEU 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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218A TYR* 2.6 51.3 + - + +
219A PHE* 3.0 18.6 + - + +
221A THR* 1.3 72.4 - - - +
223A LEU* 1.3 60.4 + - - +
225A ILE* 3.2 10.2 + - - +
226A ALA* 2.8 39.6 + - + -
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Residues in contact with LEU 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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141A CYS* 3.2 34.1 - - - +
144A ALA* 4.3 1.1 - - + -
145A LEU* 5.4 4.5 - - + -
219A PHE* 3.0 32.3 + - + +
220A PRO* 3.7 7.9 - - + +
222A LEU* 1.3 82.0 - - - +
224A LEU* 1.3 65.4 + - - +
226A ALA* 3.1 4.5 + - - +
227A LEU* 2.9 59.5 + - + +
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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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137A ILE* 5.5 4.5 - - + -
140A LEU* 3.5 36.1 - - + +
141A CYS* 5.5 1.6 - - - -
144A ALA* 4.1 20.6 - - + -
220A PRO 2.8 18.5 + - - +
221A THR* 3.9 5.4 - - - +
223A LEU* 1.3 82.0 - - - +
225A ILE* 1.3 62.2 + - - +
227A LEU* 3.9 2.3 - - - +
228A TYR* 3.1 27.3 + - + +
316A LEU 5.8 1.6 - - - +
320A LEU* 2.9 56.3 - - + -
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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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218A TYR* 5.8 5.2 - - + +
221A THR* 2.7 51.1 + - + +
222A LEU* 3.5 7.6 - - - +
224A LEU* 1.3 77.0 - - + +
226A ALA* 1.3 65.6 + - - +
228A TYR* 3.2 8.5 + - + +
229A GLY* 3.0 18.5 + - - -
320A LEU* 5.2 10.8 - - + -
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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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222A LEU* 2.8 32.4 + - + +
223A LEU* 3.7 5.4 - - - +
225A ILE* 1.3 70.7 - - - +
227A LEU* 1.3 69.9 + - + +
229A GLY* 3.0 11.8 + - - -
230A ARG* 3.1 20.9 + - + +
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Residues in contact with LEU 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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144A ALA* 2.9 45.1 - - + +
145A LEU* 3.2 11.4 - - + +
148A TYR* 4.2 26.6 - - + -
223A LEU* 2.9 44.4 + - + +
224A LEU 3.9 3.6 - - - +
226A ALA* 1.3 79.6 - - + +
228A TYR* 1.3 57.5 + - - +
230A ARG* 2.8 25.2 + - + +
231A ILE* 2.9 15.8 + - - +
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Residues in contact with TYR 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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224A LEU* 3.1 23.7 + - + +
225A ILE* 3.3 13.2 - - + +
226A ALA 3.2 0.2 - - - -
227A LEU* 1.3 75.5 - - - +
229A GLY* 1.3 66.2 + - - +
231A ILE* 2.7 39.2 - - + +
232A TYR* 3.4 14.1 + + + +
236A ARG 5.0 5.1 + - - -
237A SER* 4.7 9.7 + - - -
250A ARG* 5.9 4.0 - - - -
313A THR 5.6 0.4 - - - -
314A LYS* 5.1 8.5 + - - +
317A GLY* 3.9 32.1 + - - -
320A LEU* 5.4 7.0 - - + -
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Residues in contact with GLY 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 ILE 3.0 9.8 + - - -
226A ALA* 3.0 10.3 + - - -
228A TYR* 1.3 80.0 - - - +
230A ARG* 1.3 71.5 + - - +
232A TYR* 3.2 20.5 - - - +
233A VAL 4.4 0.7 + - - -
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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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148A TYR* 4.0 30.4 - - + -
152A THR* 3.9 4.9 + - + +
226A ALA* 3.4 17.0 - - + +
227A LEU* 2.8 14.8 + - + +
229A GLY* 1.3 81.4 + - - +
231A ILE* 1.3 52.7 + - - +
232A TYR 3.0 5.2 + - - -
233A VAL* 2.8 41.8 + - - +
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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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147A ARG* 4.3 9.6 - - + -
151A ILE* 2.9 38.4 - - + -
152A THR* 4.8 1.8 - - - +
227A LEU 2.9 7.5 + - - +
228A TYR* 2.7 57.4 - - + +
230A ARG* 1.3 73.1 - - - +
232A TYR* 1.3 63.0 + - - +
233A VAL* 3.1 1.5 + - - -
234A GLU* 3.5 2.2 + - - +
235A ALA* 2.7 46.2 + - + +
236A ARG 4.8 2.0 - - - +
250A ARG* 5.4 3.1 - - - +
313A THR* 4.8 3.4 - - - -
314A LYS* 4.3 14.1 - - - +
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Residues in contact with TYR 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 TYR* 3.4 14.9 + + - +
229A GLY* 3.2 19.6 + - - +
231A ILE* 1.3 79.0 - - - +
233A VAL* 1.3 67.4 + - - +
235A ALA 3.9 5.4 - - - -
236A ARG* 3.7 49.8 + - + +
237A SER* 5.7 0.4 - - - -
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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