Contacts of the helix formed by residues 236 - 248 (chain A) in PDB entry 4GLP
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 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A GLU* 3.2 19.2 + - - +
235A GLU* 1.3 90.1 - - + +
237A PRO* 1.3 71.6 - - - +
238A THR* 3.3 23.3 + - - -
239A GLY* 3.6 6.4 + - - -
240A VAL* 4.0 5.8 + - - +
256A LEU* 6.1 0.9 - - - -
262A ARG* 4.1 25.1 - - + +
263A ALA* 5.3 0.2 - - - -
264A THR* 4.0 29.8 - - + +
266A ASN* 5.7 1.2 + - + -
292A PRO* 6.0 0.9 - - - -
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Residues in contact with PRO 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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235A GLU 3.9 4.7 - - - +
236A THR* 1.3 84.7 - - - +
238A THR* 1.3 56.9 + - + +
240A VAL* 2.8 33.2 + - + +
241A CYS 2.8 11.1 + - - -
256A LEU* 5.1 14.8 - - + -
261A LEU* 5.5 5.8 - - + -
262A ARG 5.0 1.1 - - - +
274A TRP* 3.6 22.4 - - + -
281A LEU* 6.5 0.9 - - + -
283A LEU* 5.7 11.9 - - + -
292A PRO* 4.4 28.7 - - + -
293A LYS 4.5 9.0 - - - +
294A GLY 4.7 1.6 - - - +
295A LEU* 5.3 4.9 - - + -
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Residues in contact with THR 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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236A THR* 3.3 17.2 + - - +
237A PRO* 1.3 76.3 - - + +
239A GLY* 1.3 60.1 + - - +
241A CYS* 3.2 10.3 + - - +
242A ALA* 3.0 29.5 + - - +
264A THR 5.0 10.1 - - - +
265A VAL* 6.2 1.1 - - - -
266A ASN 4.5 12.0 + - - -
268A SER 4.6 15.9 + - - +
269A ALA* 4.9 11.2 - - + -
272A CYS* 3.9 9.3 - - - -
274A TRP* 4.8 0.7 - - - -
293A LYS* 3.6 29.6 - - + +
294A GLY* 4.4 6.1 - - - -
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Residues in contact with GLY 239 (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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209A GLU* 3.8 25.9 - - - +
236A THR* 3.6 5.9 + - - -
237A PRO 3.2 1.0 - - - -
238A THR* 1.3 82.0 + - - +
240A VAL* 1.3 53.4 + - - +
242A ALA* 3.4 6.4 + - - +
243A ALA* 2.7 36.8 + - - +
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Residues in contact with VAL 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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209A GLU* 4.3 9.4 - - + -
212A LEU* 4.8 6.3 - - + -
229A LEU* 4.9 6.3 - - + -
234A MET* 3.8 31.0 - - + -
236A THR 4.0 10.7 + - - +
237A PRO* 2.8 16.2 + - + +
239A GLY* 1.3 72.3 - - - +
241A CYS* 1.3 65.3 + - - +
243A ALA* 4.2 5.6 - - - -
244A LEU* 2.9 53.6 + - + +
254A LEU* 4.4 18.6 - - + -
256A LEU* 4.6 9.9 - - + -
274A TRP* 4.6 3.4 - - + -
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Residues in contact with CYS 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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237A PRO 2.8 5.7 + - - -
238A THR 3.3 3.8 - - - +
240A VAL* 1.3 78.1 - - - +
242A ALA* 1.3 62.0 + - - +
244A LEU* 3.5 3.5 + - - +
245A ALA* 3.3 19.6 + - - +
272A CYS* 2.0 44.9 - - - -
273A MET* 3.3 12.8 - - - +
274A TRP* 3.3 57.6 - - + -
275A SER* 5.2 2.6 + - - -
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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 THR 3.0 12.5 + - - +
239A GLY* 3.8 5.8 - - - +
241A CYS* 1.3 82.5 - - - +
243A ALA* 1.3 51.4 + - - +
245A ALA* 3.2 6.7 + - - +
246A ALA* 2.7 36.8 + - + +
268A SER 5.7 4.5 - - - +
272A CYS* 5.7 0.9 - - - -
273A MET* 4.7 11.8 - - - +
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Residues in contact with ALA 243 (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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209A GLU* 4.6 9.0 - - + +
212A LEU* 4.7 6.7 - - + -
213A MET* 3.6 34.8 - - + +
216A LEU* 6.1 0.2 - - - -
239A GLY 2.7 24.0 + - - +
240A VAL* 3.2 7.1 + - - +
242A ALA* 1.3 74.0 - - - +
244A LEU* 1.3 62.0 + - + +
246A ALA* 3.3 6.8 + - - +
247A ALA* 2.8 29.8 + - - +
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Residues in contact with LEU 244 (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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212A LEU* 4.1 20.0 - - + -
216A LEU* 5.3 5.2 - - + -
227A LEU* 4.4 13.2 - - + -
229A LEU* 5.0 3.8 - - + -
240A VAL* 2.9 52.3 + - + +
241A CYS* 4.1 2.9 - - - +
243A ALA* 1.3 78.2 - - - +
245A ALA* 1.3 63.4 + - - +
247A ALA* 4.3 4.9 - - - -
248A GLY* 3.2 21.0 + - - -
249A VAL* 3.6 29.9 + - + +
251A PRO* 3.7 31.4 - - + -
254A LEU* 4.5 7.6 - - + -
274A TRP* 5.4 5.6 - - + -
275A SER* 4.7 8.7 - - - +
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Residues in contact with ALA 245 (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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241A CYS 3.3 7.0 + - - +
242A ALA 3.2 7.4 + - - +
244A LEU* 1.3 80.0 - - - +
246A ALA* 1.3 64.3 + - - +
247A ALA 3.4 4.0 + - - +
248A GLY* 4.2 2.3 + - - -
249A VAL 5.3 1.6 - - - -
250A GLN* 5.8 1.8 - - - -
273A MET* 3.6 42.0 - - + +
275A SER* 5.4 2.9 + - - +
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Residues in contact with ALA 246 (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 MET* 3.4 28.9 - - + -
242A ALA* 2.7 22.8 + - + +
243A ALA 3.6 0.4 - - - +
245A ALA* 1.3 74.5 - - - +
247A ALA* 1.3 63.7 + - - +
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Residues in contact with ALA 247 (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 MET* 5.1 12.3 - - - +
216A LEU* 3.6 38.4 - - + +
218A PRO* 3.8 22.6 - - + +
243A ALA 2.8 17.9 + - - +
244A LEU 3.7 3.1 - - - +
245A ALA 3.2 1.6 - - - +
246A ALA* 1.3 81.8 - - - +
248A GLY* 1.3 60.3 + - - +
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Residues in contact with GLY 248 (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 PRO* 5.2 0.9 - - - +
219A HIS* 4.9 13.1 + - - -
220A LYS 4.9 1.7 - - - +
221A PHE 4.7 3.3 - - - +
222A PRO* 4.9 6.1 - - - +
244A LEU 3.2 5.2 + - - -
245A ALA 4.7 3.8 - - - -
247A ALA* 1.3 82.7 - - - +
249A VAL* 1.3 67.7 + - - +
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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