Contacts of the helix formed by residues 217 - 226 (chain B) in PDB entry 3GUU
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 SER 217 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188B HIS* 6.2 0.9 - - - -
215B PRO* 5.0 1.6 - - - -
216B VAL* 1.3 82.0 - - - +
218B ALA* 1.3 59.5 + - - +
219B LYS 3.6 0.5 + - - -
220B ASP* 3.0 39.0 + - - -
221B THR* 2.7 31.7 + - - -
309B THR* 3.5 7.6 - - - -
311B VAL* 4.3 6.7 - - - -
314B GLU* 2.7 32.2 + - - -
341B PRO* 4.8 1.0 - - - +
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Residues in contact with ALA 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ILE* 5.0 11.0 - - + +
188B HIS* 5.9 4.5 + - - +
216B VAL 4.2 0.4 - - - -
217B SER* 1.3 72.0 + - - +
219B LYS* 1.3 57.5 + - - +
221B THR* 3.3 3.7 + - - -
222B PHE* 2.9 24.8 + - - +
241B LEU* 4.3 13.2 - - + -
305B LEU* 4.2 15.7 - - + +
308B GLU* 3.3 25.2 + - + +
309B THR* 4.7 0.2 - - - -
442B 1PE 3.4 29.8 - - - +
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Residues in contact with LYS 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B SER* 3.4 0.6 + - - +
218B ALA* 1.3 77.8 - - - +
220B ASP* 1.3 65.3 + - - +
222B PHE* 3.2 8.7 + - - +
223B THR* 2.9 37.3 + - + +
296B LEU* 4.0 35.6 + - + +
297B ASN* 4.1 17.2 + - - -
305B LEU* 4.0 32.2 + - + +
308B GLU 5.1 0.2 + - - -
314B GLU* 3.6 23.7 + - - +
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Residues in contact with ASP 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B SER* 3.0 29.5 + - - +
219B LYS* 1.3 82.2 - - - +
221B THR* 1.3 65.4 + - - +
223B THR* 3.4 10.0 + - - -
224B PHE* 3.2 24.6 + - - +
311B VAL* 5.3 3.3 - - - +
314B GLU* 4.2 6.1 - - - +
338B PRO* 4.0 4.4 - - + +
341B PRO* 3.9 29.3 - - + +
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Residues in contact with THR 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B PRO* 3.7 23.2 - - + +
216B VAL 4.7 0.2 + - - -
217B SER 2.7 23.0 + - - -
218B ALA* 3.7 3.6 - - - -
220B ASP* 1.3 76.4 - - - +
222B PHE* 1.3 63.5 + - - +
224B PHE* 3.3 3.1 + - - +
225B LEU* 3.2 37.0 + - + +
336B ILE 4.6 2.9 - - - +
337B VAL* 4.9 2.0 - - - -
338B PRO* 4.2 22.9 - - + +
442B 1PE 3.5 36.3 - - - +
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Residues in contact with PHE 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ALA 2.9 8.0 + - - +
219B LYS* 3.2 9.6 + - - +
221B THR* 1.3 76.9 - - - +
223B THR* 1.3 70.8 + - + +
225B LEU 3.4 0.2 + - - -
226B ASN* 2.9 53.0 + - + +
234B ALA* 3.8 18.5 - - + +
238B VAL* 4.1 11.0 - - + -
286B VAL* 3.9 31.0 - - + -
287B PHE* 3.8 31.6 - + - -
296B LEU* 4.1 18.4 - - + -
442B 1PE 3.5 46.7 - - - -
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Residues in contact with THR 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU* 5.0 1.9 + - - +
112A ASP* 3.3 34.5 + - - +
219B LYS* 2.9 30.6 + - + +
220B ASP* 3.4 15.9 + - - -
222B PHE* 1.3 90.1 - - + +
224B PHE* 1.3 59.6 + - - +
226B ASN* 4.3 9.4 + - - +
296B LEU* 4.1 18.8 - - + -
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Residues in contact with PHE 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA* 3.1 45.7 + - - +
13A LEU 4.1 20.2 - - - -
14A PRO* 4.2 7.9 - - + -
15A ASN 4.9 3.6 - - - -
105A TYR* 5.5 2.2 - - - -
112A ASP* 3.6 11.2 + - - +
220B ASP 3.2 18.4 + - - +
221B THR 3.5 4.0 - - - +
222B PHE 3.3 0.2 - - - -
223B THR* 1.3 78.2 + - - +
225B LEU* 1.3 61.5 + - + +
226B ASN 4.5 1.4 - - - +
228B GLY* 6.0 0.2 - - - -
334B ASP 3.4 20.2 - - - -
335B GLU 3.7 14.4 - - - -
336B ILE 3.4 36.3 - - - -
338B PRO* 3.6 35.2 - - + -
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Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA 5.4 0.2 - - - -
221B THR* 3.2 39.2 + - + +
224B PHE* 1.3 80.3 - - + +
226B ASN* 1.3 67.3 + - - +
227B GLY 3.4 0.5 + - - -
228B GLY* 3.1 16.3 + - - -
230B PHE* 3.7 35.6 - - + +
231B ALA* 3.5 12.6 + - - -
233B PHE* 4.0 12.6 - - + -
234B ALA* 4.1 12.1 - - + +
335B GLU 4.9 2.5 - - - +
336B ILE* 3.2 34.5 - - + +
442B 1PE 3.8 20.2 - - - +
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Residues in contact with ASN 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLY* 3.8 10.4 - - - -
111A LEU* 3.8 22.6 + - + +
222B PHE* 2.9 37.4 + - + +
223B THR* 4.3 6.3 + - - +
224B PHE 3.7 3.2 - - - +
225B LEU* 1.3 77.5 - - - +
227B GLY* 1.3 63.5 + - - +
228B GLY* 3.2 3.1 + - - -
231B ALA* 4.6 0.4 - - - -
234B ALA* 4.1 6.7 - - - +
284B LEU 3.4 1.4 - - - +
285B ASN* 2.8 25.1 + - - -
286B VAL* 2.8 31.7 + - - +
287B PHE* 3.6 23.6 - - - -
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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