Contacts of the helix formed by residues 217 - 226 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A HIS* 6.3 0.4 - - - -
215A PRO* 5.1 1.1 - - - -
216A VAL* 1.3 82.2 - - - +
218A ALA* 1.3 60.6 + - - +
220A ASP* 3.2 38.6 + - - -
221A THR* 2.7 31.9 + - - -
309A THR* 3.6 7.2 - - - -
311A VAL* 4.3 6.5 - - - -
314A GLU* 2.6 32.9 + - - -
341A PRO* 4.8 1.3 - - - +
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Residues in contact with ALA 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE* 5.1 10.3 - - + +
188A HIS* 5.9 4.7 + - - +
215A PRO* 6.4 0.2 - - - -
216A VAL 4.2 0.6 - - - -
217A SER* 1.3 71.7 + - - +
219A LYS* 1.3 59.1 + - - +
221A THR* 3.3 3.6 + - - -
222A PHE* 2.9 30.5 + - - +
241A LEU* 4.1 17.7 - - + -
305A LEU* 4.1 17.5 + - + +
308A GLU* 3.2 27.3 + - + +
309A THR* 4.8 0.6 - - - -
442A 1PE 3.6 18.5 - - - +
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Residues in contact with LYS 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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217A SER 3.4 0.4 - - - -
218A ALA* 1.3 78.4 - - - +
220A ASP* 1.3 63.7 + - - +
222A PHE* 3.3 7.7 + - + +
223A THR* 3.0 39.3 + - + +
296A LEU* 4.6 26.8 + - + +
297A ASN* 4.4 14.8 + - - -
305A LEU* 3.8 36.2 + - + +
314A GLU* 3.6 23.2 + - + +
442A 1PE 5.3 0.7 - - - -
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Residues in contact with ASP 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A SER* 3.2 28.8 + - - +
219A LYS* 1.3 82.7 - - - +
221A THR* 1.3 65.4 + - - +
223A THR* 3.2 9.8 + - - +
224A PHE* 3.1 23.9 + - - +
311A VAL* 5.2 3.3 - - - +
314A GLU* 4.3 6.9 - - - +
338A PRO* 4.0 3.7 - - + +
341A PRO* 3.6 30.6 - - + +
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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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215A PRO* 3.7 25.0 - - + +
216A VAL 4.5 0.2 + - - -
217A SER 2.7 24.1 + - - -
218A ALA* 3.8 3.8 - - - -
220A ASP* 1.3 76.9 - - - +
222A PHE* 1.3 63.1 + - - +
224A PHE* 3.3 2.1 + - - +
225A LEU* 3.1 33.3 + - + +
336A ILE 4.7 2.7 - - - +
337A VAL* 5.0 1.6 - - - -
338A PRO* 4.1 23.2 - - + +
442A 1PE 3.4 39.5 - - - +
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Residues in contact with PHE 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 ALA 2.9 14.7 + - - +
219A LYS* 3.4 9.2 - - - +
221A THR* 1.3 75.2 - - - +
223A THR* 1.3 71.6 + - + +
225A LEU* 3.1 2.3 + - - +
226A ASN* 2.9 53.9 + - + +
234A ALA* 3.8 28.3 - - + -
238A VAL* 4.1 16.8 - - + -
286A VAL* 4.1 14.8 - - + -
287A PHE* 4.0 18.4 - + - -
296A LEU* 3.8 29.8 - - + -
442A 1PE 3.6 42.4 + - - -
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Residues in contact with THR 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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219A LYS* 3.0 31.7 + - + +
220A ASP* 3.2 18.1 + - - +
222A PHE* 1.3 86.8 - - + +
224A PHE* 1.3 61.3 + - - +
225A LEU 3.5 0.2 + - - -
226A ASN* 4.1 10.1 + - - +
296A LEU* 4.5 13.9 - - + -
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Residues in contact with PHE 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 ASP 3.1 18.9 + - - +
221A THR 3.6 4.5 - - - +
222A PHE 3.1 0.2 - - - -
223A THR* 1.3 78.3 + - - +
225A LEU* 1.3 62.3 + - + +
226A ASN 4.7 1.8 - - - +
228A GLY* 5.9 1.0 - - - -
334A ASP 3.2 21.5 - - - -
335A GLU* 3.6 29.6 - - - -
336A ILE 3.5 23.3 - - - -
338A PRO* 3.6 33.9 - - + -
339A TYR 5.6 0.2 - - - -
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Residues in contact with LEU 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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221A THR* 3.1 35.0 + - + +
222A PHE 3.1 3.0 + - - +
224A PHE* 1.3 80.7 - - + +
226A ASN* 1.3 66.1 - - - +
227A GLY 3.4 0.3 + - - -
228A GLY* 3.1 15.6 + - - -
230A PHE* 3.8 33.3 - - + +
231A ALA* 3.5 13.4 + - - -
233A PHE* 3.8 25.4 - - + -
234A ALA* 4.1 13.9 - - + +
335A GLU 5.1 1.6 - - - +
336A ILE* 3.3 32.8 - - + +
442A 1PE 3.9 11.4 - - - +
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Residues in contact with ASN 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 PHE* 2.9 40.1 + - + +
223A THR* 4.1 8.9 + - - +
224A PHE 3.7 2.2 - - - +
225A LEU* 1.3 76.1 - - - +
227A GLY* 1.3 64.8 + - - +
228A GLY 3.2 4.3 + - - -
231A ALA* 4.3 1.1 - - - -
234A ALA* 4.1 6.5 - - - +
284A LEU 3.4 1.4 - - - +
285A ASN* 3.1 21.3 + - - -
286A VAL* 2.8 32.4 + - - +
287A PHE* 3.5 20.6 - - - -
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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