Contacts of the helix formed by residues 226 - 235 (chain A) in PDB entry 5TQW
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 GLN 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A HIS 4.0 1.8 + - - -
225A LEU* 1.3 73.4 - - + +
227A PRO* 1.4 78.4 - - + +
228A PHE* 3.9 32.6 - - + +
229A THR* 3.1 23.3 + - - +
230A TRP* 3.0 20.3 + - - +
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Residues in contact with PRO 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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185A LEU* 3.7 37.9 - - + -
188A LEU* 6.6 0.2 - - + -
193A PHE* 4.9 2.2 - - + -
219A ARG* 5.1 7.0 - - - +
225A LEU 4.0 4.9 - - - +
226A GLN* 1.4 91.2 - - + +
228A PHE* 1.3 62.4 + - + +
230A TRP* 3.6 14.1 - - + -
231A HIS* 2.4 56.3 + - + +
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Residues in contact with PHE 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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185A LEU* 6.5 0.4 - - + -
193A PHE* 3.6 33.2 - + + -
226A GLN* 3.2 26.8 + - + +
227A PRO* 1.3 84.3 - - + +
229A THR* 1.3 64.4 + - + +
231A HIS* 3.6 2.1 + - - +
232A GLU* 3.4 28.8 + - - +
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Residues in contact with THR 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 LEU* 3.3 24.6 - - - +
226A GLN* 3.1 27.7 + - - +
228A PHE* 1.3 75.7 - - + +
230A TRP* 1.3 52.9 + - - +
232A GLU* 4.4 9.4 - - - +
233A LYS* 2.8 40.9 + - - +
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Residues in contact with TRP 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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185A LEU 4.0 7.6 - - - -
186A GLN* 3.2 41.1 - - + -
205A TRP* 3.5 19.7 - + - -
209A THR* 5.2 1.1 - - + -
219A ARG* 3.4 42.0 - - + +
220A PRO* 5.3 1.6 - - + -
221A PHE* 2.4 59.6 + + - -
222A LEU* 3.7 16.8 - - + +
225A LEU* 3.7 7.6 - - + -
226A GLN 3.0 18.8 + - - +
227A PRO* 3.4 11.4 - - + +
228A PHE 3.2 0.4 - - - -
229A THR* 1.3 77.4 + - - +
231A HIS* 1.3 82.6 + + - +
233A LYS* 3.9 1.0 - - - +
234A ILE* 3.0 32.8 + - - +
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Residues in contact with HIS 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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185A LEU 4.6 5.6 - - - -
188A LEU* 2.7 30.2 + - + -
190A PRO* 4.1 19.6 - - + +
193A PHE* 3.4 61.9 - + + -
194A GLU* 5.1 2.5 - - - +
205A TRP* 5.5 1.8 - + - -
227A PRO* 2.4 42.7 + - + +
228A PHE 4.1 0.7 - - - +
230A TRP* 1.3 99.4 - + - +
232A GLU* 1.3 51.4 + - + +
234A ILE* 3.6 8.6 - - + +
235A LYS* 2.8 39.1 + - - +
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Residues in contact with GLU 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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193A PHE* 5.9 1.8 - - + -
194A GLU* 4.7 12.1 - - - +
228A PHE 3.4 18.5 + - - +
229A THR* 4.4 8.1 - - - +
231A HIS* 1.3 75.2 - - + +
233A LYS* 1.3 65.3 + - - +
235A LYS* 3.2 16.3 + - + +
236A LYS* 3.2 43.2 + - - +
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Residues in contact with LYS 233 (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* 3.6 26.5 - - + -
225A LEU* 4.8 2.2 - - + -
229A THR 2.8 23.1 + - - +
230A TRP 3.9 2.7 - - - +
232A GLU* 1.3 77.4 - - - +
234A ILE* 1.3 61.5 + - - +
236A LYS* 3.2 13.5 + - + +
237A LYS* 3.2 44.3 + - - +
252A VAL* 5.3 5.3 - - - +
254A PHE* 3.6 27.7 - - + -
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Residues in contact with ILE 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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190A PRO* 5.7 8.1 - - + -
205A TRP* 5.7 2.9 - - + +
221A PHE* 3.5 54.5 - - + -
222A LEU* 5.5 1.5 - - + +
230A TRP 3.0 18.3 + - - +
231A HIS* 3.6 11.0 - - + +
233A LYS* 1.3 73.5 - - - +
235A LYS* 1.3 63.4 + - - +
236A LYS 3.1 6.2 + - - -
237A LYS* 3.5 23.6 + - + +
238A ASP 5.1 4.7 - - - +
239A PRO* 6.3 1.6 - - + -
241A CYS* 5.0 11.9 - - + +
244A ALA* 5.6 0.2 - - + -
254A PHE* 5.2 9.9 - - + -
280A LEU 5.7 4.3 - - - +
282A TRP* 3.8 23.8 - - + +
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Residues in contact with LYS 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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190A PRO* 5.2 14.1 - - + -
194A GLU* 2.4 45.8 + - - +
231A HIS 2.8 21.4 + - - +
232A GLU* 3.4 13.2 - - + +
233A LYS 3.2 0.6 - - - -
234A ILE* 1.3 78.3 - - - +
236A LYS* 1.3 63.0 + - + +
237A LYS 3.7 0.2 - - - -
282A TRP* 3.9 46.8 - - + -
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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