Contacts of the helix formed by residues 223 - 234 (chain A) in PDB entry 4QMO
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 HIS 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A LEU* 1.3 75.3 - - - +
224A PRO* 1.3 76.2 - - + +
225A MET* 3.0 48.6 + - + +
226A LYS* 2.8 44.7 + - + +
227A VAL* 4.0 1.9 + - - +
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Residues in contact with PRO 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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183A PRO* 4.2 24.4 - - + +
184A PHE* 4.2 26.2 - - + -
222A LEU 3.4 4.5 - - - +
223A HIS* 1.3 101.2 - - + +
225A MET* 1.3 60.4 + - - +
227A VAL* 3.1 24.9 - - + +
228A LEU* 3.9 3.1 + - - +
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Residues in contact with MET 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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223A HIS* 3.0 28.7 + - + +
224A PRO* 1.3 77.4 - - - +
226A LYS* 1.3 63.2 + - + +
228A LEU* 3.2 39.3 + - + +
229A PHE* 4.2 5.9 - - + -
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Residues in contact with LYS 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* 4.5 21.6 - - + +
223A HIS* 2.8 32.6 + - + +
225A MET* 1.3 79.3 - - + +
227A VAL* 1.3 58.6 + - - +
228A LEU 3.2 0.5 + - - -
229A PHE* 3.2 35.2 + - + -
230A LEU* 3.0 41.1 + - + +
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Residues in contact with VAL 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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183A PRO* 3.7 26.5 - - + +
184A PHE* 3.5 33.9 - - + -
191A ILE* 4.1 3.7 - - + +
219A HIS* 4.0 18.6 - - + -
222A LEU* 5.3 1.3 - - + -
223A HIS 4.4 4.0 - - - +
224A PRO 3.1 17.9 - - - +
226A LYS* 1.3 76.8 - - + +
228A LEU* 1.3 65.4 + - + +
229A PHE 3.1 0.2 - - - -
230A LEU* 3.7 10.8 - - + -
231A ILE* 3.0 49.6 + - + +
232A PRO* 3.5 1.0 - - - +
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Residues in contact with LEU 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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179A PHE* 3.6 37.2 - - + -
183A PRO* 6.0 3.8 - - + -
191A ILE* 3.6 18.2 - - + +
224A PRO 4.4 2.5 - - - +
225A MET* 3.2 39.0 - - + +
227A VAL* 1.3 82.0 - - + +
229A PHE* 1.3 56.9 + - + +
232A PRO* 3.5 16.9 - - - +
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Residues in contact with PHE 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 MET* 4.2 5.6 - - + -
226A LYS* 3.2 52.2 + - + -
228A LEU* 1.3 77.8 - - + +
230A LEU* 1.3 100.2 + - + +
231A ILE 3.4 2.0 - - - -
232A PRO* 3.4 4.1 - - - +
233A LYS* 3.0 43.8 + - + +
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Residues in contact with LEU 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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219A HIS* 4.4 17.7 - - + +
222A LEU* 3.5 31.9 - - + -
226A LYS* 3.0 34.3 + - + +
227A VAL* 4.0 6.7 - - + +
229A PHE* 1.3 96.8 - - + +
231A ILE* 1.3 57.8 + - - +
233A LYS* 4.7 2.5 - - + -
234A ASN* 2.8 63.3 + - - +
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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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183A PRO 3.4 25.4 - - - +
184A PHE* 4.4 10.3 - - - +
186A MET 3.9 13.9 - - - +
188A PRO* 4.0 19.3 - - + -
191A ILE* 3.5 23.1 - - + -
203A TRP* 4.2 14.6 - - + +
219A HIS* 4.3 17.9 - - + +
227A VAL* 3.0 29.4 + - + +
230A LEU* 1.3 77.4 - - - +
232A PRO* 1.4 67.8 - - + +
234A ASN* 3.7 4.8 - - - +
236A PRO* 6.1 0.2 - - - +
257A LYS* 3.5 17.2 + - - +
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Residues in contact with PRO 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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188A PRO* 4.3 11.0 - - + +
191A ILE* 3.8 12.3 - - + -
192A LYS* 3.7 39.8 - - + +
227A VAL 3.5 2.5 - - - +
228A LEU 3.5 23.1 - - - +
229A PHE* 3.4 11.2 - - - +
231A ILE* 1.4 95.0 - - + +
233A LYS* 1.3 56.6 + - - +
257A LYS* 2.8 20.7 + - - +
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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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229A PHE* 3.0 36.4 + - + +
230A LEU* 4.1 2.5 - - + +
232A PRO* 1.3 79.4 - - - +
234A ASN* 1.3 78.1 + - - +
235A ASN 4.0 0.2 + - - -
257A LYS* 4.2 1.4 + - - -
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Residues in contact with ASN 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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219A HIS* 4.6 7.2 - - - +
230A LEU* 2.8 47.3 + - - +
231A ILE* 3.7 5.2 - - - +
233A LYS* 1.3 91.3 - - - +
235A ASN* 1.3 74.5 + - - +
236A PRO* 3.7 0.3 - - - +
257A LYS* 2.8 24.2 + - - -
403A PG4 3.5 34.2 + - - +
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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