Contacts of the helix formed by residues 220 - 230 (chain A) in PDB entry 4K81
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 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A ILE* 1.3 83.9 - - - +
221A PRO* 1.4 79.3 - - - +
222A THR* 4.1 5.9 + - - -
223A GLN* 3.0 44.0 + - - +
224A ILE* 3.0 9.0 + - - +
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Residues in contact with PRO 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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200A PRO* 4.1 19.1 - - + +
201A MET* 3.6 46.9 - - + +
219A ILE 3.5 0.4 - - - +
220A SER* 1.4 90.5 - - - +
222A THR* 1.3 65.9 + - + +
224A ILE* 3.1 3.8 + - - +
225A LEU* 3.0 26.3 + - - +
85F ASN* 4.5 17.0 - - - +
86F ASN* 5.9 3.8 - - + +
124F THR* 5.8 7.6 - - + -
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Residues in contact with THR 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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200A PRO* 6.3 0.4 - - + -
220A SER* 4.1 5.4 + - - -
221A PRO* 1.3 82.0 - - + +
223A GLN* 1.3 60.9 + - - +
225A LEU* 3.7 24.1 - - + +
226A GLN* 2.9 33.3 + - - +
86F ASN* 4.9 16.9 + - - +
88F LYS* 5.4 5.6 - - + +
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Residues in contact with GLN 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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211A PHE* 5.8 7.4 - - + -
219A ILE* 3.3 18.0 + - - +
220A SER* 3.0 42.2 + - - +
221A PRO 3.0 0.4 - - - -
222A THR* 1.3 79.6 + - - +
224A ILE* 1.3 63.1 + - + +
226A GLN* 3.1 19.3 - - - +
227A MET* 3.0 44.9 + - + +
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Residues in contact with ILE 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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196A PHE* 4.0 15.7 - - + -
200A PRO 4.3 7.2 - - - +
201A MET* 3.7 23.8 - - - +
204A PHE* 5.3 2.0 - - + -
209A VAL* 6.1 3.4 - - + -
211A PHE* 3.7 25.6 - - + -
219A ILE* 3.5 35.9 - - + +
220A SER 3.0 7.3 + - - +
221A PRO 3.7 6.1 - - - +
223A GLN* 1.3 76.5 - - + +
225A LEU* 1.3 64.6 + - - +
227A MET* 3.2 7.9 + - - +
228A PHE* 3.0 48.0 + - + -
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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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196A PHE* 4.4 12.1 - - + -
197A PHE* 4.6 16.8 - - + +
200A PRO* 4.6 20.4 - - + +
221A PRO 3.0 15.8 + - - +
222A THR* 3.7 23.6 - - + +
224A ILE* 1.3 77.4 - - - +
226A GLN* 1.3 65.7 + - + +
228A PHE* 3.3 9.9 + - - +
229A LEU* 3.3 40.8 + - + +
347A TYR* 3.9 34.8 - - + +
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Residues in contact with GLN 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 THR 2.9 17.0 + - - +
223A GLN* 3.1 31.4 + - - +
225A LEU* 1.3 79.5 - - + +
227A MET* 1.3 83.8 + - - +
229A LEU* 4.1 4.7 - - - +
230A SER* 3.3 24.9 + - - -
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Residues in contact with MET 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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211A PHE* 3.7 39.5 - - + -
223A GLN* 3.0 40.3 + - + +
224A ILE* 3.2 6.3 + - - +
226A GLN* 1.3 97.2 - - - +
228A PHE* 1.3 60.4 + - - +
230A SER* 4.0 7.9 + - - -
233A THR* 4.1 16.8 + - - +
234A TYR* 4.7 0.2 - - - -
235A PRO* 3.5 16.6 - - + +
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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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196A PHE* 3.6 24.9 - + + -
204A PHE* 3.3 40.6 - + - -
209A VAL* 4.0 9.6 - - + -
211A PHE* 4.2 9.0 - + - -
224A ILE* 3.0 36.4 + - + +
225A LEU 3.3 4.0 + - - +
226A GLN 3.2 0.2 - - - -
227A MET* 1.3 79.0 - - - +
229A LEU* 1.3 58.2 + - - +
230A SER 3.5 2.5 - - - +
234A TYR* 3.6 49.3 - + - -
235A PRO* 4.0 20.4 - - + -
237A ILE* 3.7 23.6 - - + -
336A ALA* 4.7 0.4 - - + -
339A LEU* 3.8 24.7 - - + +
343A GLY* 5.2 0.5 - - - -
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Residues in contact with LEU 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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196A PHE* 5.7 0.4 - - + -
197A PHE* 4.1 5.4 - - + -
225A LEU* 3.3 37.3 + - + +
226A GLN* 4.4 4.3 - - - +
227A MET 3.4 0.2 - - - -
228A PHE* 1.3 76.9 - - + +
230A SER* 1.3 67.2 + - - +
231A SER* 3.7 1.6 + - - -
339A LEU* 3.9 23.3 - - + -
343A GLY* 3.7 24.1 - - - +
344A MET* 3.7 37.1 + - + +
347A TYR* 3.6 49.1 - - + -
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Residues in contact with SER 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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226A GLN 3.3 16.0 + - - -
227A MET* 4.0 4.2 + - - -
228A PHE 3.5 2.3 - - - +
229A LEU* 1.3 81.8 - - - +
231A SER* 1.3 54.9 + - - +
232A SER* 3.2 8.0 + - - -
233A THR* 2.8 39.4 + - - -
260A ARG* 2.6 29.3 + - - -
343A GLY* 5.7 2.1 - - - -
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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