Contacts of the helix formed by residues 220 - 231 (chain A) in PDB entry 6C9G
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 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A ASP* 3.0 17.4 + - - +
219A ASP* 1.3 76.5 - - - +
221A VAL* 1.3 65.8 + - - +
222A PRO* 3.7 32.2 - - + +
223A THR* 2.8 31.4 + - - +
224A LEU* 3.1 17.3 + - - +
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Residues in contact with VAL 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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218A ASP 5.0 1.8 - - - +
219A ASP 3.5 8.9 + - - +
220A HIS* 1.3 71.8 - - - +
222A PRO* 1.3 72.8 - - + +
224A LEU* 3.2 11.9 + - + +
225A PHE* 3.1 51.9 + - + -
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Residues in contact with PRO 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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220A HIS* 3.7 31.4 - - + +
221A VAL* 1.3 96.3 - - + +
223A THR* 1.3 59.6 + - - +
225A PHE* 3.5 8.8 + - + +
226A LYS* 3.2 21.8 + - - +
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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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218A ASP* 3.4 25.8 - - - +
220A HIS* 2.8 35.3 + - - +
222A PRO* 1.3 75.8 - - - +
224A LEU* 1.3 60.8 + - - +
226A LYS* 3.3 7.3 + - + +
227A LYS* 3.0 42.1 + - + +
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Residues in contact with LEU 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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179A PRO* 4.0 28.7 - - + -
180A ASN* 4.2 13.9 - - - +
216A PHE* 3.4 42.2 - - + +
217A ASP* 3.7 9.2 - - - +
218A ASP* 4.0 19.9 - - + +
220A HIS 3.1 12.4 + - - +
221A VAL* 3.2 14.6 + - + +
223A THR* 1.3 78.5 - - - +
225A PHE* 1.3 69.1 + - + +
227A LYS* 3.4 5.3 + - + +
228A ILE* 3.1 32.2 + - + +
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Residues in contact with PHE 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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179A PRO* 4.0 29.4 - - + -
187A ILE* 3.5 42.7 - - + +
221A VAL* 3.1 37.5 + - + +
222A PRO* 3.9 7.4 - - + +
224A LEU* 1.3 84.0 - - + +
226A LYS* 1.3 61.8 + - - +
228A ILE* 3.4 2.7 + - + -
229A CYS* 3.0 30.2 + - - -
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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 PRO 3.2 14.8 + - - +
223A THR* 3.7 9.9 - - + +
224A LEU 3.3 0.2 - - - -
225A PHE* 1.3 75.8 - - - +
227A LYS* 1.3 60.3 + - - +
229A CYS* 3.2 4.7 + - - -
230A ASP* 2.8 60.4 + - - +
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Residues in contact with LYS 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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215A PRO 5.9 0.7 - - - +
216A PHE* 3.5 24.4 - - + -
217A ASP 3.5 25.1 + - - +
218A ASP* 2.9 30.3 + - + +
223A THR* 3.0 31.1 + - + +
224A LEU* 3.6 7.0 - - - +
226A LYS* 1.3 75.7 - - + +
228A ILE* 1.3 57.7 + - - +
230A ASP* 3.5 5.9 + - - +
231A GLY 3.1 21.0 + - - -
232A ILE* 3.6 12.3 + - + +
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Residues in contact with ILE 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 PRO 3.3 26.7 - - - +
180A ASN* 4.9 2.2 - - - +
182A ALA 3.8 17.3 - - - +
184A PRO* 3.4 27.1 - - + +
187A ILE* 3.6 25.1 - - + -
200A TRP* 3.9 8.7 - - + -
216A PHE* 3.8 28.7 - - + -
224A LEU* 3.1 31.0 + - + +
225A PHE* 3.6 9.0 - - + +
226A LYS 3.2 0.4 - - - -
227A LYS* 1.3 76.6 - - - +
229A CYS* 1.3 62.9 + - - +
231A GLY* 3.1 13.3 + - - -
253A VAL* 3.9 0.2 - - - +
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Residues in contact with CYS 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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184A PRO* 4.1 14.6 - - + -
187A ILE* 3.6 20.6 - - - -
188A SER* 3.8 19.3 - - - -
190A ARG* 6.0 0.4 - - - -
225A PHE* 3.0 22.8 + - - +
226A LYS* 4.0 5.8 - - + +
228A ILE* 1.3 76.9 - - - +
230A ASP* 1.3 61.3 + - - +
253A VAL* 3.3 22.9 - - + +
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Residues in contact with ASP 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 LYS* 2.8 55.0 + - - +
227A LYS* 3.8 7.3 + - - +
229A CYS* 1.3 80.8 - - - +
231A GLY* 1.3 60.8 + - - +
232A ILE* 3.1 29.6 + - + +
253A VAL* 3.8 5.2 - - - +
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Residues in contact with GLY 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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200A TRP* 4.7 0.7 - - - -
216A PHE* 3.9 11.2 - - - -
227A LYS 3.1 7.3 + - - -
228A ILE 3.1 9.6 + - - -
229A CYS 3.3 0.2 - - - -
230A ASP* 1.3 78.0 - - - +
232A ILE* 1.3 58.1 + - - +
233A PHE* 3.4 21.3 - - - -
251A LEU 4.6 9.5 - - - +
253A VAL* 3.5 16.6 - - - -
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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