Contacts of the helix formed by residues 223 - 232 (chain A) in PDB entry 4CBS
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 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A ASN* 3.3 15.4 - - - +
200A ILE 4.0 7.4 - - - -
201A ASP* 2.8 48.7 + - - -
222A PHE* 1.3 75.3 - - - +
224A ASP* 1.3 65.7 + - - +
225A LYS* 3.2 5.2 + - - -
226A ALA* 3.2 13.6 + - - +
227A LYS* 2.9 21.9 + - - +
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Residues in contact with ASP 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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72A ASN* 4.6 4.2 + - - +
73A PRO* 5.6 5.7 - - - +
223A SER* 1.3 71.6 - - - +
225A LYS* 1.3 69.0 + - + +
227A LYS* 3.2 9.8 + - - +
228A LYS* 3.0 24.0 + - - +
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Residues in contact with LYS 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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174A HIS* 3.8 46.4 - - + +
179A LEU* 3.5 19.9 - - + +
201A ASP* 3.8 2.5 - - - +
223A SER* 3.2 5.6 + - - +
224A ASP* 1.3 86.0 - - + +
226A ALA* 1.3 62.8 + - - +
228A LYS* 3.2 8.8 + - - +
229A LYS* 3.0 23.2 + - - +
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Residues in contact with ALA 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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93A VAL* 4.9 2.5 - - + -
179A LEU* 3.8 15.2 - - + +
201A ASP* 3.7 22.2 - - + +
202A ILE* 3.9 18.2 - - + -
222A PHE* 3.9 15.7 - - + -
223A SER* 3.2 11.5 + - - +
225A LYS* 1.3 77.1 - - - +
227A LYS* 1.3 64.5 + - - +
228A LYS 3.2 0.2 + - - -
229A LYS* 3.2 2.8 + - - +
230A MET* 3.0 29.9 + - + +
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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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73A PRO* 4.8 20.6 - - + +
74A LEU* 4.1 25.9 - - + +
222A PHE* 4.5 0.4 - - - +
223A SER 2.9 18.9 + - - +
224A ASP* 3.2 8.0 + - - +
226A ALA* 1.3 75.4 - - - +
228A LYS* 1.3 56.5 + - - +
230A MET* 3.9 10.9 - - - +
231A TYR* 3.0 60.8 + - + +
253A CYS 4.9 9.1 + - - -
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Residues in contact with LYS 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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224A ASP 3.0 12.9 + - - +
225A LYS* 3.4 11.9 - - - +
227A LYS* 1.3 73.4 - - - +
229A LYS* 1.3 68.2 + - - +
230A MET 3.2 0.2 + - - -
231A TYR* 3.2 5.2 + - + +
232A SER* 3.0 46.1 + - - +
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Residues in contact with LYS 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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93A VAL* 2.7 29.7 + - - +
94A LEU* 4.4 0.2 - - - +
95A GLU* 4.3 17.7 - - - +
98A ASP* 2.6 32.3 + - - -
149A VAL* 3.4 26.8 - - + +
179A LEU* 4.4 17.5 - - + -
225A LYS 3.0 15.6 + - - +
226A ALA 3.8 3.6 - - - +
228A LYS* 1.3 77.6 - - - +
230A MET* 1.3 62.9 + - + +
232A SER* 3.6 6.2 + - - -
233A ARG* 3.3 23.5 + - - +
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Residues in contact with MET 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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74A LEU* 3.8 17.9 - - + -
92A ASN* 3.3 48.0 - - + +
93A VAL* 3.8 12.6 - - + -
222A PHE* 3.4 47.3 - - + -
226A ALA 3.0 25.9 + - - +
227A LYS* 3.9 3.1 - - - +
229A LYS* 1.3 75.5 - - - +
231A TYR* 1.3 61.6 + - + +
233A ARG* 3.3 23.8 - - - +
244A ILE* 3.9 21.1 - - + +
245A LYS* 4.1 8.2 - - - -
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Residues in contact with TYR 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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74A LEU* 4.4 12.9 - - + +
227A LYS* 3.0 53.8 + - + +
228A LYS* 4.1 4.0 - - + +
230A MET* 1.3 79.7 - - + +
232A SER* 1.3 58.6 + - - +
233A ARG 3.6 1.0 - - - +
244A ILE* 4.6 9.9 - - + -
245A LYS* 3.7 53.9 + - + +
248A ALA* 3.5 25.3 - - - +
254A ASP* 3.8 14.6 + - - -
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Residues in contact with SER 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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228A LYS* 3.0 39.1 + - - +
229A LYS* 3.6 7.3 + - - -
230A MET 3.2 0.2 - - - -
231A TYR* 1.3 78.7 - - - +
233A ARG* 1.3 67.3 + - - +
234A LYS* 3.7 9.4 + - - +
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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