Contacts of the helix formed by residues 221 - 226 (chain A) in PDB entry 1CX4
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 GLU 221 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A LEU* 3.8 20.3 - - + +
189A PHE* 3.6 26.3 - - + -
218A SER* 4.3 4.3 + - - +
219A PHE* 3.4 15.0 + - - -
220A GLY* 1.3 78.1 - - - +
222A LEU* 1.3 76.3 + - + +
224A LEU* 3.3 3.7 + - - +
225A MET* 3.1 42.0 + - + +
250A PHE* 4.0 11.7 - - + -
289A VAL* 4.7 7.2 - - + +
381A ARG* 4.7 5.5 + - - -
440A CMP 2.7 27.0 + - - -
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Residues in contact with LEU 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 GLY 3.5 1.0 - - - -
221A GLU* 1.3 86.9 - - - +
223A ALA* 1.3 62.8 + - - +
225A MET* 3.1 13.4 + - + -
226A TYR* 3.0 51.8 + - + +
228A THR* 4.4 4.5 - - - +
231A ALA* 4.6 6.7 - - + -
381A ARG* 3.5 48.0 - - - +
440A CMP 3.5 48.9 + - + +
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Residues in contact with ALA 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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186A GLY* 3.8 17.1 - - - +
222A LEU* 1.3 76.0 - - - +
224A LEU* 1.3 59.2 + - - +
227A ASN* 3.0 29.6 + - - +
228A THR* 3.1 29.0 + - - +
229A PRO 4.4 0.9 - - - -
230A ARG* 3.6 22.2 - - - +
247A ARG* 4.8 1.7 + - - -
440A CMP 3.0 21.2 + - - +
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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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186A GLY* 3.7 34.5 - - - +
187A ASP 3.7 3.8 - - - +
188A ASN 3.8 23.8 - - - +
189A PHE* 3.8 8.5 - - + +
220A GLY 3.6 13.9 - - - +
221A GLU 3.3 2.6 + - - +
222A LEU 3.1 0.8 - - - -
223A ALA* 1.3 77.2 - - - +
225A MET* 1.3 54.0 + - - +
227A ASN* 4.4 0.8 - - - +
230A ARG* 4.5 0.2 - - - +
245A LEU 4.4 0.2 - - - +
247A ARG* 3.8 39.5 - - + +
250A PHE* 3.6 35.9 - - + -
251A ARG* 2.7 39.3 + - + +
255A VAL* 4.2 0.9 - - - +
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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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152A LEU* 5.1 3.4 - - - -
221A GLU* 3.1 38.9 + - + +
222A LEU* 3.1 11.2 + - + +
224A LEU* 1.3 80.3 - - - +
226A TYR* 1.3 98.4 + - + +
227A ASN* 3.5 2.0 + - - -
250A PHE* 3.6 22.2 - - + -
251A ARG* 3.6 13.5 + - - +
255A VAL* 4.4 13.6 - - + +
258A ASN* 3.6 26.2 - - - +
288A ASP* 4.1 11.2 - - - +
289A VAL* 4.3 9.9 - - + -
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Residues in contact with TYR 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* 3.0 45.3 + - + +
225A MET* 1.3 99.8 - - + +
227A ASN* 1.3 72.7 + - - +
228A THR* 3.0 24.6 + - + +
285A LYS* 3.9 46.4 + - + +
288A ASP* 2.5 40.6 + - - +
289A VAL* 5.3 0.9 - - - +
381A ARG* 5.4 1.7 + - - -
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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