Contacts of the helix formed by residues 220 - 231 (chain A) in PDB entry 3CL1
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 ARG 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A GLY* 1.3 63.5 + - - +
222A ASP* 3.4 3.9 - - - +
223A PHE* 3.2 6.8 + - - +
224A VAL* 3.0 55.4 + - - +
230B VAL* 5.6 1.6 - - - +
236B PHE* 2.7 26.3 + - - +
237B GLN* 3.4 36.1 + - - +
238B LYS 5.6 0.2 - - - -
239B LEU 2.7 28.5 + - - +
240B GLY* 4.5 4.0 - - - -
241B PRO* 4.1 28.1 - - + +
244B LEU* 3.6 28.5 - - + +
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Residues in contact with GLY 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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220A ARG* 1.3 81.1 - - - +
222A ASP* 1.3 60.2 + - - +
224A VAL* 3.4 6.4 - - - +
225A ARG* 3.1 50.2 + - - -
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Residues in contact with ASP 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 ARG 3.4 1.7 - - - +
221A GLY* 1.3 74.1 - - - +
223A PHE* 1.3 57.1 + - - +
225A ARG* 3.1 25.3 + - - +
226A ASN* 3.1 39.0 + - - +
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Residues in contact with PHE 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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220A ARG* 3.2 17.1 + - - +
222A ASP* 1.3 78.7 - - - +
224A VAL* 1.3 71.7 + - + +
226A ASN* 3.3 8.1 + - - -
227A TRP* 3.1 39.0 - + - -
245A VAL* 4.6 3.8 - - + -
248A VAL* 3.5 25.8 - - + +
249A ARG* 4.0 31.0 - - + -
227B TRP* 3.4 22.9 - + - -
241B PRO* 3.8 39.7 - - + -
244B LEU* 4.3 3.4 - - + -
245B VAL* 3.6 25.1 - - + -
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Residues in contact with VAL 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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220A ARG* 3.0 44.0 + - - +
221A GLY* 3.4 11.4 - - - +
223A PHE* 1.3 75.7 - - + +
225A ARG* 1.3 71.0 + - - +
227A TRP* 3.6 19.9 + - - +
228A GLN* 4.0 5.9 + - - +
227B TRP* 4.8 7.9 - - + -
244B LEU* 3.6 31.2 - - + -
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Residues in contact with ARG 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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221A GLY* 3.1 46.2 + - - +
222A ASP* 3.1 31.3 + - - +
224A VAL* 1.3 82.8 - - - +
226A ASN* 1.3 63.5 + - - +
227A TRP 3.3 0.7 + - - -
228A GLN* 3.4 8.7 + - + +
229A LEU* 3.3 37.3 + - + +
253A ALA* 6.1 1.3 - - + -
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Residues in contact with ASN 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 ASP* 3.1 24.2 + - - +
223A PHE 3.7 0.2 - - - +
224A VAL 3.3 0.4 - - - -
225A ARG* 1.3 78.6 - - - +
227A TRP* 1.3 52.3 + - - +
229A LEU* 3.9 4.5 - - - +
230A VAL* 2.7 45.3 + - + +
248A VAL* 3.1 36.3 + - + -
251A LEU* 2.7 33.7 + - - +
252A ARG* 4.9 0.2 - - - +
253A ALA* 3.8 15.1 + - - +
320A LEU* 3.6 21.1 - - - +
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Residues in contact with TRP 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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223A PHE* 3.1 44.9 - + - -
224A VAL* 3.6 13.2 + - - +
225A ARG 3.2 0.8 - - - -
226A ASN* 1.3 75.9 - - - +
228A GLN* 1.3 61.4 + - - +
230A VAL* 3.6 7.0 + - + +
231A ALA* 3.4 20.6 + - - +
244A LEU* 3.8 31.0 - - + -
245A VAL* 4.0 17.9 - - + -
248A VAL* 3.5 34.2 - - + +
223B PHE* 3.6 19.5 - + - -
224B VAL* 5.0 5.2 - - + -
227B TRP* 3.3 70.9 - + + -
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Residues in contact with GLN 228 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A VAL 4.0 6.1 + - - +
225A ARG* 3.4 10.8 + - + +
226A ASN 3.3 0.4 - - - -
227A TRP* 1.3 78.1 - - - +
229A LEU* 1.3 63.9 + - + +
231A ALA* 3.7 15.8 - - - +
232A ALA* 4.3 4.0 + - - +
276A VAL* 5.5 0.2 - - - +
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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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225A ARG* 3.3 28.0 + - + +
226A ASN* 3.1 12.5 + - - +
228A GLN* 1.3 80.9 - - + +
230A VAL* 1.3 62.5 + - - +
231A ALA 3.2 1.6 - - - -
232A ALA* 3.2 19.8 + - - +
233A VAL* 4.1 1.6 + - - +
253A ALA* 3.7 30.3 - - + -
276A VAL* 3.6 40.1 - - + +
318A SER* 4.2 13.0 - - - +
319A LEU 5.6 0.4 - - - +
320A LEU* 3.9 12.9 - - + +
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Residues in contact with VAL 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 ASN* 2.7 25.2 + - + +
227A TRP* 3.9 9.4 - - + +
229A LEU* 1.3 68.5 - - - +
231A ALA* 1.3 63.6 + - - +
232A ALA 3.1 2.0 - - - -
233A VAL* 3.1 21.7 + - - +
236A PHE* 3.9 20.7 - - + +
244A LEU* 4.0 24.2 - - + -
247A ILE* 5.3 0.7 - - + -
248A VAL* 3.9 16.6 - - + -
251A LEU* 3.6 31.6 - - + -
320A LEU* 4.1 9.0 - - + -
220B ARG* 5.7 2.5 - - - +
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Residues in contact with ALA 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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227A TRP 3.4 11.2 + - - +
228A GLN* 3.7 15.3 - - - +
229A LEU 3.2 1.0 - - - -
230A VAL* 1.3 78.0 - - - +
232A ALA* 1.3 59.9 + - - +
233A VAL 3.2 4.2 + - - -
234A PRO* 4.6 5.0 - - - +
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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