Contacts of the helix formed by residues 232 - 239 (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 ALA 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A GLN 5.0 2.7 - - - +
229A LEU 3.2 14.2 + - - +
230A VAL 3.1 0.8 - - - -
231A ALA* 1.3 78.7 - - - +
233A VAL* 1.3 56.4 + - - +
234A PRO* 3.3 11.9 - - - +
276A VAL* 3.6 32.7 - - + +
292A PRO* 4.3 4.3 - - + +
293A GLY* 3.7 13.5 + - - -
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Residues in contact with VAL 233 (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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229A LEU 4.1 12.6 - - - +
230A VAL 3.1 12.9 + - - +
231A ALA 4.4 1.3 - - - -
232A ALA* 1.3 81.1 - - - +
234A PRO* 1.3 63.6 - - - +
235A LEU* 4.1 11.2 - - + -
236A PHE* 3.1 42.4 + - + +
237A GLN 4.4 0.5 + - - -
274A PHE* 3.9 30.3 - - + -
275A VAL 3.9 17.3 - - - +
276A VAL* 4.4 2.9 - - + -
293A GLY* 3.9 19.5 - - - +
320A LEU* 4.3 7.2 - - + -
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Residues in contact with PRO 234 (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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231A ALA 5.0 4.7 - - - +
232A ALA 3.3 13.0 - - - +
233A VAL* 1.3 80.0 - - - +
235A LEU* 1.3 67.2 + - - +
236A PHE 3.1 0.4 - - - -
237A GLN* 2.9 26.1 + - + +
238A LYS 4.4 0.3 + - - -
293A GLY* 3.9 15.5 - - - +
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Residues in contact with LEU 235 (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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233A VAL* 3.1 12.7 + - + +
234A PRO* 1.3 78.8 - - - +
236A PHE* 1.3 64.6 + - + +
237A GLN 3.2 4.7 + - - -
238A LYS* 3.2 21.1 + - - +
274A PHE* 3.7 17.3 - - + -
293A GLY 5.2 3.8 + - - +
295A PHE* 4.3 11.0 - - + -
337A ILE* 3.6 21.6 - - + +
340A ILE* 3.9 41.3 - - + -
341A PHE* 3.6 33.2 - - + -
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Residues in contact with PHE 236 (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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230A VAL* 3.9 30.7 - - + +
233A VAL* 3.1 39.1 + - + +
234A PRO 3.0 2.0 + - - -
235A LEU* 1.3 79.2 - - + +
237A GLN* 1.3 55.0 + - - +
238A LYS 3.1 5.8 - - - -
239A LEU* 3.2 43.3 + - + +
244A LEU* 4.2 3.1 - - + +
247A ILE* 4.1 18.8 - - + -
251A LEU* 4.1 24.2 - - + -
274A PHE* 3.6 47.1 - + - -
320A LEU* 4.7 1.3 - - + -
330A LEU* 4.1 7.2 - - + -
337A ILE* 4.8 1.8 - - + -
220B ARG* 2.9 15.7 + - - +
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Residues in contact with GLN 237 (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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233A VAL 4.4 0.6 + - - -
234A PRO* 2.9 20.5 + - + +
236A PHE* 1.3 76.2 - - - +
238A LYS* 1.3 56.8 + - - +
239A LEU 3.1 3.4 - - - -
220B ARG* 3.1 37.5 + - - +
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Residues in contact with LYS 238 (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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234A PRO 4.4 0.2 + - - -
235A LEU 3.2 14.7 + - - +
236A PHE 3.1 0.4 - - - -
237A GLN* 1.3 77.9 - - - +
239A LEU* 1.3 60.2 + - - +
240A GLY 4.0 1.6 + - - -
334A SER* 4.6 4.0 + - - +
336A GLU* 3.7 28.7 - - - +
337A ILE* 4.0 17.3 - - + -
340A ILE* 6.0 1.8 - - + -
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Residues in contact with LEU 239 (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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236A PHE* 3.4 40.4 - - + +
237A GLN 3.1 1.2 - - - -
238A LYS* 1.3 79.3 - - - +
240A GLY* 1.3 65.9 + - - +
243A VAL* 3.8 20.2 - - + -
244A LEU* 4.1 20.0 - - + +
247A ILE* 3.7 21.1 - - + -
330A LEU* 4.0 2.2 - - + -
333A SER 5.4 0.2 - - - +
334A SER* 3.5 33.2 - - - +
337A ILE* 3.5 14.4 - - + -
220B ARG* 2.7 32.6 + - - +
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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