Contacts of the helix formed by residues 240 - 251 (chain B) 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 GLY 240 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A ARG* 4.5 3.6 - - - -
238B LYS 4.2 1.2 + - - -
239B LEU* 1.3 75.6 - - - +
241B PRO* 1.3 72.6 - - - +
242B ALA 3.3 2.4 + - - -
243B VAL* 3.4 11.0 + - - +
244B LEU* 2.9 27.1 + - - +
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Residues in contact with PRO 241 (chain B).
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* 4.1 28.9 - - + +
223A PHE* 3.8 36.7 - - + -
249A ARG* 3.3 25.1 - - - +
240B GLY* 1.3 82.6 - - - +
242B ALA* 1.3 57.5 + - - +
244B LEU* 3.4 4.8 + - + +
245B VAL* 3.0 34.7 + - - +
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Residues in contact with ALA 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ARG* 3.8 13.1 - - - +
240B GLY 3.3 0.8 + - - -
241B PRO* 1.3 78.5 - - - +
243B VAL* 1.3 62.4 + - + +
245B VAL* 3.3 8.9 + - - +
246B GLU* 3.1 36.1 + - - +
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Residues in contact with VAL 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B LEU* 3.4 31.0 - - + -
240B GLY* 3.4 11.9 + - - +
242B ALA* 1.3 76.0 - - + +
244B LEU* 1.3 65.5 + - - +
246B GLU* 3.3 13.9 + - - +
247B ILE* 3.0 26.4 + - + +
330B LEU* 4.3 9.2 - - + -
333B SER* 3.7 40.2 - - - +
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Residues in contact with LEU 244 (chain B).
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* 3.6 35.0 - - + +
223A PHE* 4.3 8.3 - - + -
224A VAL* 3.6 30.5 - - + -
227B TRP* 4.0 15.3 - - + -
230B VAL* 4.1 24.2 - - + -
236B PHE* 3.8 12.8 - - + +
239B LEU* 3.7 15.2 - - + +
240B GLY 2.9 18.5 + - - +
241B PRO 3.4 5.2 - - - +
243B VAL* 1.3 73.3 - - - +
245B VAL* 1.3 61.6 + - - +
247B ILE* 3.4 5.3 - - + +
248B VAL* 2.8 34.8 + - - +
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Residues in contact with VAL 245 (chain B).
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* 3.6 21.8 - - + -
245A VAL* 3.9 34.3 - - + -
249A ARG* 6.1 0.4 - - - +
223B PHE* 4.2 10.8 - - + -
227B TRP* 3.9 13.7 - - + -
241B PRO 3.0 20.9 + - - +
242B ALA* 3.3 8.7 + - - +
243B VAL 3.3 0.2 - - - -
244B LEU* 1.3 73.9 - - - +
246B GLU* 1.3 64.9 + - + +
248B VAL* 3.2 1.2 + - - +
249B ARG* 2.9 33.8 + - + +
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Residues in contact with GLU 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B ALA* 3.1 25.1 + - - +
243B VAL* 3.5 15.5 - - + +
244B LEU 3.3 0.2 - - - -
245B VAL* 1.3 76.6 - - + +
247B ILE* 1.3 59.5 + - + +
249B ARG* 3.1 10.3 + - - +
250B ALA* 2.9 27.4 + - - +
329B MET* 5.0 7.1 - - - +
333B SER* 3.4 24.3 + - - -
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Residues in contact with ILE 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B VAL* 4.4 7.6 - - + -
236B PHE* 3.5 52.3 - - + -
239B LEU* 3.8 5.6 - - + -
243B VAL* 3.0 18.2 + - + +
244B LEU* 3.4 14.4 - - + +
246B GLU* 1.3 72.7 - - + +
248B VAL* 1.3 64.7 + - + +
250B ALA* 4.2 7.2 - - + +
251B LEU* 2.9 48.3 + - + +
322B LEU* 5.2 5.8 - - + -
326B ASP 5.7 1.1 - - - +
330B LEU* 3.8 38.1 - - + -
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Residues in contact with VAL 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B PHE* 3.5 16.5 - - + +
226B ASN* 2.9 45.9 + - + +
227B TRP* 3.5 52.0 - - + +
230B VAL* 3.7 28.5 - - + -
244B LEU* 2.8 26.1 + - - +
245B VAL 3.8 2.9 - - - +
247B ILE* 1.3 73.7 - - + +
249B ARG* 1.3 58.7 + - - +
251B LEU* 4.6 1.6 - - - -
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Residues in contact with ARG 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A PRO* 3.4 38.0 - - - +
242A ALA* 3.5 24.0 - - - +
245A VAL* 6.0 0.6 - - - +
219B ARG 6.1 1.0 - - - +
223B PHE* 3.7 20.3 - - + -
245B VAL* 2.9 24.5 + - + +
246B GLU* 3.3 11.7 - - - +
248B VAL* 1.3 78.4 - - - +
250B ALA* 1.3 61.7 + - + +
251B LEU 4.3 2.8 - - - +
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Residues in contact with ALA 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B GLU 2.9 15.6 + - - +
247B ILE* 3.2 5.6 + - + +
249B ARG* 1.3 78.1 - - - +
251B LEU* 1.3 63.1 + - - +
252B ARG* 3.5 3.6 + - - +
321B SER 4.3 2.4 - - - +
322B LEU* 3.8 11.4 - - + +
323B HIS* 4.9 8.5 + - - -
326B ASP* 3.4 45.3 - - + +
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Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B ASP* 6.1 0.5 - - - +
226B ASN* 2.8 29.3 + - - +
230B VAL* 3.5 31.9 - - + -
236B PHE* 4.1 7.2 - - + -
247B ILE* 2.9 39.6 + - + +
248B VAL* 4.2 1.6 + - - +
249B ARG 3.5 3.0 - - - +
250B ALA* 1.3 77.7 - - - +
252B ARG* 1.3 58.9 + - - +
274B PHE* 4.0 28.7 - - + -
320B LEU* 4.2 17.9 - - + -
321B SER 3.4 13.0 - - - +
322B LEU* 3.6 21.5 - - + -
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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