Contacts of the helix formed by residues 284 - 297 (chain B) in PDB entry 2C2L
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 ASN 284 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A ILE* 3.9 8.0 - - - +
284A ASN* 2.5 41.1 + - - +
244B PRO* 3.0 26.2 + - + +
246B ILE* 3.7 23.1 - - + +
252B THR* 3.6 16.6 + - - +
282B ILE 3.0 5.0 + - - -
283B PRO* 1.3 67.5 - - - +
285B LEU* 1.3 62.5 + - - +
286B ALA 3.7 1.4 + - - -
287B MET* 2.8 42.8 + - + +
288B LYS* 3.4 14.0 + - - +
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Residues in contact with LEU 285 (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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246A ILE* 4.1 0.4 - - - +
249A SER 4.9 2.2 - - - +
250A GLY* 3.1 35.2 + - - +
251A ILE* 4.5 11.2 - - + +
283B PRO* 2.9 27.6 + - + +
284B ASN* 1.3 69.5 - - - +
286B ALA* 1.3 69.2 + - - +
287B MET 3.1 1.8 - - - -
288B LYS* 2.8 26.5 + - + +
289B GLU* 3.0 12.9 + - - +
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A TYR* 4.7 3.4 - - + +
235A LYS* 6.3 0.7 - - - +
241A MET* 5.9 0.2 - - + -
250A GLY 4.8 1.6 + - - -
252A THR* 4.0 26.5 + - - +
287A MET* 3.5 31.5 - - + +
284B ASN* 3.6 2.6 + - - +
285B LEU* 1.3 77.6 - - - +
287B MET* 1.3 62.9 + - - +
289B GLU* 3.1 15.4 + - - +
290B VAL* 3.0 26.3 + - - +
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Residues in contact with MET 287 (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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284A ASN* 3.7 4.0 - - - +
286A ALA* 3.3 48.0 - - + +
287A MET* 3.3 26.5 - - + +
290A VAL* 3.8 20.4 - - - -
231B TYR 4.5 7.9 - - - +
232B LEU* 5.2 3.1 - - - -
241B MET* 5.9 1.1 - - + -
244B PRO* 3.8 13.9 - - + -
252B THR* 4.5 4.9 - - + -
284B ASN* 2.8 32.3 + - - +
286B ALA* 1.3 70.5 - - - +
288B LYS* 1.3 60.7 + - - +
290B VAL* 3.0 9.9 + - - +
291B ILE* 2.7 49.0 + - + +
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Residues in contact with LYS 288 (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 ARG 3.9 21.5 - - - +
243B GLU* 4.4 7.9 - - - +
244B PRO* 3.5 22.3 + - + +
283B PRO* 6.2 2.0 - - - +
284B ASN 3.4 10.1 + - - +
285B LEU* 2.8 22.7 + - - +
287B MET* 1.3 74.4 - - - +
289B GLU* 1.3 58.8 + - - +
291B ILE* 3.9 5.6 - - + +
292B ASP* 3.0 43.1 + - - +
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Residues in contact with GLU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A TYR* 3.4 37.7 - - + +
235A LYS* 4.9 8.7 + - - -
285B LEU* 3.0 11.0 + - - +
286B ALA* 3.3 14.2 - - - +
288B LYS* 1.3 78.7 - - - +
290B VAL* 1.3 61.3 + - - +
292B ASP* 3.6 7.4 - - + +
293B ALA* 3.4 20.6 + - - +
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Residues in contact with VAL 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A TYR* 3.6 30.3 - - + -
287A MET* 4.0 21.3 - - + -
290A VAL* 3.8 30.5 - - + -
232B LEU* 4.5 15.3 - - + -
286B ALA 3.0 22.2 + - - +
287B MET* 3.0 12.5 + - - +
289B GLU* 1.3 74.5 - - - +
291B ILE* 1.3 65.7 + - - +
292B ASP 3.1 1.5 + - - -
293B ALA* 3.3 5.0 + - - +
294B PHE* 3.1 20.3 + - - +
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Residues in contact with ILE 291 (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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232B LEU* 4.5 22.7 - - + +
240B LEU* 4.6 8.3 - - + -
241B MET* 3.1 56.3 - - + +
242B ARG* 5.0 5.6 - - - +
244B PRO* 3.7 19.3 - - + -
287B MET* 2.7 36.3 + - + +
288B LYS* 3.9 6.5 - - + +
290B VAL* 1.3 69.7 - - + +
292B ASP* 1.3 68.7 + - - +
294B PHE* 3.2 16.9 - - - +
295B ILE* 2.8 35.1 - - + +
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Residues in contact with ASP 292 (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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288B LYS* 3.0 38.2 + - - +
289B GLU* 3.6 10.3 - - + +
291B ILE* 1.3 78.3 - - - +
293B ALA* 1.3 59.0 + - - +
295B ILE* 2.8 30.4 + - - +
296B SER* 3.2 13.4 + - - -
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Residues in contact with ALA 293 (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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231A TYR* 3.5 30.5 - - + +
289B GLU 3.4 9.5 + - - +
290B VAL 3.3 8.0 + - - +
292B ASP* 1.3 78.4 - - - +
294B PHE* 1.3 61.4 + - - +
296B SER* 3.3 15.6 + - - -
297B GLU* 3.0 26.6 - - - +
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Residues in contact with PHE 294 (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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227B ASP 4.7 3.1 - - - -
228B ILE* 3.3 34.8 - - + -
229B PRO* 3.8 25.4 - - + -
232B LEU* 3.5 25.4 - - + -
240B LEU* 3.9 19.5 - - + -
290B VAL* 3.1 13.5 + - + +
291B ILE 3.2 10.3 - - - +
293B ALA* 1.3 78.6 - - - +
295B ILE* 1.3 64.8 + - + +
297B GLU* 3.4 3.8 + - - +
298B ASN* 2.5 58.2 + - - +
300B TRP* 4.7 2.9 - + - -
301B VAL* 4.2 8.1 - - + -
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Residues in contact with ILE 295 (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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240B LEU* 4.1 21.5 - - + -
242B ARG* 4.9 10.1 - - - +
291B ILE* 2.8 41.3 - - + +
292B ASP* 2.8 12.7 + - - +
294B PHE* 1.3 74.3 - - + +
296B SER* 1.3 57.9 + - - +
297B GLU 3.0 2.2 - - - -
298B ASN* 2.6 35.6 + - - +
299B GLY* 3.4 4.4 + - - -
301B VAL* 4.6 6.5 - - + -
302B GLU* 3.7 34.3 - - + +
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Residues in contact with SER 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ASP 3.2 14.3 + - - -
293B ALA* 3.4 15.6 + - - -
294B PHE 3.3 0.2 - - - -
295B ILE* 1.3 78.1 - - - +
297B GLU* 1.3 75.4 + - - +
298B ASN 3.7 0.2 + - - -
299B GLY* 4.8 2.1 + - - -
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Residues in contact with GLU 297 (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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224A LYS* 6.3 0.7 - - - +
293B ALA* 3.0 23.7 - - - +
294B PHE* 3.4 6.9 + - - +
295B ILE 3.0 0.4 - - - -
296B SER* 1.3 94.2 - - - +
298B ASN* 1.3 76.7 + - - +
299B GLY 3.9 1.1 - - - -
300B TRP* 4.5 0.9 + - - -
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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