Contacts of the helix formed by residues 241 - 251 (chain C) in PDB entry 6CNB
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 241 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240C LYS* 1.3 84.0 - - - +
242C GLU* 1.3 69.2 + - - +
243C SER 3.6 0.9 - - - -
244C ALA* 3.4 11.5 - - - +
245C ARG* 3.9 8.7 + - - -
258C ILE* 5.7 0.7 - - - +
261C GLY* 3.6 16.7 + - - +
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Residues in contact with GLU 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C GLY* 1.3 71.3 - - - -
243C SER* 1.3 58.0 + - - +
245C ARG* 2.4 62.8 + - + +
246C ARG* 3.7 5.7 + - - -
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Residues in contact with SER 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C ILE 5.8 0.2 - - - -
240C LYS 5.0 2.0 + - - -
241C GLY 3.6 0.4 - - - -
242C GLU* 1.3 80.7 - - - +
244C ALA* 1.3 57.8 + - - +
245C ARG 3.1 0.4 - - - -
246C ARG* 3.0 32.1 + - - +
247C PHE 2.9 22.7 + - - -
284C GLU* 5.1 5.2 + - - -
285C PHE* 3.6 23.1 - - - -
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Residues in contact with ALA 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C ILE* 3.1 35.6 + - + +
240C LYS* 3.8 10.5 + - - -
241C GLY 3.4 14.5 + - - +
242C GLU 2.8 0.8 + - - -
243C SER* 1.3 75.7 - - - +
245C ARG* 1.3 62.8 + - - +
247C PHE* 3.0 25.1 - - - +
248C GLN* 3.4 4.3 + - - +
258C ILE* 3.7 22.2 - - + +
264C GLU* 4.9 1.3 - - - -
265C ALA* 4.7 4.2 - - - +
285C PHE* 5.3 0.9 - - - -
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Residues in contact with ARG 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C GLY 3.9 7.0 + - - -
242C GLU* 2.4 57.1 + - + +
244C ALA* 1.3 66.4 - - - +
246C ARG* 1.3 63.1 + - - +
248C GLN* 3.1 34.5 + - - +
249C LYS* 3.6 4.0 + - - +
258C ILE* 4.3 22.9 - - + +
261C GLY* 5.3 10.1 - - - -
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Residues in contact with ARG 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C GLU* 3.7 6.1 + - - -
243C SER* 3.0 32.5 + - - +
245C ARG* 1.3 77.6 - - - +
247C PHE* 1.3 61.7 + - - +
249C LYS* 3.1 21.9 + - - +
250C CYS* 3.0 19.4 + - - +
282C TYR* 5.6 13.9 - - + -
285C PHE* 4.6 16.1 - - + -
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Residues in contact with PHE 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C ILE* 5.1 1.3 - - + -
235C ILE* 4.4 12.3 - - + -
239C ILE* 4.1 20.0 - - + -
243C SER 2.9 9.0 + - - +
244C ALA* 3.0 20.8 + - - +
246C ARG* 1.3 77.2 - - - +
248C GLN* 1.3 60.5 + - - +
250C CYS* 3.1 18.1 - - - +
251C PHE* 3.6 27.2 + + - -
256C ILE* 3.5 37.7 - - + -
265C ALA* 4.4 5.6 - - + -
279C VAL* 3.8 18.2 - - + -
285C PHE* 3.7 33.2 - + + -
288C LYS* 6.5 0.2 - - - -
289C VAL* 3.9 29.4 - - + -
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Residues in contact with GLN 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C ALA 3.4 2.9 + - - +
245C ARG* 3.1 31.1 + - - +
247C PHE* 1.3 76.6 - - - +
249C LYS* 1.3 67.4 + - + +
251C PHE* 3.1 21.9 + - - +
252C PRO 5.1 0.3 - - - -
253C PRO* 5.1 5.5 - - - +
255C VAL* 4.3 5.3 - - + +
256C ILE* 3.5 30.6 - - + +
257C GLY* 3.8 5.0 - - - -
258C ILE* 3.5 35.1 + - + +
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Residues in contact with LYS 249 (chain C).
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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989B LYS* 5.8 4.4 - - - +
992B VAL* 6.1 0.7 - - - +
993B ASP* 6.2 0.2 - - - -
245C ARG 3.6 4.7 + - - +
246C ARG* 3.1 22.8 + - - +
248C GLN* 1.3 83.6 - - + +
250C CYS* 1.3 62.4 + - - +
251C PHE 3.2 7.8 + - - +
282C TYR* 4.9 10.7 + - - -
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Residues in contact with CYS 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992B VAL* 4.8 7.0 - - - +
246C ARG 3.0 11.2 + - - +
247C PHE* 3.1 18.6 - - - +
248C GLN 3.0 0.6 - - - -
249C LYS* 1.3 79.9 - - - +
251C PHE* 1.3 58.6 + - - +
252C PRO* 4.8 0.2 - - - +
278C GLU* 3.5 27.5 - - - +
279C VAL* 3.4 44.6 - - + -
282C TYR* 3.5 30.7 - - + -
285C PHE* 4.8 2.5 - - + -
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Residues in contact with PHE 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992B VAL 5.6 2.5 - - - -
993B ASP* 6.0 1.4 - - - -
233C ILE* 3.5 30.3 - - + -
247C PHE* 3.6 28.9 + + - -
248C GLN 3.1 12.8 + - - +
249C LYS* 3.4 9.5 - - - +
250C CYS* 1.3 85.0 - - - +
252C PRO* 1.3 75.4 - - + +
253C PRO* 3.8 1.2 - - - +
255C VAL* 3.3 35.9 - - + -
256C ILE* 4.2 10.8 - - + -
273C ASP* 4.5 6.3 - - - -
276C SER 6.3 0.2 - - - -
277C ARG 5.4 3.8 - - - -
278C GLU* 4.6 9.4 - - - -
279C VAL* 3.3 42.4 - - + -
289C VAL* 5.4 0.9 - - + -
291C LEU* 5.3 7.6 - - + -
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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