Contacts of the helix formed by residues 236 - 250 (chain P) 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 THR 236 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235P LEU* 1.3 79.7 - - - +
237P PRO* 1.3 77.0 - - - +
238P SER* 3.9 11.7 + - - +
239P ASN* 3.0 37.1 + - + +
240P ILE* 3.1 10.8 + - - +
532S ARG* 6.1 1.2 - - - +
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Residues in contact with PRO 237 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218P THR 5.9 3.4 - - - +
219P GLN* 4.2 22.4 - - - +
222P LEU* 3.6 23.3 - - + -
235P LEU 4.0 0.4 - - - +
236P THR* 1.3 91.8 - - - +
238P SER* 1.3 61.3 + - - +
240P ILE* 3.2 25.6 - - + +
241P ARG* 3.4 21.8 + - - +
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Residues in contact with SER 238 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236P THR* 3.2 14.2 + - - -
237P PRO* 1.3 77.6 - - - +
239P ASN* 1.3 62.4 + - - +
241P ARG* 3.3 31.4 + - - +
242P SER* 3.1 23.3 + - - -
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Residues in contact with ASN 239 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169P GLU* 2.7 51.2 + - - +
235P LEU* 3.4 27.4 - - + +
236P THR* 3.0 18.2 + - + +
238P SER* 1.3 75.5 - - - +
240P ILE* 1.3 66.9 + - - +
242P SER* 3.0 12.7 + - - -
243P LEU* 2.9 23.1 + - - +
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Residues in contact with ILE 240 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217P THR* 5.1 4.0 - - - +
218P THR* 4.5 8.7 - - - +
221P ILE* 3.5 40.6 - - + -
222P LEU* 3.8 18.2 - - + -
225P ILE* 4.4 11.0 - - + -
235P LEU* 3.4 17.9 - - + +
236P THR 3.1 13.2 + - - +
237P PRO* 3.2 14.4 - - + +
239P ASN* 1.3 74.3 - - - +
241P ARG* 1.3 64.0 + - + +
243P LEU* 2.8 31.4 + - + +
244P CYS* 2.9 14.8 + - + +
261P TYR* 6.3 2.0 - - + -
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Residues in contact with ARG 241 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218P THR* 5.4 8.2 - - + +
237P PRO* 3.4 19.2 + - - +
238P SER* 3.3 33.6 + - - +
240P ILE* 1.3 81.9 - - + +
242P SER* 1.3 64.0 + - - +
244P CYS* 3.0 5.1 + - - +
245P GLU* 2.9 35.2 + - + +
255P LYS* 6.1 0.2 - - - +
258P HIS* 5.6 1.1 - - - -
259P ASP* 3.2 38.9 + - + -
261P TYR* 4.0 21.5 - - + +
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Residues in contact with SER 242 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524O SER 6.1 0.7 - - - -
525O THR 4.5 4.0 - - - +
238P SER* 3.1 15.6 + - - -
239P ASN* 3.0 21.3 + - - -
241P ARG* 1.3 77.1 - - - +
243P LEU* 1.3 63.5 + - - +
245P GLU* 3.9 9.0 + - - +
246P VAL* 3.5 19.9 + - - +
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Residues in contact with LEU 243 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527O LEU* 5.8 4.5 - - + -
169P GLU* 3.1 15.9 - - + +
175P ILE* 4.9 5.6 - - + -
178P LEU* 3.4 32.8 - - + -
179P LEU* 4.1 17.7 - - + -
182P VAL* 5.6 8.7 - - + -
235P LEU* 4.9 9.9 - - + -
239P ASN* 2.9 39.7 + - - +
240P ILE* 2.8 23.7 + - + +
242P SER* 1.3 71.4 - - - +
244P CYS* 1.3 65.3 + - - +
246P VAL* 2.9 23.9 + - - +
247P LEU* 3.4 11.3 + - + +
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Residues in contact with CYS 244 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182P VAL* 6.5 1.1 - - + -
186P ILE* 4.9 6.7 - - - -
240P ILE* 2.9 15.8 + - + +
241P ARG* 3.0 7.8 + - - +
243P LEU* 1.3 75.6 - - - +
245P GLU* 1.3 57.0 + - - +
247P LEU* 3.1 9.5 + - - +
248P VAL* 2.9 29.5 + - - +
253P LEU* 3.4 26.9 - - - -
261P TYR* 3.3 49.6 - - + +
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Residues in contact with GLU 245 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513O ASP* 5.5 2.1 - - - +
525O THR* 5.7 3.6 - - + +
241P ARG* 2.9 27.3 + - + +
242P SER* 4.0 9.2 - - - +
244P CYS* 1.3 76.8 - - - +
246P VAL* 1.3 62.3 + - + +
248P VAL* 3.0 12.6 + - - +
249P TYR* 2.9 45.4 + - + +
255P LYS* 2.4 44.2 + - - -
261P TYR* 3.2 12.3 + - - -
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Residues in contact with VAL 246 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506O ARG* 3.5 36.6 - - - +
525O THR 3.5 24.9 - - - +
526O ALA* 4.4 2.9 - - - -
527O LEU* 4.3 23.8 - - + +
179P LEU* 5.0 6.7 - - + -
242P SER 3.5 13.7 + - - +
243P LEU* 2.9 10.6 + - - +
245P GLU* 1.3 75.8 - - - +
247P LEU* 1.3 64.3 + - + +
249P TYR* 2.8 13.9 + - + +
250P ASP* 2.8 28.3 + - - +
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Residues in contact with LEU 247 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179P LEU* 3.7 43.3 - - + +
182P VAL* 4.6 8.3 - - + -
183P TRP* 4.0 21.8 - - + -
243P LEU* 3.7 14.8 - - + +
244P CYS* 3.1 5.8 + - - +
246P VAL* 1.3 75.7 - - + +
248P VAL* 1.3 60.8 + - - +
250P ASP* 4.3 7.2 - - + +
251P ASP* 2.8 22.3 + - - -
252P LYS* 2.8 35.2 + - + -
253P LEU* 3.4 36.6 + - + -
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Residues in contact with VAL 248 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509O ARG* 4.3 11.8 + - - +
513O ASP* 4.9 8.5 - - - +
244P CYS 2.9 20.9 + - - +
245P GLU* 3.1 22.9 - - - +
247P LEU* 1.3 77.8 - - - +
249P TYR* 1.3 61.4 + - + +
251P ASP* 2.7 29.1 + - - +
253P LEU* 3.5 27.0 - - + +
254P GLU* 5.4 0.7 - - - -
255P LYS* 4.1 31.6 - - + +
261P TYR* 4.4 4.7 - - + -
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Residues in contact with TYR 249 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505O MET* 4.7 3.8 - - - +
506O ARG* 3.3 29.7 + - + +
509O ARG* 3.3 30.7 - - + +
510O CYS* 3.6 49.8 + - + -
513O ASP* 3.5 33.4 + - - +
514O ASN* 4.8 3.6 + - - -
525O THR* 4.1 18.1 - - + +
526O ALA* 5.3 3.6 - - - -
245P GLU* 2.9 38.7 + - + +
246P VAL* 2.8 17.7 + - + +
248P VAL* 1.3 79.0 - - + +
250P ASP* 1.3 59.8 + - - +
251P ASP* 3.0 10.7 + - - +
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Residues in contact with ASP 250 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502O PRO* 4.2 11.0 - - - +
503O SER* 5.0 0.7 - - - -
505O MET* 4.6 16.3 - - - +
506O ARG* 3.0 54.4 + - - +
179P LEU* 6.2 0.2 - - - +
246P VAL* 2.8 16.9 + - - +
247P LEU* 4.2 6.4 - - + +
249P TYR* 1.3 70.6 - - - +
251P ASP* 1.3 69.4 + - - +
252P LYS* 3.1 24.6 + - + +
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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