Contacts of the helix formed by residues 236 - 251 (chain A) in PDB entry 3BPT
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 SER 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A PRO* 4.8 0.2 - - - -
234A SER 3.6 2.2 + - - -
235A PRO* 1.3 76.4 - - - +
237A LYS* 1.3 62.6 + - - +
238A GLU* 3.3 19.7 + - - +
239A ASN* 3.0 42.1 + - - +
240A ILE* 3.1 15.6 + - - +
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Residues in contact with LYS 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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134A PRO* 3.9 24.2 - - + +
155A GLN* 2.8 35.7 - - - +
156A PHE* 4.1 4.3 - - + -
236A SER* 1.3 71.9 - - - +
238A GLU* 1.3 72.2 + - + +
240A ILE* 3.2 6.7 + - - +
241A ALA* 2.9 28.7 + - + +
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Residues in contact with GLU 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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236A SER* 3.1 20.8 - - - +
237A LYS* 1.3 91.2 + - + +
239A ASN* 1.3 62.2 + - - +
241A ALA* 3.2 7.7 + - - +
242A SER* 2.8 33.6 + - - +
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Residues in contact with ASN 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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232A LEU* 4.6 8.7 - - + -
233A LYS 5.1 1.4 - - - +
234A SER 4.4 1.7 - - - +
235A PRO* 3.5 17.2 - - + +
236A SER* 3.0 40.3 + - - +
238A GLU* 1.3 76.1 - - - +
240A ILE* 1.3 64.2 + - - +
242A SER* 3.3 8.9 + - - -
243A VAL* 3.2 27.8 + - - +
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Residues in contact with ILE 240 (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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82A PHE 3.9 9.2 - - - +
83A LEU* 3.9 14.8 - - + -
134A PRO* 3.6 30.1 - - + -
136A VAL* 4.0 20.0 - - + -
156A PHE* 3.9 21.3 - - + -
229A LEU* 4.2 10.8 - - + -
232A LEU* 4.0 22.2 - - + -
235A PRO* 4.1 11.2 - - + -
236A SER 3.1 19.0 + - - +
237A LYS* 3.5 6.3 - - - +
239A ASN* 1.3 76.1 - - - +
241A ALA* 1.3 62.4 + - - +
243A VAL* 3.2 6.2 + - - +
244A LEU* 3.1 24.1 + - + +
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Residues in contact with ALA 241 (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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156A PHE* 4.1 24.2 - - + -
215A HIS* 4.6 3.7 + - - +
237A LYS* 2.9 18.3 + - + +
238A GLU* 3.5 9.0 - - - +
240A ILE* 1.3 75.6 - - - +
242A SER* 1.3 57.5 + - - +
244A LEU* 3.4 4.2 + - - +
245A GLU* 2.9 33.5 + - - +
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Residues in contact with SER 242 (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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238A GLU* 2.8 18.5 + - - +
239A ASN* 3.5 11.8 + - - -
240A ILE 3.2 0.4 - - - -
241A ALA* 1.3 76.6 - - - +
243A VAL* 1.3 62.9 + - - +
245A GLU* 3.3 9.5 + - - +
246A ASN* 3.0 38.4 + - - +
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Residues in contact with VAL 243 (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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225A LEU* 3.6 23.6 - - + -
228A ASP* 4.3 14.8 - - + +
229A LEU* 3.8 13.2 - - + -
232A LEU* 4.1 28.5 - - + -
239A ASN 3.2 13.2 + - - +
240A ILE 3.2 7.3 + - - +
242A SER* 1.3 75.5 - - - +
244A LEU* 1.3 63.1 + - - +
246A ASN* 3.2 9.3 + - - +
247A TYR* 3.1 40.5 + - + -
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Residues in contact with LEU 244 (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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136A VAL* 4.5 3.6 - - + -
156A PHE* 3.4 50.3 - - + -
158A VAL* 3.7 24.5 - - + -
215A HIS* 3.5 26.3 - - + +
217A VAL* 5.2 1.7 - - + +
225A LEU* 3.9 25.4 - - + -
229A LEU* 4.5 13.0 - - + -
240A ILE* 3.1 18.2 + - + +
241A ALA 3.8 3.8 - - - +
243A VAL* 1.3 75.6 - - - +
245A GLU* 1.3 57.3 + - - +
247A TYR* 3.4 2.9 + - - +
248A HIS* 2.9 29.3 + - - +
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Residues in contact with GLU 245 (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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215A HIS* 3.9 7.5 - - - +
241A ALA 2.9 18.4 + - - +
242A SER* 3.6 9.8 + - - +
244A LEU* 1.3 77.7 - - - +
246A ASN* 1.3 62.8 + - - +
248A HIS* 3.6 7.7 - - + +
249A THR* 2.8 45.4 + - - +
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Residues in contact with ASN 246 (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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242A SER* 3.0 30.7 + - - +
243A VAL* 3.2 8.9 + - - +
245A GLU* 1.3 84.9 - - - +
247A TYR* 1.3 66.2 + - + +
249A THR* 3.6 4.3 + - - -
250A GLU* 3.5 27.6 + - - +
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Residues in contact with TYR 247 (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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217A VAL* 3.8 22.9 - - + +
221A LYS* 3.8 31.4 - - + -
224A MSE 3.4 25.1 - - + +
225A LEU* 3.5 42.8 - - + -
228A ASP* 2.6 30.3 + - - -
243A VAL* 3.1 32.0 + - + +
244A LEU 3.8 5.2 - - - +
246A ASN* 1.3 77.8 - - + +
248A HIS* 1.3 65.0 + - - +
250A GLU* 3.3 5.5 + - - +
251A SER* 3.2 22.7 + - - -
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Residues in contact with HIS 248 (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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205A ARG* 4.1 11.2 + - - -
208A TYR* 3.4 48.0 + + - -
214A THR 4.9 0.4 - - - -
215A HIS* 3.5 17.1 - + + -
216A PHE* 2.9 44.8 + - + +
217A VAL* 4.5 0.4 - - - +
244A LEU 2.9 22.1 + - - +
245A GLU* 3.2 6.9 + - + +
247A TYR* 1.3 72.4 - - - +
249A THR* 1.3 72.8 + - - +
251A SER* 2.9 20.1 + - - +
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Residues in contact with THR 249 (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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245A GLU* 2.8 32.7 + - - +
246A ASN* 3.9 6.7 - - - -
247A TYR 3.3 0.2 - - - -
248A HIS* 1.3 81.5 - - - +
250A GLU* 1.3 64.6 + - + +
251A SER 4.2 0.2 - - - +
255A ARG* 2.9 20.8 + - - -
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Residues in contact with GLU 250 (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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218A ASP* 4.8 0.2 - - - +
221A LYS* 4.3 22.8 + - + +
246A ASN 3.5 15.5 + - - +
247A TYR* 3.3 5.6 + - - +
248A HIS 3.2 0.8 - - - -
249A THR* 1.3 82.0 - - + +
251A SER* 1.3 66.7 + - - +
252A LYS* 3.5 21.5 + - - +
255A ARG* 3.9 4.3 - - - +
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Residues in contact with SER 251 (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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205A ARG* 3.0 24.0 + - - -
216A PHE* 3.2 21.8 + - - -
217A VAL* 3.9 1.1 - - - -
218A ASP* 3.6 28.7 - - - -
221A LYS* 6.5 0.9 - - - -
247A TYR 3.2 8.9 + - - -
248A HIS 2.9 18.4 + - - +
249A THR 4.2 0.7 - - - +
250A GLU* 1.3 76.8 - - - +
252A LYS* 1.3 59.9 + - - +
255A ARG* 3.1 21.1 + - - +
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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