Contacts of the helix formed by residues 246 - 262 (chain A) in PDB entry 3J8B
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 TRP 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A ILE* 6.3 0.2 - - - +
244A GLU* 3.1 9.4 + - - +
245A LEU* 1.3 72.4 - - - +
247A GLN* 1.3 60.5 + - - +
249A ALA* 3.2 10.3 + - + +
250A PHE* 2.9 28.6 + - - +
282A VAL* 5.8 6.1 - - + +
285A LYS* 5.1 13.7 - - + -
518C GLY* 4.6 19.7 - - - -
519C PRO 5.4 2.7 - - - +
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Residues in contact with GLN 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU 3.4 0.6 - - - -
246A TRP* 1.3 78.1 - - - +
248A GLU* 1.3 62.5 + - - +
250A PHE* 3.4 7.8 + - - +
251A LYS* 3.2 21.0 + - - +
516C LEU* 5.1 10.5 - - + +
518C GLY* 5.7 2.9 - - - +
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Residues in contact with GLU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ARG* 5.7 11.0 - - + -
198A CYS* 6.4 2.2 - - + -
240A ALA* 4.3 7.4 - - + -
245A LEU* 3.0 23.1 + - + +
247A GLN* 1.3 76.2 - - - +
249A ALA* 1.3 66.7 + - - +
251A LYS* 3.2 7.7 + - - +
252A ALA* 3.0 23.9 + - - +
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Residues in contact with ALA 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LEU* 4.9 7.2 - - + +
240A ALA* 3.5 25.7 - - + +
241A ILE* 4.5 7.2 - - + +
245A LEU 2.8 13.1 + - - +
246A TRP* 3.3 15.7 - - - +
248A GLU* 1.3 75.9 - - - +
250A PHE* 1.3 58.1 + - - +
252A ALA* 3.0 6.5 + - - +
253A VAL* 2.9 27.3 + - - +
282A VAL* 5.0 14.6 - - + -
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Residues in contact with PHE 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TRP 2.9 15.2 + - - +
247A GLN 3.7 5.6 - - - +
248A GLU 3.3 0.4 - - - -
249A ALA* 1.3 75.6 - - - +
251A LYS* 1.3 62.0 + - - +
253A VAL* 3.2 19.9 + - - +
254A GLU* 3.5 7.6 + - - +
282A VAL* 5.8 4.4 - - + +
516C LEU* 4.1 24.5 - - + -
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Residues in contact with LYS 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A GLN 3.2 12.4 + - - +
248A GLU* 3.2 11.2 + - - +
250A PHE* 1.3 77.2 - - - +
252A ALA* 1.3 61.6 + - - +
254A GLU* 3.5 7.0 + - - +
255A ASP* 3.2 19.6 + - - +
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Residues in contact with ALA 252 (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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198A CYS* 6.5 0.4 - - + -
233A ARG* 4.8 4.1 - - + +
236A GLN* 4.4 13.0 - - + +
237A LEU* 4.1 28.3 - - - +
240A ALA* 5.2 0.7 - - + -
248A GLU 3.0 15.8 + - - +
249A ALA* 3.0 6.2 + - - +
251A LYS* 1.3 75.3 - - - +
253A VAL* 1.3 59.9 + - - +
255A ASP* 3.3 11.5 - - + +
256A ILE* 2.9 27.9 + - - +
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Residues in contact with VAL 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LEU* 5.1 5.6 - - + +
249A ALA 2.9 11.4 + - - +
250A PHE* 3.5 13.7 - - - +
251A LYS 3.2 0.2 - - - -
252A ALA* 1.3 74.9 - - - +
254A GLU* 1.3 60.5 + - - +
256A ILE* 3.2 8.3 + - - +
257A HIS* 2.8 27.5 + - - +
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Residues in contact with GLU 254 (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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250A PHE 3.5 7.8 + - - +
251A LYS* 4.0 7.4 - - - +
253A VAL* 1.3 76.0 - - - +
255A ASP* 1.3 66.7 + - - +
257A HIS* 3.4 9.2 - - + +
258A GLY* 2.9 22.9 + - - -
358A LEU* 6.1 0.9 - - - -
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Residues in contact with ASP 255 (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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233A ARG* 4.7 13.0 - - + +
251A LYS 3.2 14.7 + - - +
252A ALA* 3.3 15.3 - - + +
254A GLU* 1.3 78.8 - - - +
256A ILE* 1.3 61.3 + - - +
258A GLY* 3.5 1.2 + - - -
259A LEU* 3.4 18.7 + - - +
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Residues in contact with ILE 256 (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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230A LEU* 5.9 1.2 - - - +
233A ARG* 4.4 22.2 - - + +
234A LEU* 5.1 4.5 - - - +
237A LEU* 5.7 3.8 - - + -
252A ALA 2.9 13.8 + - - +
253A VAL* 3.4 11.7 - - - +
255A ASP* 1.3 74.7 - - - +
257A HIS* 1.3 64.1 + - - +
259A LEU* 3.1 7.2 + - - +
260A PHE* 3.0 22.3 + - - +
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Residues in contact with HIS 257 (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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253A VAL 2.8 17.5 + - - +
254A GLU* 3.4 13.7 - - + +
256A ILE* 1.3 73.1 - - - +
258A GLY* 1.3 63.1 + - - +
260A PHE* 3.1 18.8 + - - +
261A SER* 3.1 13.3 + - - -
358A LEU* 4.7 26.7 - - + +
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Residues in contact with GLY 258 (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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254A GLU 2.9 19.0 + - - -
255A ASP 4.1 1.6 - - - -
257A HIS* 1.3 73.0 - - - +
259A LEU* 1.3 60.6 + - - +
261A SER* 3.7 7.8 + - - -
262A LEU* 3.6 18.2 + - - +
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Residues in contact with LEU 259 (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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226A GLN* 5.6 3.3 - - + +
229A HIS* 5.6 3.4 - - + -
230A LEU* 4.4 26.5 - - + +
233A ARG* 5.7 2.9 - - + -
255A ASP 3.4 11.8 + - - +
256A ILE* 3.1 10.1 + - - +
258A GLY* 1.3 77.0 - - - +
260A PHE* 1.3 59.8 + - - +
262A LEU* 3.3 8.1 + - - +
263A SER* 2.9 27.5 + - - -
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Residues in contact with PHE 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LEU* 5.6 1.7 - - - +
256A ILE 3.0 12.7 + - - +
257A HIS* 3.1 11.6 + - - +
259A LEU* 1.3 77.4 - - - +
261A SER* 1.3 61.6 + - - +
263A SER* 3.1 25.8 + - - +
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Residues in contact with SER 261 (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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257A HIS 3.1 11.8 + - - -
258A GLY* 3.9 10.3 - - - -
259A LEU 3.2 0.2 - - - -
260A PHE* 1.3 78.1 - - - +
262A LEU* 1.3 61.3 + - - +
263A SER 3.4 4.3 + - - +
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Residues in contact with LEU 262 (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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220A LEU* 5.1 11.0 - - + +
226A GLN* 5.5 5.6 - - + +
258A GLY 3.6 10.4 + - - +
259A LEU* 3.3 11.6 + - - +
261A SER* 1.3 76.9 - - - +
263A SER* 1.3 62.4 + - - +
264A LYS* 3.6 4.0 + - - +
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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