Contacts of the helix formed by residues 237 - 251 (chain A) in PDB entry 1SEJ
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 GLU 237 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A HIS* 2.9 26.0 + - + +
236A TYR* 1.3 77.3 - - - +
238A PHE* 1.3 56.8 + - - +
239A GLN 3.1 0.9 - - - -
240A TYR* 3.2 5.8 + - - +
241A LEU* 3.0 37.1 + - + +
272A PHE* 4.6 3.1 - - - -
281A LEU* 3.6 19.5 - - + +
282A THR* 2.6 47.8 + - - +
283A THR* 2.9 30.7 + - - -
481A PRO* 3.8 8.5 - - + +
484A PHE* 3.5 13.1 - - + -
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Residues in contact with PHE 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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159A MET* 4.0 22.0 - - + -
225A ASN* 3.4 25.1 - - - -
226A THR* 4.5 2.5 - - - -
229A ILE* 4.3 15.7 - - + -
233A ARG* 3.6 63.0 - - + +
235A HIS* 3.1 39.6 + + + +
236A TYR 2.9 0.2 - - - -
237A GLU* 1.3 77.3 - - - +
239A GLN* 1.3 61.5 + - + +
240A TYR 3.1 0.2 - - - -
241A LEU* 4.2 11.9 - - + -
242A ASP* 2.8 47.9 + - - +
481A PRO* 4.0 11.7 - - + -
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Residues in contact with GLN 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ARG 5.5 4.6 + - - -
235A HIS 5.6 1.0 + - - -
236A TYR* 2.9 33.2 + - + +
238A PHE* 1.3 82.0 - - - +
240A TYR* 1.3 56.6 + - - +
242A ASP* 4.7 1.4 - - - +
243A LEU* 3.6 13.3 + - - +
246A ARG* 4.8 3.2 + - - +
269A MET* 4.5 6.9 - - - +
270A MET* 3.4 22.9 - - + +
271A ARG* 3.0 53.4 + - - +
272A PHE* 4.1 6.5 - - + -
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Residues in contact with TYR 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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237A GLU 3.2 7.0 + - - +
239A GLN* 1.3 77.7 - - - +
241A LEU* 1.3 76.6 + - + +
242A ASP 3.1 1.1 - - - -
243A LEU* 3.0 4.4 + - + +
244A LEU* 3.0 54.8 + - + +
270A MET* 3.7 17.0 - - + -
272A PHE* 4.4 7.6 - - + -
281A LEU* 3.5 38.1 - - + -
427A LEU* 2.6 34.7 + - + -
428A GLY* 4.1 5.0 + - - -
431A SER* 3.9 23.8 - - - -
432A PRO* 3.7 11.4 - - + +
435A ILE* 4.1 9.2 - - + -
476A GLN* 3.7 18.2 + - - -
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Residues in contact with LEU 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ASN* 3.6 30.7 - - + +
237A GLU* 3.0 28.4 + - + +
238A PHE* 4.2 9.9 - - + -
240A TYR* 1.3 90.0 - - + +
242A ASP* 1.3 60.6 + - - +
244A LEU* 3.1 12.1 - - + +
245A SER* 3.0 28.0 + - - -
283A THR* 3.9 21.5 - - + +
476A GLN* 4.7 6.5 - - + -
477A LEU* 3.8 20.0 - - + +
481A PRO* 3.5 31.9 - - + -
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Residues in contact with ASP 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A PRO* 4.8 0.9 - - + +
224A TYR* 3.3 21.6 + - + -
225A ASN 5.1 1.2 + - - -
233A ARG* 2.4 40.9 + - - +
238A PHE* 2.8 31.7 + - - +
239A GLN* 4.7 0.9 - - - +
241A LEU* 1.3 77.8 - - - +
243A LEU* 1.3 60.4 + - - +
244A LEU 3.1 1.3 - - - -
245A SER* 3.2 7.2 + - - -
246A ARG* 2.8 47.9 + - - +
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Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLN 3.6 13.9 + - - +
240A TYR* 3.0 10.6 + - + +
242A ASP* 1.3 78.0 - - - +
244A LEU* 1.3 62.8 + - - +
246A ARG* 3.3 12.1 + - - +
247A VAL* 3.0 41.2 + - + +
265A ILE* 4.3 1.3 - - + -
268A GLN* 3.5 48.0 - - + +
269A MET 5.0 0.7 - - - +
270A MET* 3.9 34.1 - - + -
427A LEU* 3.9 24.9 - - + -
460A ILE* 4.5 7.0 - - + -
463A ALA* 4.4 2.9 - - + -
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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
----------------------------------------------------------
240A TYR* 3.0 54.4 + - + +
241A LEU* 3.1 15.0 - - + +
243A LEU* 1.3 79.2 - - - +
245A SER* 1.3 62.6 + - - +
247A VAL* 3.3 5.6 + - - +
248A LEU* 3.0 25.4 + - + +
427A LEU* 3.7 29.6 - - + +
465A ILE* 4.0 16.3 - - + +
473A LEU* 4.0 22.2 - - + +
476A GLN* 4.6 4.5 - - - +
477A LEU* 4.4 24.5 - - + -
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Residues in contact with SER 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A PRO* 3.8 20.4 - - - -
223A ILE* 2.7 31.3 + - - +
224A TYR* 3.8 13.8 - - - -
225A ASN 4.2 0.9 + - - -
241A LEU 3.0 12.6 + - - -
242A ASP* 3.2 8.1 + - - -
244A LEU* 1.3 77.9 - - - +
246A ARG* 1.3 58.5 + - - +
248A LEU* 3.2 8.7 + - - +
249A GLU* 2.9 30.8 + - - +
477A LEU* 3.9 6.5 - - - +
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Residues in contact with ARG 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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216A HIS* 6.3 0.9 - - - -
217A LYS 4.9 2.7 - - - +
219A PRO* 3.9 21.1 - - + +
239A GLN* 4.8 3.4 + - - +
242A ASP* 2.8 38.3 + - - +
243A LEU* 3.5 27.9 - - - +
244A LEU 3.2 0.2 - - - -
245A SER* 1.3 78.2 - - - +
247A VAL* 1.3 57.9 + - - +
249A GLU 3.4 0.3 + - - -
250A ASN* 2.9 41.2 + - - +
265A ILE* 4.3 11.4 - - + +
268A GLN* 2.7 31.9 - - - +
269A MET 4.0 14.6 + - - -
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Residues in contact with VAL 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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243A LEU* 3.0 20.3 + - + +
244A LEU 3.7 0.7 - - - +
246A ARG* 1.3 72.2 - - - +
248A LEU* 1.3 67.5 + - + +
249A GLU 3.0 1.6 - - - -
251A GLY* 2.5 32.7 + - - +
263A TYR* 3.9 21.3 - - + +
265A ILE* 3.6 31.4 - - + -
427A LEU* 3.8 20.0 - - + -
463A ALA 4.2 2.7 - - - +
465A ILE* 3.2 39.7 - - + +
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Residues in contact with LEU 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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223A ILE* 3.9 23.0 - - + +
244A LEU* 3.0 14.6 + - + +
245A SER* 3.2 5.8 + - - +
247A VAL* 1.3 79.4 - - + +
249A GLU* 1.3 59.6 + - - +
251A GLY 4.9 0.3 + - - +
263A TYR* 5.8 6.4 - - + -
465A ILE* 3.2 31.9 - - + -
470A LEU* 4.1 21.5 - - + -
473A LEU* 5.3 6.5 - - + -
474A LYS* 4.0 23.8 - - + +
477A LEU* 3.8 29.8 - - + -
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Residues in contact with GLU 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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217A LYS* 3.8 37.1 - - + +
218A PHE 3.9 9.1 - - - +
219A PRO* 3.9 5.2 - - + -
220A LYS* 2.9 59.6 + - - +
223A ILE* 3.1 13.6 - - + +
245A SER 2.9 16.1 + - - +
246A ARG* 3.7 1.3 - - - +
248A LEU* 1.3 80.9 - - - +
250A ASN* 1.3 65.7 + - - +
251A GLY 3.8 0.2 - - - -
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Residues in contact with ASN 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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214A ASN 4.4 1.2 + - - -
215A ARG 3.3 21.5 + - - +
216A HIS* 4.2 3.1 - - - -
217A LYS* 2.7 58.6 - - - +
246A ARG* 2.9 27.6 + - - +
249A GLU* 1.3 80.7 + - - +
251A GLY* 1.3 69.0 + - - +
252A ALA* 3.1 5.0 + - - +
265A ILE* 3.8 14.2 - - + +
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Residues in contact with GLY 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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247A VAL 2.5 29.4 + - - +
248A LEU 5.7 0.2 - - - +
249A GLU 3.8 0.4 - - - -
250A ASN* 1.3 71.7 - - - +
252A ALA* 1.3 66.0 + - - -
253A TYR 3.7 0.7 + - - -
263A TYR* 3.5 19.1 - - - -
264A SER 3.5 18.6 - - - -
265A ILE* 3.5 8.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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