Contacts of the helix formed by residues 248 - 266 (chain A) in PDB entry 1JPW
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 VAL 248 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A VAL* 4.1 34.3 - - + +
212A ARG* 4.5 18.8 - - + +
246A SER* 2.7 13.7 + - - +
247A PRO* 1.3 91.6 - - + +
249A ASP* 1.3 68.7 + - - +
250A SER* 4.3 8.1 - - - +
251A VAL* 3.0 21.0 + - + +
252A LEU* 2.9 19.5 + - - +
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Residues in contact with ASP 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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247A PRO 3.8 5.4 + - - +
248A VAL* 1.3 71.8 - - - +
250A SER* 1.3 53.8 + - - +
252A LEU* 2.8 20.3 + - - +
253A PHE* 2.4 70.9 + - + -
288A LYS* 4.6 13.2 + - - +
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Residues in contact with SER 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ARG* 3.1 45.0 + - - -
248A VAL* 3.1 5.4 + - - +
249A ASP* 1.3 75.2 - - - +
251A VAL* 1.3 66.5 + - - +
253A PHE* 3.0 10.6 + - - +
254A TYR* 2.8 40.1 + - - +
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Residues in contact with VAL 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A VAL* 5.8 2.0 - - - -
211A ALA* 4.0 10.8 - - + -
212A ARG* 3.8 31.4 - - + +
215A ALA* 4.7 9.3 - - + +
243A MET* 3.8 33.0 - - + -
246A SER* 3.7 21.1 - - - +
248A VAL* 3.0 26.6 + - + +
250A SER* 1.3 78.1 - - - +
252A LEU* 1.3 66.6 + - - +
254A TYR* 3.4 8.2 + - - +
255A ALA* 2.9 24.9 + - - +
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Residues in contact with LEU 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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243A MET 3.6 3.1 - - - +
244A LEU* 3.0 46.2 - - + +
246A SER 3.6 21.1 - - - +
247A PRO 5.5 0.7 - - - -
248A VAL 2.9 8.3 + - - +
249A ASP* 2.8 24.4 + - - +
251A VAL* 1.3 77.0 - - - +
253A PHE* 1.3 68.5 + - + +
255A ALA* 2.9 15.0 + - - +
256A ILE* 3.0 15.9 + - - +
285A LEU* 3.9 28.7 - - + -
288A LYS* 4.0 20.6 - - + +
293A PHE* 4.6 9.9 - - + -
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Residues in contact with PHE 253 (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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249A ASP* 2.4 66.7 + - + +
250A SER* 3.5 8.5 - - - +
252A LEU* 1.3 70.2 - - + +
254A TYR* 1.3 64.9 + - + +
255A ALA 3.0 0.9 + - - -
256A ILE* 3.4 6.6 + - - +
257A THR* 3.2 27.9 + - - -
290A ASN* 3.5 27.6 - - + -
293A PHE* 3.7 36.1 - + + -
48D LEU* 3.5 42.2 - - + +
49D VAL* 4.8 5.2 - - + -
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Residues in contact with TYR 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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176A HIS* 4.6 11.8 + - - -
212A ARG* 3.5 29.7 - - + +
215A ALA* 4.1 18.7 - - + +
216A GLY* 3.5 26.9 - - - -
218A LEU* 5.4 0.2 - - - +
219A HIS* 3.5 22.9 - - + +
220A ASN* 6.1 0.2 - - - -
240A LEU* 5.9 0.2 - - - -
250A SER* 2.8 31.1 + - - +
251A VAL 3.7 3.8 - - - +
253A PHE* 1.3 73.8 - - + +
255A ALA* 1.3 56.8 - - - +
257A THR* 4.1 1.8 - - - -
258A THR* 2.6 33.1 + - - -
49D VAL* 3.7 38.3 + - + -
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Residues in contact with ALA 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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215A ALA* 5.3 1.5 - - + +
240A LEU* 4.1 15.7 - - + +
243A MET* 3.9 22.2 - - + -
244A LEU* 3.9 17.5 - - + -
251A VAL 2.9 19.1 + - - +
252A LEU* 2.9 7.0 + - - +
254A TYR* 1.3 74.2 - - - +
256A ILE* 1.3 64.5 + - - +
257A THR 3.2 1.6 - - - -
258A THR* 3.5 2.4 + - - -
259A LEU* 3.1 29.8 + - - +
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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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244A LEU* 4.1 15.9 - - + +
252A LEU 3.0 7.0 + - - +
253A PHE* 3.6 10.5 - - - +
255A ALA* 1.3 77.4 - - - +
257A THR* 1.3 64.0 + - - +
259A LEU* 3.9 2.9 - - + +
260A HIS* 2.9 28.4 + - - +
282A MET* 4.0 23.3 - - + -
285A LEU* 5.1 1.3 - - + -
293A PHE* 3.9 30.1 - - + -
296A ILE* 3.7 17.6 - - + +
297A THR* 3.5 34.1 - - + +
300A CYS* 3.9 17.4 - - - -
48D LEU* 4.7 4.7 - - + -
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Residues in contact with THR 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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219A HIS* 3.1 34.1 - - + +
223A HIS* 5.6 0.2 - - - +
253A PHE 3.2 16.1 + - - -
254A TYR 4.1 3.6 - - - -
255A ALA 3.2 0.6 - - - -
256A ILE* 1.3 82.9 - - - +
258A THR* 1.3 58.7 + - - +
260A HIS* 3.4 5.4 + - - +
261A ASN* 3.0 34.5 + - - +
296A ILE* 4.7 0.8 - - - +
45D LYS* 3.9 38.1 + - + +
48D LEU* 4.6 5.5 - - - +
49D VAL* 4.2 7.9 - - + +
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Residues in contact with THR 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LEU* 3.5 20.7 - - + +
219A HIS* 3.3 19.6 - - - +
222A SER* 3.8 27.4 - - - +
231A ILE* 4.4 6.5 - - + -
240A LEU* 3.3 27.1 - - + -
254A TYR 2.6 23.4 + - - -
255A ALA 4.0 0.7 - - - -
257A THR* 1.3 74.4 - - - +
259A LEU* 1.3 65.7 + - - +
261A ASN* 3.2 3.9 + - - +
262A LEU* 3.0 27.2 + - + +
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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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237A ILE* 4.4 9.0 - - + +
240A LEU* 3.4 37.0 - - + +
241A VAL* 4.3 5.8 - - + +
244A LEU* 3.7 37.0 - - + -
255A ALA 3.1 24.9 + - - +
256A ILE* 3.9 6.1 - - + +
258A THR* 1.3 78.6 - - - +
260A HIS* 1.3 61.6 + - - +
262A LEU* 3.3 11.7 + - + +
263A LEU* 3.0 31.7 + - + +
273A VAL* 4.3 20.1 - - + +
282A MET* 4.2 17.9 - - + -
300A CYS* 5.1 0.2 - - - -
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Residues in contact with HIS 260 (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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256A ILE 2.9 20.0 + - - +
257A THR 3.5 6.1 - - - +
258A THR 3.3 0.2 - - - -
259A LEU* 1.3 77.0 - - - +
261A ASN* 1.3 57.8 + - - +
263A LEU* 3.3 5.5 + - - +
264A LEU* 3.0 52.6 + - + +
296A ILE* 3.6 32.5 - - + -
299A ASP* 2.6 32.8 + - + -
300A CYS* 3.9 14.5 - - - -
303A ILE* 4.6 6.6 - - + +
41D LEU* 3.6 19.8 - - + +
45D LYS* 2.9 26.7 + - + +
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Residues in contact with ASN 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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222A SER* 3.5 39.1 + - - +
223A HIS* 3.9 14.6 + - - -
228A LEU* 4.1 3.2 - - - +
257A THR* 3.0 18.2 + - - +
258A THR 3.5 8.3 - - - +
259A LEU 3.2 0.2 - - - -
260A HIS* 1.3 76.8 - - - +
262A LEU* 1.3 60.7 + - - +
264A LEU* 3.4 6.4 + - - +
265A HIS* 3.1 36.1 + - + +
45D LYS* 2.4 38.2 - - - +
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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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228A LEU* 3.6 44.0 - - + +
231A ILE* 4.3 16.8 - - + -
232A PHE* 4.5 5.4 - - + -
237A ILE* 3.6 28.0 - - + -
240A LEU* 4.0 20.0 - - + -
258A THR* 3.0 23.2 + - + +
259A LEU* 3.3 7.2 + - + +
261A ASN* 1.3 73.2 - - - +
263A LEU* 1.3 62.5 + - + +
266A GLN* 2.8 46.2 + - + +
269A ALA* 3.1 15.5 - - + +
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Residues in contact with LEU 263 (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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259A LEU* 3.0 23.6 + - + +
260A HIS* 3.3 4.7 + - - +
262A LEU* 1.3 80.1 - - + +
264A LEU* 1.3 62.5 + - - +
266A GLN 4.4 5.2 + - - +
269A ALA* 4.0 4.4 - - + +
270A LYS* 3.9 39.4 + - + +
273A VAL* 4.3 14.1 - - + -
282A MET* 4.7 5.6 - - + -
300A CYS* 3.8 39.3 - - + +
303A ILE* 4.4 20.8 - - + +
304A LEU* 3.7 33.7 - - + -
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Residues in contact with LEU 264 (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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260A HIS* 3.0 45.9 + - + +
261A ASN* 3.8 4.3 - - - +
263A LEU* 1.3 78.3 - - - +
265A HIS* 1.3 88.1 + - + +
299A ASP* 5.2 1.6 - - - +
303A ILE* 3.9 20.4 - - + -
45D LYS* 4.5 6.7 - - - +
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Residues in contact with HIS 265 (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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222A SER 5.5 1.6 - - - -
223A HIS 6.6 0.2 - - - -
225A ARG* 3.7 40.3 + - - +
228A LEU* 3.8 15.5 - - + -
261A ASN* 3.1 25.7 + - + -
264A LEU* 1.3 108.2 + - + +
266A GLN* 1.3 62.7 + - - +
267A GLU 3.7 2.6 + - - -
500B PRO* 4.9 18.6 - - + +
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Residues in contact with GLN 266 (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 ARG* 5.4 0.4 - - - +
228A LEU* 3.4 17.3 - - + +
229A LEU* 3.0 34.5 - - - +
232A PHE* 3.8 41.7 - - + -
262A LEU* 2.8 37.7 + - + +
263A LEU 4.4 3.9 + - - +
264A LEU 4.0 0.2 - - - -
265A HIS* 1.3 71.9 - - - +
267A GLU* 1.3 95.4 + - - +
268A GLY 3.4 0.2 + - - -
269A ALA* 3.1 19.1 + - + +
270A LYS 4.7 0.5 + - - -
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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
------------------------------------------------------------
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