Contacts of the helix formed by residues 249 - 260 (chain C) in PDB entry 1JPM
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 249 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97C MET* 5.0 17.7 - - + -
247C VAL* 3.8 2.3 - - - +
248C PHE* 1.3 91.0 - - + +
250C PRO* 1.3 72.3 - - + +
251C ARG* 3.7 8.3 + - - +
252C GLN* 3.2 31.0 + - - +
253C ALA* 2.9 25.6 + - - +
271C LYS 4.7 5.2 - - - +
272C ALA* 5.1 3.8 - - - +
281C ILE* 4.0 3.6 - - - -
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Residues in contact with PRO 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C PHE 4.7 0.2 - - - +
249C THR* 1.3 87.6 - - + +
251C ARG* 1.3 56.0 + - - +
253C ALA* 3.9 2.5 - - + -
254C PHE* 2.8 28.6 + - - +
272C ALA* 5.6 2.5 - - + +
277C GLY* 4.3 13.5 - - - +
280C LYS* 3.9 31.9 - - + -
281C ILE* 3.8 19.1 - - + +
284C MET* 3.2 33.3 - - + +
287D ALA* 4.7 6.3 - - + -
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Residues in contact with ARG 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C THR* 3.2 8.9 - - - +
250C PRO* 1.3 81.4 - - + +
252C GLN* 1.3 65.4 + - + +
254C PHE* 3.1 10.8 + - + +
255C GLU* 3.0 20.3 + - - +
260D ARG* 5.8 3.4 - - - +
287D ALA* 3.5 31.4 + - + +
288D CYS* 4.3 16.6 + - - +
289D GLY* 4.6 3.6 - - - +
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Residues in contact with GLN 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C GLU 5.0 0.2 + - - -
246C SER 3.9 15.6 + - - +
247C VAL* 3.6 5.4 - - - +
248C PHE* 2.6 54.0 - - - +
249C THR* 3.2 21.9 + - - +
251C ARG* 1.3 75.4 - - + +
253C ALA* 1.3 65.5 + - - +
255C GLU* 3.1 9.8 + - - +
256C VAL* 3.0 26.3 + - - +
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Residues in contact with ALA 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C VAL* 3.7 22.8 - - + +
249C THR 2.9 14.3 + - - +
250C PRO* 3.2 12.5 + - + +
252C GLN* 1.3 76.0 - - - +
254C PHE* 1.3 62.6 + - - +
256C VAL* 3.4 1.4 + - - +
257C LEU* 3.0 33.7 + - + +
265C ILE* 4.4 7.0 - - + -
281C ILE* 3.7 21.5 - - + -
284C MET* 4.2 7.4 - - - -
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Residues in contact with PHE 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C PRO 2.8 14.4 + - - +
251C ARG* 3.2 14.6 - - + +
253C ALA* 1.3 77.8 - - - +
255C GLU* 1.3 56.6 + - - +
257C LEU* 3.4 4.7 + - - +
258C GLN* 2.9 47.9 + - - +
284C MET* 3.8 19.7 - - + -
254D PHE* 3.2 43.0 - + - -
257D LEU* 3.9 4.0 - - + -
258D GLN* 3.8 32.3 - - - -
284D MET* 4.2 11.0 - - + -
287D ALA* 5.6 0.9 - - + -
288D CYS* 3.6 34.5 - - - -
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Residues in contact with GLU 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C LEU* 3.3 29.4 - - + +
251C ARG 3.0 11.5 + - - +
252C GLN* 3.1 13.2 + - - +
254C PHE* 1.3 77.6 - - - +
256C VAL* 1.3 53.7 + - - +
258C GLN* 3.2 25.8 + - - +
259C THR* 2.8 60.9 + - - +
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Residues in contact with VAL 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C LEU* 3.9 29.4 - - + -
230C LEU* 5.1 0.9 - - + -
243C ALA* 4.4 7.9 - - + -
246C SER* 4.2 6.3 - - - +
247C VAL* 3.6 22.2 - - + -
252C GLN 3.0 18.6 + - - +
253C ALA* 3.9 3.6 - - - +
255C GLU* 1.3 75.5 - - - +
257C LEU* 1.3 59.9 - - + +
259C THR* 3.4 4.7 + - - -
260C ARG* 3.0 21.3 + - - -
261C SER* 3.1 16.7 + - - -
262C ALA* 4.0 32.0 + - + +
265C ILE* 4.7 9.9 - - + -
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Residues in contact with LEU 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C ALA* 3.0 28.2 + - + +
254C PHE 3.8 3.1 - - - +
256C VAL* 1.3 77.0 - - + +
258C GLN* 1.3 64.0 + - - +
260C ARG* 3.3 19.7 + - - +
262C ALA 5.7 3.1 - - - +
265C ILE* 4.1 17.9 - - + -
281C ILE 4.9 0.2 - - - +
284C MET* 3.7 20.2 - - + +
285C ALA* 3.5 30.3 - - + +
288C CYS* 4.1 13.8 - - + +
290C VAL* 3.6 38.4 - - + -
254D PHE* 3.9 15.0 - - + -
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Residues in contact with GLN 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C PHE* 2.9 31.7 + - + +
255C GLU* 3.2 44.0 + - - +
257C LEU* 1.3 77.7 - - - +
259C THR* 1.3 69.4 + - + +
260C ARG* 3.7 6.1 + - - +
254D PHE* 3.8 16.1 - - + -
258D GLN* 3.3 52.1 - - + +
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Residues in contact with THR 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C LEU* 5.2 3.6 - - + +
231C LYS* 2.9 33.5 + - - +
255C GLU* 2.8 40.3 + - - +
256C VAL* 3.4 4.7 + - - -
258C GLN* 1.3 83.3 - - + +
260C ARG* 1.3 67.7 + - - +
261C SER* 2.6 25.3 + - - -
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Residues in contact with ARG 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C LYS* 3.9 13.8 - - - +
234C THR* 4.4 8.7 - - - +
235C ASP* 4.6 4.2 - - - +
256C VAL 3.0 8.4 + - - -
257C LEU* 3.3 14.8 + - - +
258C GLN 4.5 4.8 + - - +
259C THR* 1.3 81.1 - - - +
261C SER* 1.3 62.1 + - - +
262C ALA 3.3 9.8 + - - +
288C CYS 5.9 0.4 + - - -
251D ARG* 4.4 17.4 - - - +
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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