Contacts of the helix formed by residues 274 - 288 (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 GLY 274 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101C ALA* 3.4 17.2 - - - +
104C GLU* 3.5 10.5 - - - -
105C MET 5.5 0.2 - - - -
269C LEU* 2.9 22.6 + - - +
272C ALA* 3.7 5.4 - - - +
273C GLY* 1.3 80.1 - - - +
275C ILE* 1.3 63.5 + - - -
276C SER 3.6 0.9 - - - -
277C GLY 4.5 1.3 - - - -
278C ALA* 3.5 20.8 + - - +
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Residues in contact with ILE 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C GLU* 2.9 4.9 + - - +
105C MET* 4.8 11.7 - - + -
108C TYR* 3.8 42.8 - - + -
119C LEU* 3.8 29.2 - - + -
123C LEU* 4.2 19.5 - - + -
269C LEU* 4.0 25.1 - - + -
274C GLY* 1.3 74.0 - - - -
276C SER* 1.3 61.7 + - - +
277C GLY 3.4 0.4 - - - -
278C ALA* 3.7 5.0 - - - +
279C GLU* 2.9 31.3 + - + +
306C ALA* 4.7 9.2 - - + +
310C PHE* 4.4 13.5 - - + -
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Residues in contact with SER 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LEU* 4.0 17.1 - - - +
90C GLN* 4.5 7.3 + - - +
104C GLU* 2.6 32.0 + - - -
108C TYR* 3.5 19.6 + - - -
275C ILE* 1.3 78.3 - - - +
277C GLY* 1.3 68.3 + - - +
279C GLU* 3.3 7.5 + - - +
280C LYS* 3.1 43.1 + - - +
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Residues in contact with GLY 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C GLN* 6.1 0.6 - - - -
104C GLU* 4.9 0.2 + - - -
250C PRO* 4.3 13.9 - - - +
272C ALA* 4.1 20.2 + - - -
274C GLY 4.2 3.4 + - - -
276C SER* 1.3 81.2 + - - +
278C ALA* 1.3 66.1 + - - +
280C LYS* 2.9 10.6 + - - +
281C ILE* 2.9 28.0 + - - +
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Residues in contact with ALA 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C ILE* 3.6 28.9 - - + +
269C LEU* 3.8 11.0 - - + -
272C ALA* 3.6 8.0 - - + +
274C GLY 3.5 20.3 + - - +
275C ILE 3.4 5.1 + - - +
276C SER 3.4 0.2 - - - -
277C GLY* 1.3 74.3 - - - +
279C GLU* 1.3 62.1 + - - +
281C ILE* 3.3 5.5 + - - +
282C ASN 3.1 18.9 + - - -
310C PHE* 3.4 24.2 - - + -
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Residues in contact with GLU 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C TYR* 4.4 12.1 + - - -
123C LEU* 3.4 24.6 - - - +
275C ILE* 2.9 19.5 + - - +
276C SER* 3.4 5.8 - - - +
278C ALA* 1.3 79.4 - - - +
280C LYS* 1.3 56.5 + - + +
282C ASN* 3.7 3.2 + - - +
283C ALA* 3.1 27.6 + - + +
310C PHE* 3.7 11.8 - - + -
314C LYS* 2.9 38.9 + - - +
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Residues in contact with LYS 280 (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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86C LEU* 6.1 0.2 - - - +
250C PRO* 3.9 27.8 - - + -
276C SER* 3.1 35.3 + - - +
277C GLY* 2.9 11.0 + - - +
279C GLU* 1.3 74.7 - - + +
281C ILE* 1.3 67.7 + - - +
283C ALA* 3.4 6.8 + - - +
284C MET* 3.0 30.1 + - + +
283D ALA* 4.3 31.2 - - + +
286D GLU* 4.3 19.5 - - - -
287D ALA* 6.0 1.3 - - + -
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Residues in contact with ILE 281 (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* 4.3 6.7 - - + +
248C PHE 3.4 27.1 - - - +
249C THR 4.0 8.3 - - - +
250C PRO* 3.8 19.1 - - + -
253C ALA* 3.7 21.7 - - + +
265C ILE* 4.0 18.2 - - + -
267C ILE* 3.8 27.8 - - + -
272C ALA* 4.3 10.8 - - + -
277C GLY 2.9 18.4 + - - +
278C ALA* 3.5 9.0 - - - +
280C LYS* 1.3 77.6 - - - +
282C ASN* 1.3 57.7 + - - +
284C MET* 3.2 6.1 + - - +
285C ALA* 3.0 26.7 + - - +
292C CYS* 5.0 1.1 - - - -
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Residues in contact with ASN 282 (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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267C ILE* 3.9 10.3 - - + +
278C ALA 3.1 13.1 + - - +
279C GLU* 3.9 4.6 + - - +
281C ILE* 1.3 80.3 - - - +
283C ALA* 1.3 59.7 + - - +
286C GLU* 2.9 33.1 + - - +
292C CYS* 4.0 11.7 - - - -
310C PHE* 4.3 7.0 - - + -
314C LYS* 3.4 33.7 - - - +
316C ASN* 2.8 38.4 + - - +
317C ILE* 3.6 16.9 - - + +
83D GLU* 5.2 1.0 + - - -
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Residues in contact with ALA 283 (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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279C GLU* 3.1 19.2 + - + +
280C LYS* 3.7 7.2 - - - +
281C ILE 3.3 0.2 - - - -
282C ASN* 1.3 79.4 - - - +
284C MET* 1.3 62.8 + - - +
286C GLU* 3.5 4.3 + - - +
287C ALA* 3.1 23.7 + - - +
280D LYS* 3.9 37.9 + - + +
283D ALA* 6.1 3.6 - - + -
284D MET* 4.8 2.3 - - - +
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Residues in contact with MET 284 (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* 3.2 46.7 - - + +
253C ALA* 4.2 5.2 - - - -
254C PHE* 3.8 29.6 - - + -
257C LEU* 3.7 10.5 - - + -
280C LYS* 3.0 17.3 + - + +
281C ILE 3.3 8.1 - - - +
283C ALA* 1.3 77.0 - - - +
285C ALA* 1.3 63.1 + - - +
287C ALA* 3.2 7.6 + - - +
288C CYS* 3.2 23.0 + - - -
254D PHE* 4.6 2.0 - - + -
283D ALA 4.8 2.0 - - - +
284D MET* 4.1 35.5 - - + +
287D ALA* 3.8 21.5 - - + -
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Residues in contact with ALA 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C LEU* 3.5 15.5 - - + +
265C ILE* 4.6 4.5 - - + -
281C ILE 3.0 13.6 + - - +
282C ASN 3.7 0.9 - - - +
284C MET* 1.3 74.8 - - - +
286C GLU* 1.3 54.9 + - - +
288C CYS* 2.7 22.7 + - - +
290C VAL* 2.8 47.0 + - + +
292C CYS* 3.5 24.7 - - - -
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Residues in contact with GLU 286 (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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282C ASN* 2.9 21.8 + - - +
283C ALA* 3.6 4.8 - - - +
285C ALA* 1.3 74.6 - - - +
287C ALA* 1.3 59.3 + - - +
289C GLY* 2.8 20.3 + - - +
290C VAL 4.1 0.9 - - - +
315C ARG* 4.6 12.1 + - - +
316C ASN* 3.5 44.1 + - + +
83D GLU* 4.4 10.7 - - - +
87D HIS* 5.5 3.8 - - - -
280D LYS* 3.0 26.7 + - - +
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Residues in contact with ALA 287 (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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283C ALA 3.1 13.4 + - - +
284C MET 3.4 10.3 - - - +
285C ALA 3.2 0.2 - - - -
286C GLU* 1.3 77.0 - - - +
288C CYS* 1.3 61.6 + - - +
289C GLY 3.3 1.0 + - - -
250D PRO* 4.4 17.0 - - + -
251D ARG* 3.6 36.9 + - - +
254D PHE* 5.7 0.9 - - + -
280D LYS* 5.4 3.3 - - + +
284D MET* 3.9 20.6 - - + -
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Residues in contact with CYS 288 (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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257C LEU* 4.1 25.6 - - + +
260C ARG* 5.9 0.3 + - - -
284C MET 3.2 14.3 + - - +
285C ALA 2.7 9.3 + - - +
287C ALA* 1.3 78.4 - - - +
289C GLY* 1.3 62.8 + - - +
290C VAL* 3.1 8.3 + - + +
251D ARG* 4.5 20.9 + - - +
254D PHE* 3.7 45.3 - - - -
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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