Contacts of the helix formed by residues 274 - 288 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101D ALA* 3.6 15.4 - - - +
104D GLU* 3.3 10.1 - - - -
105D MET* 6.2 0.4 - - - -
269D LEU* 2.8 29.9 + - - +
272D ALA* 3.7 5.5 - - - +
273D GLY* 1.3 81.0 - - - +
275D ILE* 1.3 63.0 + - - -
276D SER 3.5 0.9 - - - -
277D GLY 4.4 1.3 - - - -
278D ALA* 3.5 14.9 + - - +
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Residues in contact with ILE 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D GLU* 2.7 8.0 + - + +
105D MET* 4.9 11.4 - - + -
108D TYR* 3.7 46.7 - - + -
119D LEU* 4.0 21.5 - - + -
123D LEU* 4.1 22.2 - - + -
269D LEU* 4.0 26.7 - - + -
274D GLY* 1.3 72.6 - - - -
276D SER* 1.3 65.8 + - - +
277D GLY 3.3 0.4 - - - -
278D ALA* 4.2 1.1 - - - -
279D GLU* 2.9 25.6 + - + +
306D ALA* 4.4 12.8 - - + +
310D PHE* 4.2 15.0 - - + -
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Residues in contact with SER 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D LEU* 3.9 17.3 - - - +
90D GLN* 4.3 10.9 + - - +
104D GLU* 2.5 37.6 + - - -
108D TYR* 3.7 19.1 + - - -
275D ILE* 1.3 73.8 - - - +
277D GLY* 1.3 67.0 + - - +
279D GLU* 3.4 8.3 + - - +
280D LYS* 3.2 32.5 + - - +
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Residues in contact with GLY 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D GLN* 5.8 1.1 - - - +
250D PRO* 4.2 11.3 - - - +
272D ALA* 4.1 21.5 + - - -
274D GLY 4.0 3.6 + - - -
275D ILE 3.3 0.2 - - - -
276D SER* 1.3 80.2 + - - +
278D ALA* 1.3 65.3 + - - +
280D LYS* 3.0 14.8 + - - +
281D ILE* 2.9 27.2 + - - +
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Residues in contact with ALA 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D ILE* 3.6 23.2 - - + +
269D LEU* 3.9 10.3 - - + -
272D ALA* 3.7 6.7 - - + +
274D GLY 3.5 19.1 + - - +
275D ILE* 3.3 5.3 + - - +
277D GLY* 1.3 74.7 - - - +
279D GLU* 1.3 62.2 + - - +
281D ILE* 3.2 5.3 + - - +
282D ASN* 3.1 19.4 + - - +
310D PHE* 3.4 33.5 - - + -
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Residues in contact with GLU 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D TYR* 4.3 13.3 + - - -
123D LEU* 3.8 21.1 - - - +
275D ILE* 2.9 18.2 + - - +
276D SER* 3.5 7.3 - - - +
277D GLY 3.2 0.2 - - - -
278D ALA* 1.3 78.8 - - - +
280D LYS* 1.3 56.0 + - + +
282D ASN* 3.7 3.0 + - - +
283D ALA* 3.1 30.6 + - + +
310D PHE* 3.6 13.4 - - + -
314D LYS* 2.8 35.4 + - - +
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Residues in contact with LYS 280 (chain D).
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* 3.9 37.7 + - + +
286C GLU* 3.0 29.1 + - - +
287C ALA* 5.4 2.7 - - + +
250D PRO* 3.7 31.4 - - + -
276D SER* 3.2 23.5 + - - +
277D GLY* 3.0 10.4 + - - +
279D GLU* 1.3 74.4 - - + +
281D ILE* 1.3 66.2 + - - +
283D ALA* 3.4 5.2 + - - +
284D MET* 3.0 30.5 + - + +
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Residues in contact with ILE 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D VAL* 4.3 6.3 - - + +
248D PHE 3.4 27.4 - - - +
249D THR 3.9 9.6 - - - +
250D PRO* 3.7 20.2 - - + -
253D ALA* 3.8 18.1 - - + +
265D ILE* 3.9 17.9 - - + -
267D ILE* 3.8 26.2 - - + -
272D ALA* 4.2 9.9 - - + -
277D GLY 2.9 19.4 + - - +
278D ALA* 3.6 8.3 - - - +
280D LYS* 1.3 76.3 - - - +
282D ASN* 1.3 58.1 + - - +
284D MET* 3.2 8.0 + - - +
285D ALA* 2.8 27.5 + - - +
292D CYS* 4.9 0.9 - - - -
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Residues in contact with ASN 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C GLU* 5.1 0.7 - - - +
267D ILE* 4.0 9.8 - - + +
278D ALA 3.1 13.3 + - - +
279D GLU 4.0 3.1 - - - +
281D ILE* 1.3 80.8 - - - +
283D ALA* 1.3 60.4 + - - +
285D ALA 3.2 0.2 + - - -
286D GLU* 2.8 33.8 + - - +
292D CYS* 3.9 12.3 - - - -
310D PHE* 4.3 8.3 - - + -
314D LYS* 3.6 23.4 - - - +
316D ASN* 3.0 42.7 + - - +
317D ILE* 3.3 24.1 - - + +
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Residues in contact with ALA 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C LYS* 4.3 33.5 - - + +
283C ALA* 6.1 3.4 - - + -
284C MET* 4.8 3.1 - - - +
279D GLU* 3.1 21.4 + - + +
280D LYS* 3.9 5.6 - - - +
281D ILE 3.4 0.2 - - - -
282D ASN* 1.3 80.4 + - - +
284D MET* 1.3 62.4 + - - +
286D GLU* 3.5 11.1 + - - +
287D ALA* 3.2 22.3 + - - +
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Residues in contact with MET 284 (chain D).
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* 4.2 14.1 - - + -
283C ALA 4.8 1.6 - - - +
284C MET* 4.1 31.2 - - + -
287C ALA* 3.9 24.9 - - + -
250D PRO* 3.1 35.2 - - + +
253D ALA* 4.1 5.2 - - + -
254D PHE* 3.6 28.7 - - + -
257D LEU* 3.7 12.8 - - + -
280D LYS* 3.0 22.1 + - + +
281D ILE 3.2 5.4 - - - +
283D ALA* 1.3 78.0 - - - +
285D ALA* 1.3 61.8 + - - +
287D ALA* 3.2 13.3 + - - +
288D CYS* 3.4 17.5 + - - -
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Residues in contact with ALA 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D LEU* 3.6 16.1 - - + +
265D ILE* 4.4 4.9 - - + -
281D ILE 2.8 20.1 + - - +
282D ASN 3.6 0.9 - - - +
284D MET* 1.3 73.4 - - - +
286D GLU* 1.3 57.4 + - - +
288D CYS* 2.8 14.4 + - - -
290D VAL* 2.8 50.2 + - + +
292D CYS* 3.5 21.5 - - - -
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Residues in contact with GLU 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C GLU* 4.4 9.5 - - - +
87C HIS* 4.6 14.8 + - - -
280C LYS* 4.3 18.6 - - - -
282D ASN* 2.8 26.0 + - - +
283D ALA* 3.8 5.8 - - - +
285D ALA* 1.3 71.7 - - - +
287D ALA* 1.3 63.8 + - - +
289D GLY* 3.1 13.1 + - - +
290D VAL 4.1 0.7 - - - +
315D ARG* 4.6 13.2 + - - +
316D ASN* 3.4 42.1 + - + +
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Residues in contact with ALA 287 (chain D).
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* 4.7 11.7 - - + -
251C ARG* 3.5 39.8 + - + +
254C PHE* 5.6 0.9 - - + -
280C LYS* 6.0 2.0 - - + -
284C MET* 3.8 23.3 - - + -
283D ALA 3.2 12.6 + - - +
284D MET 3.5 9.6 - - - +
285D ALA 3.1 0.6 - - - -
286D GLU* 1.3 77.5 - - - +
288D CYS* 1.3 63.8 + - - +
289D GLY 3.4 0.4 + - - -
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Residues in contact with CYS 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C ARG* 4.3 13.8 + - - +
254C PHE* 3.6 46.0 - - - -
257D LEU* 4.1 24.9 - - + +
284D MET 3.6 13.0 - - - +
285D ALA 2.8 8.7 + - - +
287D ALA* 1.3 82.3 - - - +
289D GLY* 1.3 59.6 + - - +
290D VAL* 3.2 6.9 + - + +
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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