Contacts of the helix formed by residues 300 - 314 (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 300 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C ILE* 3.7 25.6 - - + -
13C VAL* 4.2 9.0 - - + -
29C ALA* 5.8 3.1 - - + +
31C SER* 4.9 1.6 - - - +
47C GLU* 2.8 28.6 + - - +
299C GLU* 1.3 77.4 - - - +
301C LYS* 1.3 65.9 + - - +
302C LEU 3.2 3.1 + - - -
303C GLY 3.5 1.6 + - - -
304C ILE* 3.3 17.3 + - - +
325C PRO* 3.8 4.3 - - - -
328C LEU* 3.8 26.7 - - + -
331C ASP* 5.7 0.7 - - - -
332C VAL* 4.4 4.3 - - + -
333C PHE* 3.1 24.7 - - + -
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Residues in contact with LYS 301 (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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300C THR* 1.3 73.6 - - - +
302C LEU* 1.3 55.7 + - - +
304C ILE* 3.8 2.2 - - - -
305C THR* 2.5 47.8 + - - +
325C PRO* 3.9 19.5 - - + +
328C LEU* 5.3 0.2 - - - +
331C ASP* 2.7 38.0 + - - +
333C PHE* 2.8 29.6 + - + -
335C GLY 2.8 28.4 + - - +
336C GLY* 4.9 0.2 - - - -
337C ILE* 3.5 34.6 + - + +
339C TYR* 5.0 7.0 - - + -
354C ILE* 5.1 1.6 - - + -
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Residues in contact with LEU 302 (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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33C ILE* 4.0 7.4 - - + -
45C TRP* 3.6 18.8 - - + -
46C GLY* 3.3 35.7 - - - +
47C GLU* 3.4 14.1 - - + +
105C MET* 5.5 1.1 - - - -
300C THR* 3.1 7.1 + - - +
301C LYS* 1.3 77.1 - - - +
303C GLY* 1.3 66.4 + - - +
305C THR* 3.0 13.3 + - - -
306C ALA* 3.1 12.0 + - - +
333C PHE* 3.8 34.8 - - + -
352C LEU* 4.4 9.0 - - + -
354C ILE* 3.5 35.7 - - + -
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Residues in contact with GLY 303 (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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47C GLU* 2.7 28.5 + - - -
105C MET* 4.4 13.1 - - - +
269C LEU* 4.9 0.2 - - - +
299C GLU* 3.2 26.9 - - - +
300C THR 3.5 0.9 + - - -
302C LEU* 1.3 73.7 - - - +
304C ILE* 1.3 62.1 + - - +
306C ALA* 3.5 3.1 + - - +
307C ALA* 3.1 22.2 + - - +
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Residues in contact with ILE 304 (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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296C SER* 3.2 36.6 - - - +
299C GLU* 4.1 4.9 - - + +
300C THR 3.3 10.0 + - - +
301C LYS* 3.9 2.9 - - - +
302C LEU 3.1 0.6 - - - -
303C GLY* 1.3 74.7 - - - +
305C THR* 1.3 57.6 + - - +
307C ALA* 3.3 3.5 + - - +
308C ALA* 2.7 33.8 + - + +
322C PHE* 3.7 31.0 - - + -
324C ALA* 4.3 3.6 - - + -
325C PRO* 3.1 35.9 - - + -
337C ILE* 4.5 12.6 - - + -
339C TYR* 3.6 19.7 - - - +
344C ILE* 5.0 0.2 - - + -
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Residues in contact with THR 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C LYS* 2.5 29.7 + - - +
302C LEU* 3.0 6.7 + - - -
304C ILE* 1.3 77.4 - - - +
306C ALA* 1.3 57.2 + - - +
308C ALA* 3.3 1.7 + - - +
309C HIS* 2.9 46.2 + - + +
336C GLY* 3.6 13.6 - - - -
337C ILE* 3.3 30.8 + - + +
352C LEU* 3.4 34.1 - - + +
354C ILE* 4.2 5.2 - - + +
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Residues in contact with ALA 306 (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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105C MET* 3.5 41.5 - - + -
119C LEU* 5.2 0.4 - - - -
269C LEU* 3.9 7.6 - - + +
275C ILE* 4.7 6.9 - - + +
302C LEU 3.1 9.5 + - - +
303C GLY 3.8 3.6 - - - +
305C THR* 1.3 74.9 - - - +
307C ALA* 1.3 64.8 + - - +
309C HIS* 3.2 3.6 + - - +
310C PHE* 3.0 22.7 + - - +
352C LEU* 3.6 24.6 - - + +
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Residues in contact with ALA 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C LEU* 3.8 19.9 - - + +
294C VAL* 3.9 8.0 - - + +
295C GLY 4.0 10.5 - - - +
296C SER* 5.1 3.1 - - - -
303C GLY 3.1 15.1 + - - +
304C ILE* 3.5 6.7 - - - +
306C ALA* 1.3 78.7 - - - +
308C ALA* 1.3 56.1 + - - +
310C PHE* 3.3 3.7 + - - +
311C ALA* 2.8 29.8 + - - +
322C PHE* 3.6 23.9 - - + -
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Residues in contact with ALA 308 (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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130C LEU* 4.0 3.7 - - + +
304C ILE* 2.7 22.2 + - + +
305C THR 3.7 4.0 - - - +
307C ALA* 1.3 71.8 - - - +
309C HIS* 1.3 55.9 + - - +
311C ALA* 3.7 1.2 - - - +
312C ALA* 2.7 38.3 + - - +
322C PHE* 3.8 23.8 - - + -
337C ILE* 4.0 10.3 - - + -
344C ILE* 4.6 5.2 - - + -
346C MET* 3.6 21.7 - - + +
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Residues in contact with HIS 309 (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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118C PRO* 4.4 2.5 - - + -
119C LEU* 3.7 18.1 - - + +
120C TYR* 2.9 68.1 + + - +
123C LEU* 4.3 1.3 - - - +
305C THR* 2.9 42.8 + - + +
306C ALA 3.6 5.2 - - - +
308C ALA* 1.3 75.6 - - - +
310C PHE* 1.3 64.8 + - - +
313C SER* 3.3 9.4 + - - -
337C ILE* 4.9 0.4 - - + -
346C MET* 4.1 6.3 - - - -
347C PRO* 3.8 20.2 - - + +
351C GLY 3.5 17.5 - - - -
352C LEU* 3.0 28.5 + - + -
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Residues in contact with PHE 310 (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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119C LEU* 5.3 0.2 - - - +
123C LEU* 3.9 13.4 - - + +
267C ILE* 4.1 7.4 - - + -
269C LEU* 4.3 12.3 - - + -
275C ILE* 4.4 24.9 - - + -
278C ALA* 3.4 38.1 - - + -
279C GLU* 3.7 23.3 - - + -
282C ASN* 4.3 5.6 - - + -
294C VAL* 3.8 16.8 - - + -
306C ALA 3.0 13.7 + - - +
307C ALA 3.6 7.6 - - - +
309C HIS* 1.3 77.2 - - - +
311C ALA* 1.3 64.1 + - - +
313C SER* 2.6 27.0 + - - -
314C LYS* 3.8 23.1 + - + +
317C ILE* 3.5 24.2 - - + -
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Residues in contact with ALA 311 (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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127C ARG* 3.0 19.2 + - - -
130C LEU* 4.6 0.2 - - + -
294C VAL* 3.8 18.8 - - + -
307C ALA 2.8 18.6 + - - +
308C ALA 3.7 3.1 - - - +
310C PHE* 1.3 78.1 - - - +
312C ALA* 1.3 58.9 + - - +
313C SER 3.3 0.7 + - - -
314C LYS 3.6 4.9 + - - -
317C ILE* 3.7 20.2 - - + +
320C PHE* 3.7 28.5 - - + -
322C PHE* 3.9 6.3 - - + -
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Residues in contact with ALA 312 (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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120C TYR* 4.3 3.6 - - + -
126C TYR* 3.4 2.5 + - - +
127C ARG* 3.0 61.8 + - + +
128C ASP 5.6 0.4 - - - -
130C LEU* 4.0 7.4 - - + +
308C ALA 2.7 22.2 + - - +
309C HIS 4.1 2.2 - - - +
311C ALA* 1.3 73.7 - - - +
313C SER* 1.3 60.0 + - - +
314C LYS 3.4 0.2 - - - -
346C MET* 3.9 24.2 - - + -
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Residues in contact with SER 313 (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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120C TYR 3.1 24.2 + - - -
123C LEU* 3.3 28.4 - - - +
124C GLY* 3.6 3.8 - - - -
125C GLY* 3.7 8.1 - - - +
126C TYR* 3.4 16.7 + - - +
309C HIS 3.3 7.2 + - - -
310C PHE* 2.6 20.1 + - - -
312C ALA* 1.3 79.7 - - - +
314C LYS* 1.3 67.4 + - - +
83D GLU* 3.6 14.7 - - - +
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Residues in contact with LYS 314 (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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123C LEU* 2.9 24.5 + - - +
126C TYR* 4.0 1.6 - - - -
127C ARG* 2.9 26.1 + - - -
279C GLU* 2.9 40.5 + - - +
282C ASN* 3.4 31.2 - - - +
310C PHE* 3.9 16.2 - - + +
311C ALA 3.6 3.0 + - - +
312C ALA 3.4 0.4 - - - -
313C SER* 1.3 92.1 - - - +
315C ARG* 1.3 64.0 + - - +
316C ASN 4.3 0.7 - - - +
317C ILE* 3.3 22.5 + - + -
83D GLU* 3.4 15.0 + - - +
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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