Contacts of the helix formed by residues 300 - 314 (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 THR 300 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D ILE* 3.7 28.0 - - + -
13D VAL* 4.2 11.2 - - + -
29D ALA* 5.6 4.7 - - + +
31D SER* 4.7 0.9 - - - +
47D GLU* 2.6 28.5 + - - +
299D GLU* 1.3 78.6 - - - +
301D LYS* 1.3 66.9 + - - +
302D LEU 3.2 8.1 + - - -
303D GLY 3.5 1.7 + - - -
304D ILE* 3.2 18.0 + - - +
325D PRO* 4.0 4.3 - - - -
328D LEU* 3.8 22.9 - - + -
331D ASP* 5.9 1.3 - - - -
332D VAL* 4.5 3.4 - - + -
333D PHE* 3.2 18.1 - - + -
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Residues in contact with LYS 301 (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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300D THR* 1.3 76.0 - - - +
302D LEU* 1.3 50.6 + - - +
304D ILE* 3.7 0.6 - - - +
305D THR* 2.6 52.7 + - - +
325D PRO* 4.0 22.0 - - + +
328D LEU* 5.2 0.4 - - - +
331D ASP* 2.9 32.0 + - - +
333D PHE* 2.7 40.0 + - + -
335D GLY 3.0 26.2 + - - +
336D GLY* 4.9 0.2 - - - -
337D ILE* 3.4 31.1 + - + +
338D THR* 6.1 0.6 - - - +
339D TYR* 5.4 5.2 - - + -
354D ILE* 5.9 0.9 - - + -
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Residues in contact with LEU 302 (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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33D ILE* 4.2 5.2 - - + -
45D TRP* 3.7 22.0 - - + -
46D GLY* 3.5 27.8 - - - +
47D GLU* 3.4 16.6 - - + +
105D MET* 5.3 1.1 - - - -
300D THR* 3.1 6.6 + - - +
301D LYS* 1.3 77.1 - - - +
303D GLY* 1.3 65.6 + - - +
305D THR* 3.0 13.2 + - - -
306D ALA* 3.1 11.8 + - - +
333D PHE* 3.6 38.2 - - + +
352D LEU* 4.1 16.4 - - + -
354D ILE* 3.5 26.5 - - + -
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Residues in contact with GLY 303 (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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47D GLU* 3.0 14.6 + - - -
105D MET* 4.0 20.8 - - - +
269D LEU* 4.7 0.2 - - - +
299D GLU* 3.2 25.4 - - - +
300D THR 3.5 1.7 + - - -
302D LEU* 1.3 79.1 - - - +
304D ILE* 1.3 61.6 + - - +
306D ALA* 3.3 4.9 + - - +
307D ALA* 3.1 22.2 + - - +
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Residues in contact with ILE 304 (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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296D SER* 3.1 37.5 - - - +
299D GLU* 4.1 8.5 - - + +
300D THR 3.2 17.2 + - - +
301D LYS* 3.9 2.7 - - - +
302D LEU 3.2 0.4 - - - -
303D GLY* 1.3 74.2 - - - +
305D THR* 1.3 60.3 + - - +
307D ALA* 3.7 3.7 - - - +
308D ALA* 2.8 29.2 + - - +
322D PHE* 3.7 35.7 - - + -
324D ALA* 4.0 11.4 - - + -
325D PRO* 3.2 22.0 - - + -
337D ILE* 4.1 10.3 - - + -
339D TYR* 3.8 13.2 - - - +
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Residues in contact with THR 305 (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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301D LYS* 2.6 32.6 + - - +
302D LEU* 3.0 8.4 + - - -
304D ILE* 1.3 74.5 - - - +
306D ALA* 1.3 57.0 + - - +
308D ALA* 3.3 1.4 + - - +
309D HIS* 2.9 39.8 + - + +
336D GLY* 3.6 13.6 - - - -
337D ILE* 3.3 29.6 + - + +
352D LEU* 3.4 36.8 - - + +
354D ILE* 4.4 3.4 - - + +
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Residues in contact with ALA 306 (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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105D MET* 3.6 35.9 - - + -
119D LEU* 5.1 0.2 - - - -
269D LEU* 4.0 7.7 - - + +
275D ILE* 4.4 8.7 - - + +
302D LEU 3.1 6.1 + - - +
303D GLY 3.6 8.1 - - - +
305D THR* 1.3 80.2 - - - +
307D ALA* 1.3 61.4 - - - +
309D HIS* 3.4 3.5 + - - +
310D PHE* 3.2 21.0 + - - +
352D LEU* 3.7 25.5 - - + +
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Residues in contact with ALA 307 (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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269D LEU* 3.8 20.4 - - + +
294D VAL* 4.1 11.6 - - + +
295D GLY 4.3 6.1 - - - +
296D SER* 5.3 3.6 - - - -
303D GLY 3.1 16.3 + - - +
304D ILE* 3.7 6.5 - - - +
306D ALA* 1.3 78.3 - - - +
308D ALA* 1.3 51.3 + - - +
310D PHE* 3.2 6.1 + - - +
311D ALA* 2.8 34.3 + - - +
322D PHE* 3.8 22.3 - - + -
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Residues in contact with ALA 308 (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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130D LEU* 4.1 3.3 - - + +
304D ILE 2.8 22.4 + - - +
305D THR 3.7 4.3 - - - +
307D ALA* 1.3 69.7 - - - +
309D HIS* 1.3 58.7 + - - +
311D ALA* 3.8 0.6 - - - +
312D ALA* 2.7 37.4 + - - +
322D PHE* 3.7 25.3 - - + -
337D ILE* 4.0 25.1 - - + -
344D ILE* 4.8 4.3 - - + -
346D MET* 3.9 7.9 - - - -
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Residues in contact with HIS 309 (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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118D PRO* 4.4 3.1 - - + -
119D LEU* 3.8 16.6 - - + +
120D TYR* 2.9 59.3 + + - +
123D LEU* 4.5 1.3 - - - +
305D THR* 2.9 39.8 + - + +
306D ALA 3.6 5.6 - - - +
308D ALA* 1.3 75.5 - - - +
310D PHE* 1.3 63.0 + - - +
313D SER* 3.3 10.9 + - - -
346D MET* 3.2 26.4 - - + +
347D PRO* 3.6 16.1 - - + +
351D GLY 3.5 14.8 - - - -
352D LEU* 3.0 30.5 + - + -
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Residues in contact with PHE 310 (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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123D LEU* 4.1 12.5 - - + +
267D ILE* 4.2 6.3 - - + -
269D LEU* 4.5 7.2 - - + -
275D ILE* 4.2 25.4 - - + -
278D ALA* 3.4 41.7 - - + -
279D GLU* 3.7 23.8 - - + -
282D ASN* 4.3 4.5 - - + -
294D VAL* 3.9 16.4 - - + -
306D ALA 3.2 10.2 + - - +
307D ALA* 3.2 10.8 + - - +
308D ALA 3.2 0.4 - - - -
309D HIS* 1.3 80.0 - - - +
311D ALA* 1.3 64.1 + - - +
313D SER* 2.8 23.2 + - - -
314D LYS* 3.7 26.2 + - + +
317D ILE* 3.5 24.9 - - + -
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Residues in contact with ALA 311 (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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127D ARG* 3.1 15.6 + - - -
130D LEU* 4.6 0.2 - - + -
294D VAL* 3.8 19.7 - - + -
307D ALA 2.8 19.3 + - - +
308D ALA 3.8 3.4 - - - +
310D PHE* 1.3 75.9 - - - +
312D ALA* 1.3 61.3 + - - +
313D SER 3.3 0.9 + - - -
314D LYS 3.5 7.3 + - - +
317D ILE* 3.8 18.2 - - + +
320D PHE* 3.7 28.9 - - + -
322D PHE* 3.9 7.4 - - + -
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Residues in contact with ALA 312 (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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120D TYR* 4.3 4.5 - - + -
126D TYR 3.5 0.2 + - - -
127D ARG* 3.0 61.0 + - + +
128D ASP* 5.2 0.2 - - - -
130D LEU* 3.8 17.2 - - + +
308D ALA 2.7 21.2 + - - +
309D HIS 4.1 2.7 - - - +
311D ALA* 1.3 74.1 - - - +
313D SER* 1.3 60.7 + - - +
346D MET* 3.9 17.7 - - + -
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Residues in contact with SER 313 (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* 3.6 5.7 - - - +
120D TYR* 3.0 29.1 - - - +
123D LEU* 3.3 30.0 + - - +
124D GLY* 3.6 12.1 - - - -
125D GLY* 4.2 0.4 - - - -
126D TYR* 3.4 20.6 + - - +
309D HIS 3.3 10.3 + - - -
310D PHE* 2.8 17.3 + - - -
311D ALA 3.2 0.2 - - - -
312D ALA* 1.3 77.9 - - - +
314D LYS* 1.3 64.7 + - - +
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Residues in contact with LYS 314 (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* 3.6 16.5 + - - +
123D LEU* 2.9 21.2 + - - -
126D TYR* 3.9 1.6 - - - -
127D ARG* 2.8 27.4 + - - -
279D GLU* 2.8 43.5 + - - +
282D ASN* 3.6 26.2 - - - +
310D PHE* 3.8 20.0 - - + +
311D ALA 3.5 3.0 + - - +
312D ALA 3.4 0.8 - - - -
313D SER* 1.3 91.8 - - - +
315D ARG* 1.3 63.1 + - - +
316D ASN 4.3 0.7 - - - +
317D ILE* 3.3 26.8 + - + +
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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