Contacts of the helix formed by residues 300 - 314 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 3.7 27.4 - - + -
13B VAL* 4.3 9.2 - - + -
29B ALA* 5.8 3.6 - - + +
31B SER* 4.5 1.3 - - - +
47B GLU* 2.6 37.0 + - - +
299B GLU* 1.3 79.1 - - - +
301B LYS* 1.3 65.1 + - - +
302B LEU 3.0 6.9 + - - -
303B GLY 3.6 0.9 + - - -
304B ILE* 3.3 17.8 + - - +
325B PRO* 3.8 3.4 - - - -
328B LEU* 3.8 24.2 - - + -
331B ASP* 5.9 0.9 - - - -
332B VAL* 4.5 5.8 - - + -
333B PHE* 3.5 16.6 - - - -
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Residues in contact with LYS 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B THR* 1.3 74.0 - - - +
302B LEU* 1.3 56.2 + - - +
304B ILE* 3.8 2.0 - - - -
305B THR* 2.5 47.0 + - - +
325B PRO* 3.9 19.5 - - + +
328B LEU* 5.3 0.4 - - - +
331B ASP* 2.7 40.7 + - - +
333B PHE* 2.8 30.1 + - + -
335B GLY 2.9 25.3 + - - +
336B GLY* 4.9 0.7 - - - -
337B ILE* 3.4 32.6 + - + +
339B TYR* 5.1 8.5 - - + -
354B ILE* 5.0 1.3 - - - -
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Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ILE* 4.1 5.2 - - + -
45B TRP* 3.6 26.0 - - + +
46B GLY 3.3 35.0 - - - +
47B GLU* 3.1 16.2 - - + +
105B MET* 5.3 1.3 - - - -
300B THR* 3.0 6.8 + - - +
301B LYS* 1.3 76.9 - - - +
303B GLY* 1.3 65.1 + - - +
305B THR* 3.0 14.0 + - - -
306B ALA* 3.2 10.9 + - - +
333B PHE* 3.7 36.4 - - + -
352B LEU* 4.2 9.4 - - + -
354B ILE* 3.6 28.9 - - + -
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Residues in contact with GLY 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLU* 2.8 21.0 + - - -
105B MET* 4.1 20.8 - - - +
299B GLU* 3.3 25.2 - - - +
300B THR 3.6 1.5 + - - -
301B LYS 3.5 0.2 - - - -
302B LEU* 1.3 73.0 - - - +
304B ILE* 1.3 56.5 + - - +
306B ALA* 3.4 3.8 + - - +
307B ALA* 3.0 27.4 + - - +
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Residues in contact with ILE 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B SER* 3.1 38.1 - - - +
299B GLU* 4.1 6.1 - - + +
300B THR 3.3 10.5 + - - +
301B LYS* 4.0 3.1 - - - +
302B LEU 3.2 0.6 - - - -
303B GLY* 1.3 75.6 - - - +
305B THR* 1.3 59.5 + - - +
307B ALA* 3.7 2.3 - - + +
308B ALA* 2.8 27.3 + - - +
322B PHE* 3.7 28.7 - - + -
324B ALA* 4.5 3.1 - - + -
325B PRO* 3.2 31.9 - - + -
337B ILE* 3.9 11.7 - - + -
339B TYR* 3.6 21.5 - - - +
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Residues in contact with THR 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B LYS* 2.5 29.5 + - - +
302B LEU 3.0 5.6 + - - -
304B ILE* 1.3 75.8 - - - +
306B ALA* 1.3 65.9 + - - +
308B ALA* 3.2 1.2 + - - +
309B HIS* 2.9 41.0 + - + +
336B GLY* 3.6 15.0 - - - -
337B ILE* 3.4 28.1 + - + +
352B LEU* 3.3 34.3 - - + +
354B ILE* 4.1 6.0 - - + +
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Residues in contact with ALA 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B MET* 3.6 37.9 - - + -
119B LEU* 4.7 3.4 - - - +
269B LEU* 4.0 8.1 - - + +
275B ILE* 4.8 5.3 - - + +
302B LEU 3.2 5.6 + - - +
303B GLY 3.7 6.5 - - - +
304B ILE 3.4 0.2 - - - -
305B THR* 1.3 78.0 - - - +
307B ALA* 1.3 63.9 + - - +
309B HIS* 3.2 3.2 + - - +
310B PHE* 3.1 21.8 + - - +
352B LEU* 3.6 24.1 - - + +
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Residues in contact with ALA 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B LEU* 3.8 20.1 - - + +
294B VAL* 4.0 7.5 - - + +
295B GLY 4.3 9.2 - - - +
296B SER* 5.2 2.0 - - - -
299B GLU* 5.9 0.2 - - - +
303B GLY 3.0 17.3 + - - +
304B ILE* 3.7 9.6 - - + +
305B THR 3.2 0.2 - - - -
306B ALA* 1.3 77.1 - - - +
308B ALA* 1.3 57.2 + - - +
310B PHE* 3.3 5.4 + - - +
311B ALA* 3.0 28.1 + - - +
322B PHE* 3.7 23.5 - - + -
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LEU* 4.0 2.8 - - + +
304B ILE 2.8 22.4 + - - +
305B THR 3.2 4.0 + - - +
307B ALA* 1.3 72.0 - - - +
309B HIS* 1.3 59.4 + - - +
311B ALA* 3.8 0.4 - - - +
312B ALA* 2.8 33.6 + - - +
322B PHE* 3.8 24.2 - - + -
337B ILE* 4.0 25.4 - - + -
344B ILE* 4.6 4.9 - - + -
346B MET* 3.9 7.4 - - - +
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Residues in contact with HIS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B PRO* 4.4 2.2 - - + -
119B LEU* 3.7 23.5 - - + +
120B TYR* 3.0 50.8 + + - +
123B LEU* 4.4 1.5 - - - +
305B THR* 2.9 40.3 + - + +
306B ALA 3.2 5.1 + - - +
308B ALA* 1.3 76.1 - - - +
310B PHE* 1.3 64.9 + - - +
313B SER* 3.3 8.7 + - - -
346B MET* 3.1 27.0 - - + +
347B PRO* 3.7 17.7 - - + +
351B GLY 3.6 16.6 - - - -
352B LEU* 3.0 29.0 + - + -
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Residues in contact with PHE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B LEU* 5.1 0.2 - - - +
123B LEU* 4.0 15.7 - - + +
267B ILE* 4.2 7.2 - - + -
269B LEU* 4.5 7.9 - - + -
275B ILE* 4.1 25.8 - - + -
278B ALA* 3.3 39.0 - - + -
279B GLU* 3.6 31.2 - - + -
282B ASN* 4.4 5.6 - - + -
294B VAL* 3.9 18.2 - - + -
306B ALA 3.1 11.4 + - - +
307B ALA* 3.6 8.7 - - - +
309B HIS* 1.3 77.6 - - - +
311B ALA* 1.3 63.2 + - - +
313B SER* 2.7 23.2 + - - -
314B LYS* 3.7 14.8 + - + +
317B ILE* 3.5 23.6 - - + -
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Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ARG* 3.0 17.3 + - - -
130B LEU* 4.6 0.4 - - + -
294B VAL* 3.8 19.5 - - + -
307B ALA 3.0 16.9 + - - +
308B ALA 3.8 3.1 - - - +
310B PHE* 1.3 78.8 - - - +
312B ALA* 1.3 62.0 + - - +
313B SER 3.2 0.5 + - - -
314B LYS 3.4 7.6 + - - +
317B ILE* 3.9 17.8 - - + +
320B PHE* 3.7 28.0 - - + -
322B PHE* 3.9 5.8 - - + -
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Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B TYR* 4.1 4.9 - - + -
126B TYR* 3.4 1.6 + - - +
127B ARG* 2.9 59.5 + - + +
130B LEU* 3.8 11.4 - - + +
308B ALA 2.8 22.4 + - - +
309B HIS 4.0 3.1 - - - +
311B ALA* 1.3 74.3 - - - +
313B SER* 1.3 60.9 + - - +
314B LYS 3.5 0.7 + - - -
346B MET* 3.8 21.1 - - + -
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Residues in contact with SER 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLU* 3.8 3.8 - - - +
120B TYR 3.1 27.8 + - - -
123B LEU* 3.3 30.6 - - - +
124B GLY* 3.6 12.6 - - - -
126B TYR* 3.4 18.8 + - - +
309B HIS 3.3 8.3 + - - -
310B PHE* 2.7 18.3 + - - -
311B ALA 3.1 0.4 - - - -
312B ALA* 1.3 79.2 - - - +
314B LYS* 1.3 70.0 + - - +
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Residues in contact with LYS 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLU* 3.4 14.7 + - - +
123B LEU* 2.9 22.7 + - - +
126B TYR* 3.9 1.8 - - - -
127B ARG* 2.7 28.0 + - - -
279B GLU* 2.8 43.0 + - - +
282B ASN* 3.7 28.0 - - - +
310B PHE* 3.8 8.3 - - + +
311B ALA 3.4 3.1 + - - +
312B ALA 3.4 0.6 - - - -
313B SER* 1.3 94.3 - - - +
315B ARG* 1.3 62.4 + - - +
316B ASN 4.3 0.4 - - - +
317B ILE* 3.4 30.9 + - + +
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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