Contacts of the helix formed by residues 300 - 314 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ILE* 3.7 27.8 - - + -
13A VAL* 4.2 10.5 - - + -
29A ALA* 5.8 3.6 - - + +
31A SER* 5.3 1.6 - - - -
47A GLU* 2.6 28.6 + - - +
299A GLU* 1.3 76.0 - - - +
301A LYS* 1.3 66.4 + - - +
302A LEU 3.2 7.8 + - - -
303A GLY 3.4 1.6 + - - -
304A ILE* 3.2 18.4 + - - +
325A PRO* 3.9 4.0 - - - -
328A LEU* 3.9 24.7 - - + -
331A ASP* 5.9 0.7 - - - -
332A VAL* 4.4 6.3 - - + -
333A PHE* 3.3 19.1 - - - -
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Residues in contact with LYS 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A THR* 1.3 72.9 - - - +
302A LEU* 1.3 53.1 + - - +
304A ILE* 4.3 0.7 - - - -
305A THR* 2.6 53.2 + - - +
325A PRO* 3.9 20.6 - - + +
328A LEU* 5.3 0.4 - - - +
331A ASP* 2.9 36.2 + - - +
333A PHE* 3.0 32.8 + - + -
334A ASN* 4.4 0.2 - - - +
335A GLY 2.9 32.7 + - - +
337A ILE* 3.5 26.3 + - + +
339A TYR* 5.5 4.9 - - + -
354A ILE* 4.6 1.6 - - + -
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 4.2 4.7 - - + -
45A TRP* 3.6 24.7 - - + +
46A GLY* 3.4 33.9 - - - +
47A GLU* 3.6 16.2 - - + +
105A MET* 5.2 1.3 - - - -
300A THR* 3.2 6.2 + - - +
301A LYS* 1.3 76.2 - - - +
303A GLY* 1.3 66.1 + - - +
305A THR* 3.0 5.2 + - - -
306A ALA* 3.0 19.2 + - - +
333A PHE* 3.8 34.2 - - + -
352A LEU* 4.1 12.3 - - + -
354A ILE* 3.6 31.4 - - + +
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Residues in contact with GLY 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLU* 3.0 19.6 + - - -
105A MET* 4.0 19.8 - - - +
299A GLU* 3.3 25.8 - - - +
300A THR 3.4 0.9 + - - -
302A LEU* 1.3 74.3 - - - +
304A ILE* 1.3 61.6 + - - +
306A ALA* 3.2 5.2 + - - +
307A ALA* 3.0 21.5 + - - +
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Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A SER* 3.1 38.4 - - - +
299A GLU* 4.1 8.3 - - + +
300A THR 3.2 17.7 + - - +
301A LYS* 3.8 2.7 - - - +
302A LEU 3.2 0.4 - - - -
303A GLY* 1.3 74.3 - - - +
305A THR* 1.3 60.8 + - - +
307A ALA* 3.2 4.4 + - - +
308A ALA* 2.8 28.6 + - - +
322A PHE* 3.6 34.9 - - + -
324A ALA* 4.1 9.6 - - + -
325A PRO* 3.2 22.4 - - + -
337A ILE* 3.9 11.7 - - + -
339A TYR* 3.7 13.9 - - - +
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Residues in contact with THR 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A LYS* 2.6 36.4 + - - +
302A LEU 3.0 5.6 + - - -
304A ILE* 1.3 74.4 - - - +
306A ALA* 1.3 62.4 + - - +
308A ALA* 3.7 0.9 - - - +
309A HIS* 3.0 39.2 + - + +
336A GLY* 3.5 11.7 - - - -
337A ILE* 3.3 30.3 + - + +
352A LEU* 3.2 35.9 - - + +
354A ILE* 3.9 6.0 - - + +
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Residues in contact with ALA 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A MET* 3.6 36.3 - - + -
269A LEU* 4.0 7.0 - - + -
275A ILE* 4.2 8.9 - - + +
302A LEU 3.0 8.7 + - - +
303A GLY 3.2 8.7 + - - +
305A THR* 1.3 78.2 - - - +
307A ALA* 1.3 61.6 + - - +
309A HIS* 3.4 4.0 + - - +
310A PHE* 3.3 20.3 + - - +
352A LEU* 3.7 24.2 - - + +
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Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A LEU* 3.8 20.1 - - + +
294A VAL* 4.0 12.3 - - + +
295A GLY 4.2 5.8 - - - +
296A SER* 5.3 3.8 - - - -
303A GLY 3.0 13.2 + - - +
304A ILE* 3.2 8.7 + - - +
306A ALA* 1.3 75.5 - - - +
308A ALA* 1.3 57.7 + - - +
310A PHE* 3.3 5.9 + - - +
311A ALA* 2.8 29.1 + - - +
322A PHE* 3.7 21.4 - - + -
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LEU* 4.1 4.7 - - + +
304A ILE 2.8 20.8 + - - +
305A THR 3.7 4.0 - - - +
306A ALA 3.3 0.2 - - - -
307A ALA* 1.3 70.2 - - - +
309A HIS* 1.3 57.9 + - - +
311A ALA* 3.8 0.2 - - - +
312A ALA* 2.7 37.6 + - - +
322A PHE* 3.7 26.4 - - + -
337A ILE* 3.9 24.0 - - + -
344A ILE* 4.7 3.8 - - + -
346A MET* 3.7 8.3 - - - -
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Residues in contact with HIS 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A PRO* 4.5 2.9 - - + -
119A LEU* 3.5 21.0 - - + +
120A TYR* 2.9 54.1 + + - +
123A LEU* 4.6 1.7 - - - +
305A THR* 3.0 36.1 + - + -
306A ALA 3.6 8.3 - - - +
308A ALA* 1.3 77.2 - - - +
310A PHE* 1.3 63.1 + - - +
313A SER* 3.3 8.5 + - - -
346A MET* 3.3 22.9 - - + +
347A PRO* 3.5 17.4 - - + +
351A GLY 3.5 17.0 - - - -
352A LEU* 2.9 29.2 + - + -
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Residues in contact with PHE 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A LEU* 5.2 0.2 - - - +
123A LEU* 4.1 8.9 - - + +
267A ILE* 4.2 7.6 - - + -
269A LEU* 4.5 6.5 - - + -
275A ILE* 4.3 22.7 - - + -
278A ALA* 3.3 41.1 - - + -
279A GLU* 3.6 35.9 - - + -
282A ASN* 4.1 5.6 - - + -
294A VAL* 3.9 17.9 - - + -
306A ALA 3.3 8.1 + - - +
307A ALA* 3.3 8.6 + - - +
308A ALA 3.3 0.2 - - - -
309A HIS* 1.3 80.3 - - - +
311A ALA* 1.3 63.7 + - - +
313A SER* 2.8 24.0 + - - -
314A LYS* 3.7 21.4 - - + +
317A ILE* 3.5 23.3 - - + -
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Residues in contact with ALA 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ARG* 3.0 18.3 + - - -
130A LEU* 4.7 0.4 - - + -
294A VAL* 3.7 21.1 - - + -
307A ALA 2.8 17.9 + - - +
308A ALA 3.8 3.1 - - - +
310A PHE* 1.3 78.8 - - - +
312A ALA* 1.3 58.6 + - - +
313A SER 3.3 0.7 + - - -
314A LYS 3.5 7.4 + - - +
317A ILE* 3.8 17.9 - - + +
320A PHE* 3.7 27.5 - - + -
322A PHE* 4.0 6.5 - - + -
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Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A TYR* 4.1 4.9 - - + -
126A TYR 3.4 0.2 + - - -
127A ARG* 2.9 61.0 + - + +
130A LEU* 4.0 10.7 - - + +
308A ALA 2.7 22.4 + - - +
309A HIS 4.1 3.4 - - - +
311A ALA* 1.3 74.2 - - - +
313A SER* 1.3 60.2 + - - +
346A MET* 3.9 21.5 - - + -
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Residues in contact with SER 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A TYR 3.1 27.1 - - - -
123A LEU* 3.3 29.6 - - - +
124A GLY* 3.6 3.8 - - - -
126A TYR* 3.3 20.6 + - - +
309A HIS 3.3 8.0 + - - -
310A PHE* 2.8 19.1 + - - -
311A ALA 3.2 0.4 - - - -
312A ALA* 1.3 79.4 - - - +
314A LYS* 1.3 66.9 + - - +
83B GLU* 3.6 14.4 - - - +
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Residues in contact with LYS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 3.0 16.9 + - - +
126A TYR* 4.0 1.8 - - - -
127A ARG* 2.8 26.5 + - - -
279A GLU* 2.7 42.8 + - - +
282A ASN* 3.7 25.6 - - - +
310A PHE* 3.7 15.5 - - + +
311A ALA 3.5 2.6 + - - +
312A ALA 3.4 0.8 - - - -
313A SER* 1.3 100.8 - - - +
315A ARG* 1.3 63.7 + - - +
316A ASN 4.3 0.7 - - - +
317A ILE* 3.4 26.7 + - + +
83B GLU* 3.6 14.8 + - - +
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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