Contacts of the strand formed by residues 337 - 346 (chain A) in PDB entry 5JPM
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 ARG 337 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A LEU* 3.5 5.4 - - - +
287A LEU* 2.8 76.4 + - + +
288A ASP 4.4 7.6 + - - -
289A GLU* 4.4 16.4 + - - +
335A GLY 4.6 2.4 + - - -
336A LEU* 1.3 79.1 - - - +
338A LEU* 1.3 64.1 + - - +
339A TYR* 3.3 0.6 + - - -
358A THR* 2.8 36.1 + - - +
360A TRP 3.2 13.5 - - - +
361A TYR* 3.1 49.3 + - + -
362A PHE* 3.9 4.3 - - - -
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Residues in contact with LEU 338 (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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252A ILE* 3.8 20.0 - - + -
262A MET* 3.9 18.2 - - + -
284A PHE* 4.0 12.8 - - + -
285A GLY 3.6 13.5 - - - +
286A LEU* 4.4 1.3 - - + -
296A PHE* 4.2 9.6 - - + -
314A LEU* 4.9 4.7 - - + -
319A PHE* 3.9 28.3 - - + -
337A ARG* 1.3 72.0 - - - +
339A TYR* 1.3 67.4 + - - +
340A VAL* 3.7 17.8 + - + +
357A LEU 3.9 6.1 - - - +
360A TRP* 2.8 48.5 + - + +
362A PHE* 3.7 12.1 - - + -
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Residues in contact with TYR 339 (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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283A ARG 3.7 1.1 - - - +
284A PHE* 3.3 7.4 - - - -
285A GLY* 2.7 46.4 + - - +
286A LEU 4.2 1.6 - - - +
287A LEU* 4.1 24.7 - - + +
293A LYS* 3.9 28.5 - - + +
295A PHE* 3.7 32.7 - + - -
337A ARG 3.3 1.2 + - - -
338A LEU* 1.3 72.0 - - - +
340A VAL* 1.3 62.1 + - - +
341A ALA* 3.6 27.5 - - + +
356A GLU* 2.7 42.5 + - + +
357A LEU 3.7 13.2 - - - -
358A THR* 4.0 13.9 - - + -
770B ASP 5.8 0.2 + - - -
771B ASP* 5.9 1.0 - - - -
772B ILE* 4.3 7.1 + - - +
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Residues in contact with VAL 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ILE* 4.0 13.7 - - + +
264A LEU* 3.6 27.8 - - + -
282A VAL* 3.7 20.2 - - + -
283A ARG 3.7 2.9 - - - -
284A PHE* 3.8 11.7 - - + -
338A LEU* 3.7 22.2 - - + +
339A TYR* 1.3 77.6 - - - +
341A ALA* 1.3 61.6 + - - +
342A ALA* 5.2 0.7 - - + -
356A GLU* 3.3 4.7 - - - +
357A LEU* 2.8 47.4 + - + -
360A TRP* 4.0 17.7 - - + -
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Residues in contact with ALA 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A TYR 3.7 0.5 - - - +
282A VAL* 3.4 3.4 - - - +
283A ARG* 2.9 68.5 + - + +
339A TYR* 3.6 30.2 - - + +
340A VAL* 1.3 73.4 - - - +
342A ALA* 1.3 59.8 + - - +
355A ALA 3.7 7.0 - - - +
356A GLU* 4.4 0.2 - - - +
772B ILE* 5.2 4.0 - - + -
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Residues in contact with ALA 342 (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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243A VAL* 5.5 2.1 - - + +
245A ILE* 3.7 23.5 - - + +
266A ILE* 4.1 30.7 - - + -
280A ALA* 5.8 0.4 - - + -
281A TYR 3.3 6.1 - - - +
282A VAL* 4.7 3.8 - - + -
283A ARG* 6.2 0.4 - - - -
341A ALA* 1.3 74.7 - - - +
343A ALA* 1.3 60.8 + - - +
344A ILE* 5.2 4.4 - - + +
353A GLU 4.3 0.2 - - - +
354A GLU* 3.4 5.6 - - - +
355A ALA* 3.0 34.7 + - + +
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Residues in contact with ALA 343 (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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280A ALA* 3.4 0.5 - - - -
281A TYR* 2.6 45.4 + - + +
283A ARG* 6.1 0.9 - - - +
342A ALA* 1.3 73.2 - - - +
344A ILE* 1.3 61.0 + - - +
345A ILE* 3.7 8.7 - - + +
352A MET* 3.7 26.7 - - + -
353A GLU 3.7 4.3 - - - -
354A GLU* 4.1 6.7 - - + +
767B ILE* 4.3 25.1 - - + -
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Residues in contact with ILE 344 (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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241A PHE* 3.8 22.6 - - + -
243A VAL* 3.6 27.1 - - + -
266A ILE* 3.7 22.0 - - + -
267A GLN 4.5 0.2 - - - +
268A ALA* 3.6 24.0 - - + -
276A VAL* 4.8 4.0 - - + -
278A GLY 5.4 0.2 - - - -
279A VAL 3.4 4.0 - - - +
280A ALA* 3.9 15.0 - - + -
305A LEU* 3.8 25.4 - - + -
342A ALA* 5.2 2.5 - - + -
343A ALA* 1.3 76.7 - - - +
345A ILE* 1.3 66.7 + - - +
352A MET* 3.2 2.1 - - - -
353A GLU 2.9 36.6 + - - +
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Residues in contact with ILE 345 (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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278A GLY* 3.2 1.0 - - - -
279A VAL* 2.9 55.8 + - + +
281A TYR* 4.5 12.3 - - + -
343A ALA* 3.7 22.2 - - + +
344A ILE* 1.3 72.6 - - - +
346A GLU* 1.3 68.8 + - - +
347A SER* 4.5 0.2 + - - -
350A GLY* 3.3 27.8 - - - +
351A GLU 3.8 2.9 - - - +
352A MET* 3.6 26.5 - - + -
762B GLN* 6.3 0.2 - - - +
767B ILE* 5.2 5.4 - - + -
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Residues in contact with GLU 346 (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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241A PHE* 4.7 10.1 - - + -
270A TYR* 3.1 37.5 + - - -
276A VAL* 3.9 17.6 - - + +
277A GLN 3.4 19.5 + - - +
278A GLY* 4.1 0.9 - - - -
344A ILE* 4.0 1.4 + - - +
345A ILE* 1.3 76.9 - - - +
347A SER* 1.3 59.8 + - - +
348A PRO* 3.7 12.8 - - + +
349A GLY* 4.2 14.1 + - - +
350A GLY* 3.0 30.0 + - - +
351A GLU* 2.9 24.1 + - - +
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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