Contacts of the helix formed by residues 340 - 354 (chain A) in PDB entry 4JQF
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 SER 340 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A GLN 4.9 2.9 + - - -
328A LEU* 4.3 1.1 - - - -
332A ARG* 4.1 4.3 - - - +
338A GLY 3.1 7.2 + - - -
339A LEU* 1.3 94.4 - - - +
341A GLU* 1.3 63.5 + - - +
342A ALA* 3.5 8.2 + - - +
343A VAL* 3.1 31.5 + - - +
344A LEU 3.0 7.8 + - - -
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Residues in contact with GLU 341 (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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324A PHE* 3.5 29.1 - - + -
325A LEU* 4.2 14.6 - - - +
328A LEU* 3.7 22.0 - - + +
332A ARG* 4.3 5.8 - - - +
339A LEU 4.1 0.6 + - - -
340A SER* 1.3 72.7 - - - +
342A ALA* 1.3 58.2 + - - +
344A LEU* 3.3 2.1 + - - -
345A GLN* 2.9 29.3 + - - +
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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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275A GLN 4.4 0.7 - - - +
276A GLU* 3.3 27.8 - - - +
277A LYS 3.9 3.0 - - - +
278A GLY* 3.6 13.5 - - - +
340A SER* 3.2 8.5 + - - +
341A GLU* 1.3 76.7 - - - +
343A VAL* 1.3 63.9 + - - +
345A GLN* 3.4 7.3 + - - +
346A GLN* 3.1 27.2 + - - +
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Residues in contact with VAL 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A GLN 4.8 2.0 - - - +
278A GLY* 3.7 23.1 - - - +
280A VAL 4.0 5.2 - - - +
281A PHE* 3.9 31.0 - - + -
294A THR* 3.8 20.9 - - + +
300A LEU* 4.4 7.2 - - + -
339A LEU* 3.5 24.5 - - + -
340A SER* 3.1 22.5 + - - +
342A ALA* 1.3 71.7 - - - +
344A LEU* 1.3 67.2 + - - +
346A GLN* 3.1 4.5 + - - +
347A VAL* 3.0 20.5 + - + +
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Residues in contact with LEU 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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304A ILE* 3.9 34.1 - - + -
324A PHE* 3.6 33.9 - - + +
327A ILE* 3.9 13.2 - - + -
328A LEU* 3.7 36.1 - - + +
331A ALA* 5.4 0.7 - - + -
339A LEU* 3.6 19.9 - - + +
340A SER 3.0 7.4 + - - +
341A GLU 3.7 6.7 - - - +
343A VAL* 1.3 78.7 - - - +
345A GLN* 1.3 62.6 + - - +
347A VAL* 3.1 5.8 + - + +
348A LEU* 2.9 32.9 + - + +
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Residues in contact with GLN 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A PHE* 3.4 26.0 - - + -
341A GLU 2.9 18.6 + - - +
342A ALA* 3.7 9.0 - - - +
343A VAL 3.2 0.2 - - - -
344A LEU* 1.3 75.1 - - - +
346A GLN* 1.3 59.9 + - - +
348A LEU* 3.3 4.3 + - - +
349A GLU* 3.0 61.1 + - - +
363A HIS* 4.9 11.4 + - - -
365A TYR* 4.1 17.6 + - - -
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Residues in contact with GLN 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LYS 3.5 16.9 - - - +
278A GLY 3.5 22.2 - - - +
279A LEU* 3.5 22.7 - - + +
294A THR* 4.1 9.0 - - + -
342A ALA 3.1 17.4 + - - +
343A VAL 3.1 7.6 + - - +
345A GLN* 1.3 78.1 - - - +
347A VAL* 1.3 61.4 + - - +
349A GLU* 3.5 25.7 + - - +
350A LEU* 3.1 22.5 + - - +
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Residues in contact with VAL 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A THR* 3.7 19.3 - - + -
300A LEU* 3.8 23.1 - - + -
301A HIS* 4.0 28.0 - - - +
304A ILE* 4.0 33.4 - - + -
339A LEU* 6.1 0.2 - - + -
343A VAL* 3.0 16.1 + - + +
344A LEU* 3.1 10.5 + - + +
346A GLN* 1.3 75.7 - - - +
348A LEU* 1.3 58.7 + - - +
350A LEU* 3.2 7.2 + - - +
351A LEU* 2.9 31.5 + - + +
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Residues in contact with LEU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ILE* 4.0 14.6 - - + -
308A ILE* 3.6 31.0 - - + -
324A PHE* 3.4 38.4 - - + -
327A ILE* 4.5 7.4 - - + -
344A LEU* 2.9 27.3 + - + +
345A GLN* 3.7 7.4 - - - +
347A VAL* 1.3 74.8 - - - +
349A GLU* 1.3 58.8 + - - +
351A LEU* 3.3 1.4 + - + -
352A GLU* 2.8 32.8 + - - +
357A ILE* 3.7 18.0 - - + +
365A TYR* 3.7 27.6 - - + +
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Residues in contact with GLU 349 (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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345A GLN* 3.0 49.3 + - - +
346A GLN* 3.8 26.5 + - - +
348A LEU* 1.3 76.4 - - - +
350A LEU* 1.3 55.9 + - - +
352A GLU* 3.3 12.0 + - - +
353A ASP* 2.9 38.1 + - - +
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Residues in contact with LEU 350 (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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295A ARG* 3.7 49.8 - - + +
301A HIS* 3.4 41.1 - - + +
346A GLN 3.1 13.7 + - - +
347A VAL* 3.2 8.7 + - - +
349A GLU* 1.3 74.6 - - - +
351A LEU* 1.3 63.5 + - + +
353A ASP* 3.1 13.1 + - + +
354A GLN* 2.9 51.8 + - + +
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Residues in contact with LEU 351 (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 HIS* 3.8 27.4 - - + +
304A ILE* 3.9 18.2 - - + -
305A HIS* 3.9 36.1 - - + +
308A ILE* 4.7 0.4 - - + -
347A VAL* 2.9 24.7 + - + +
348A LEU* 3.7 4.3 - - - +
350A LEU* 1.3 76.5 - - + +
352A GLU* 1.3 59.0 + - - +
354A GLN* 3.4 18.0 + - - +
355A SER 3.3 2.6 + - - -
356A ASP* 2.9 40.7 + - + +
357A ILE* 3.5 28.2 + - + -
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Residues in contact with GLU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU 2.8 16.9 + - - +
349A GLU* 3.5 13.1 - - - +
351A LEU* 1.3 74.3 - - - +
353A ASP* 1.3 66.9 + - - +
355A SER* 3.0 16.8 + - - -
357A ILE* 3.8 21.5 - - + +
358A VAL* 5.1 2.2 - - - -
359A SER* 3.4 25.0 + - - -
365A TYR* 3.8 22.5 + - - -
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Residues in contact with ASP 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ARG* 5.3 4.0 + - - -
349A GLU* 2.9 25.9 + - - +
350A LEU* 3.1 16.0 + - + +
352A GLU* 1.3 78.4 - - - +
354A GLN* 1.3 60.1 + - + +
355A SER* 3.2 4.8 + - - -
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Residues in contact with GLN 354 (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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298A LYS* 6.3 0.8 - - - +
301A HIS* 5.2 5.7 - - - +
350A LEU* 2.9 49.0 + - + +
351A LEU* 3.8 13.0 - - - +
352A GLU 3.2 0.4 - - - -
353A ASP* 1.3 75.6 - - + +
355A SER* 1.3 68.5 - - - +
356A ASP* 3.0 29.0 + - - +
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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