Contacts of the helix formed by residues 339 - 357 (chain A) in PDB entry 2FQ3
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 339 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A PHE* 3.5 8.1 - - - +
335A ILE 3.9 4.9 - - - +
336A PRO* 3.5 22.9 - - + +
338A LYS* 1.3 78.6 - - - +
340A PRO* 1.3 77.6 - - + +
341A GLU* 3.2 17.8 + - - +
342A VAL* 3.1 23.3 + - - +
343A TYR* 2.9 22.2 + - - +
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Residues in contact with PRO 340 (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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319A ILE* 3.6 24.0 - - + +
330A PHE 3.7 6.1 - - - +
331A PHE* 3.9 23.1 - - + -
333A ASN* 5.7 7.9 - - - +
339A THR* 1.3 89.0 - - - +
341A GLU* 1.3 68.8 + - - +
343A TYR* 3.3 5.9 + - + +
344A MET* 2.9 36.7 + - - +
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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
----------------------------------------------------------
339A THR* 3.2 21.8 + - - +
340A PRO* 1.3 90.8 - - - +
342A VAL* 1.3 61.5 + - + +
344A MET* 4.8 1.1 - - - -
345A ARG* 2.7 57.9 + - - +
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Residues in contact with VAL 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A PHE* 4.3 7.9 - - + -
336A PRO 5.2 1.3 - - - +
337A SER* 3.5 28.5 - - - +
338A LYS* 5.7 0.2 - - + -
339A THR* 3.1 22.9 + - + +
341A GLU* 1.3 75.1 - - + +
343A TYR* 1.3 67.2 + - - +
345A ARG* 3.1 9.7 + - - +
346A TYR* 3.1 55.2 + - + +
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Residues in contact with TYR 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ILE* 4.0 12.1 - - + -
323A GLU* 2.6 45.0 + - + +
327A LEU* 3.6 25.8 - - + +
330A PHE* 3.6 39.7 - + + -
331A PHE* 3.8 22.0 - + + -
339A THR 2.9 12.7 + - - +
340A PRO* 3.4 8.3 - - + +
342A VAL* 1.3 79.5 - - - +
344A MET* 1.3 62.3 + - + +
346A TYR* 3.3 2.7 + - - +
347A ARG* 2.8 54.6 + - + +
381A LEU* 3.8 13.4 - - + +
384A PHE* 3.8 13.2 - - - -
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Residues in contact with MET 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LEU 3.1 27.4 - - - +
317A GLU* 3.5 28.9 - - - +
318A LYS* 3.8 0.9 - - - +
319A ILE* 3.7 30.7 - - + -
340A PRO* 2.9 18.9 + - - +
341A GLU* 5.3 0.9 - - - -
342A VAL 3.3 0.2 - - - -
343A TYR* 1.3 77.9 - - + +
345A ARG* 1.3 85.8 + - - +
347A ARG* 3.6 15.7 - - - +
348A ASN* 2.8 39.8 + - - +
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Residues in contact with ARG 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A GLU* 2.7 48.4 + - - +
342A VAL* 3.1 12.4 + - - +
344A MET* 1.3 112.9 - - - +
346A TYR* 1.3 68.6 - - + +
348A ASN* 4.2 2.6 + - - +
349A PHE* 3.2 23.2 + - - +
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Residues in contact with TYR 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A PHE* 4.3 21.1 - + - -
342A VAL* 3.1 38.2 + - + +
343A TYR 3.9 1.8 - - - +
345A ARG* 1.3 82.3 - - + +
347A ARG* 1.3 64.2 + - - +
349A PHE* 3.3 7.2 + - - +
350A MET* 3.2 25.8 + - - +
371A VAL* 3.4 32.8 - - + +
372A SER 3.4 17.1 + - - -
373A GLY* 3.5 14.3 - - - -
374A ASP* 4.6 3.0 + - + -
377A ALA* 5.8 4.7 - - + -
378A LEU* 3.9 17.3 - - + -
381A LEU* 3.5 17.3 - - + -
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Residues in contact with ARG 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A PHE* 3.6 19.4 - - - -
315A ASN 3.5 0.6 + - - -
316A LEU* 2.9 31.9 + - - +
318A LYS 2.8 26.3 + - - -
319A ILE* 4.1 2.8 - - - +
323A GLU* 2.8 43.8 + - - -
343A TYR* 2.8 36.3 + - + +
344A MET* 3.6 17.1 - - - +
346A TYR* 1.3 77.1 - - - +
348A ASN* 1.3 81.8 + - - +
350A MET* 3.1 4.9 + - - +
351A VAL* 3.0 26.2 + - + +
381A LEU* 3.6 17.0 - - + +
385A LEU* 4.1 22.0 - - + -
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Residues in contact with ASN 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LEU* 3.0 42.1 - - + +
317A GLU* 4.8 3.5 - - - +
344A MET* 2.8 28.8 + - - +
345A ARG* 4.2 3.4 + - - +
347A ARG* 1.3 110.1 + - - +
349A PHE* 1.3 57.3 + - - +
351A VAL* 4.5 0.4 - - - +
352A ASN* 2.8 47.0 + - - +
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Residues in contact with PHE 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ARG 3.2 19.1 + - - +
346A TYR 3.6 4.7 - - - +
347A ARG 3.2 0.4 - - - -
348A ASN* 1.3 77.2 - - - +
350A MET* 1.3 62.7 + - + +
352A ASN* 4.0 4.2 - - + +
353A SER* 2.8 53.8 + - - -
362A PHE* 4.5 13.5 - + - -
367A ALA* 4.9 2.0 - - - -
370A ASN* 3.5 36.8 - - + -
371A VAL* 3.1 33.2 - - + -
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Residues in contact with MET 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A TYR 3.5 9.0 - - - +
347A ARG 3.1 7.7 + - - +
349A PHE* 1.3 80.7 - - + +
351A VAL* 1.3 57.2 + - - +
353A SER* 3.3 2.3 + - - -
354A TYR* 3.0 30.1 + - - +
362A PHE* 3.5 34.7 - - + -
367A ALA* 4.0 16.6 - - + -
371A VAL* 6.1 1.3 - - + -
378A LEU* 3.5 48.7 - - + +
381A LEU* 4.1 12.8 - - + -
382A HIS* 4.0 19.7 - - + -
385A LEU* 3.7 24.7 - - + -
391A ILE* 4.0 4.6 - - + +
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Residues in contact with VAL 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A PHE* 4.2 19.1 - - + -
316A LEU* 4.1 16.4 - - + -
347A ARG 3.0 15.9 + - - +
348A ASN 4.1 2.5 - - - +
350A MET* 1.3 74.8 - - - +
352A ASN* 1.3 63.7 + - - +
354A TYR* 3.3 2.3 + - - +
355A ARG* 2.9 61.4 + - + +
385A LEU* 4.2 23.8 - - + -
390A LEU* 4.3 11.2 - - + +
391A ILE* 4.0 12.6 - - + -
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Residues in contact with ASN 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LEU* 3.7 30.6 - - - +
348A ASN* 2.8 36.1 + - - +
349A PHE* 4.0 4.8 - - + +
351A VAL* 1.3 73.6 - - - +
353A SER* 1.3 62.3 + - - +
355A ARG* 3.4 9.9 + - - +
356A LEU* 3.2 27.3 + - - +
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Residues in contact with SER 353 (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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349A PHE* 2.8 48.1 + - - -
350A MET 3.6 0.7 - - - -
352A ASN* 1.3 77.4 - - - +
354A TYR* 1.3 63.2 + - - +
356A LEU* 3.2 24.8 + - - +
357A ASN* 3.7 6.2 + - - +
362A PHE* 3.5 27.7 - - - -
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Residues in contact with TYR 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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350A MET 3.0 17.1 + - - +
351A VAL 3.8 3.1 - - - +
353A SER* 1.3 77.0 - - - +
355A ARG* 1.3 65.4 + - + +
357A ASN 3.0 15.9 + - - -
358A PRO* 2.6 48.3 + - + -
360A GLU 3.3 24.7 - - - -
362A PHE* 4.1 14.1 - - + -
390A LEU 4.4 1.8 - - - -
391A ILE* 3.8 17.5 - - + -
392A ASN* 3.2 45.5 - - - -
393A TYR* 3.2 34.2 + + - -
394A GLN* 2.8 27.7 + - - +
395A VAL* 3.5 1.2 + - + -
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Residues in contact with ARG 355 (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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311A SER* 6.0 2.4 + - - -
314A PHE* 3.7 27.1 - - - -
316A LEU* 4.0 24.7 - - - +
351A VAL* 2.9 37.4 + - + +
352A ASN* 3.9 10.1 - - - +
353A SER 3.3 0.2 - - - -
354A TYR* 1.3 79.0 - - + +
356A LEU* 1.3 61.2 + - - +
357A ASN 3.3 0.2 - - - -
358A PRO* 3.5 18.3 - - - +
390A LEU* 5.0 6.9 + - - +
393A TYR* 3.9 23.9 + - + +
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Residues in contact with LEU 356 (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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352A ASN 3.2 17.3 + - - +
353A SER* 3.4 15.0 - - - +
354A TYR 3.1 1.0 - - - -
355A ARG* 1.3 80.2 - - - +
357A ASN* 1.3 77.7 + - - +
358A PRO* 3.6 3.4 - - - +
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Residues in contact with ASN 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A SER 3.7 5.6 + - - +
354A TYR* 3.0 9.1 + - - +
356A LEU* 1.3 100.1 - - - +
358A PRO* 1.3 57.3 - - - +
359A ASN* 3.1 15.3 + - - +
360A GLU* 3.0 53.6 + - + +
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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
------------------------------------------------------------
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