Contacts of the helix formed by residues 347 - 362 (chain A) in PDB entry 3E4E
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 MET 347 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A LEU* 6.2 0.4 - - + -
328A GLU* 3.3 22.9 - - - +
329A ILE* 3.6 35.9 - - + +
332A VAL* 3.9 17.3 - - + -
333A ILE* 3.6 23.8 - - + -
343A ASP* 3.2 23.3 - - - +
344A ARG* 2.6 18.5 + - - +
346A GLU* 1.3 74.6 - - - +
348A PRO* 1.3 65.5 - - - +
349A TYR 3.2 3.8 + - - -
350A MET* 3.6 11.8 + - + -
351A ASP* 3.1 22.2 + - - +
448A PHE* 4.0 9.0 - - + -
452A CYS* 3.9 15.9 - - - -
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Residues in contact with PRO 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A GLU* 3.4 9.6 - - - +
331A ARG* 5.7 2.9 - - - +
344A ARG 4.9 0.9 - - - +
345A GLN 5.2 2.0 - - - +
346A GLU* 3.3 13.7 - - - +
347A MET* 1.3 86.2 - - - +
349A TYR* 1.3 64.0 + - + +
351A ASP* 4.0 6.5 - - + +
352A ALA* 3.2 19.8 + - - +
415A LEU* 3.5 5.6 - - - +
419A GLY 3.5 25.6 - - - +
420A LYS* 4.2 3.1 - - - -
421A PHE* 3.9 22.5 - - + +
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Residues in contact with TYR 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ILE* 3.4 46.9 - - + +
324A LYS* 3.3 54.2 + - + +
325A LEU* 3.6 21.8 - - + -
328A GLU* 2.9 22.7 + - + +
348A PRO* 1.3 76.4 - - - +
350A MET* 1.3 58.2 + - - +
352A ALA* 2.8 22.7 + - - +
353A VAL* 3.0 16.0 + - + +
411A PRO* 3.8 21.5 - - + +
412A GLU* 4.9 5.3 + - - -
415A LEU* 4.0 23.3 - - + +
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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
----------------------------------------------------------
325A LEU* 3.5 30.2 - - + +
328A GLU* 3.3 16.0 + - - +
329A ILE* 5.1 3.1 - - - -
347A MET* 3.8 14.8 - - + +
349A TYR* 1.3 77.2 - - - +
351A ASP* 1.3 52.1 + - - +
353A VAL* 3.0 2.8 + - - +
354A VAL* 2.7 41.5 + - + +
448A PHE* 3.6 30.3 - - + +
451A LEU* 3.4 42.8 - - + +
452A CYS* 3.4 31.2 - - - +
455A LEU* 5.0 1.8 - - - -
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Residues in contact with ASP 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ARG* 3.2 43.4 + - + +
345A GLN* 6.1 0.2 - - - -
347A MET 3.1 16.3 + - - +
348A PRO* 4.0 4.7 - - + +
350A MET* 1.3 79.2 - - - +
352A ALA* 1.3 58.7 + - - +
354A VAL* 4.1 4.6 - - - +
355A HIS* 2.6 57.4 + - - -
421A PHE* 3.5 36.1 - - + +
448A PHE* 4.7 3.7 - - - -
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Residues in contact with ALA 352 (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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348A PRO 3.2 13.4 + - - +
349A TYR 2.8 12.6 + - - +
351A ASP* 1.3 74.8 - - - +
353A VAL* 1.3 58.4 + - - +
355A HIS* 3.6 2.6 + - - +
356A GLU* 2.9 30.9 + - - +
411A PRO* 3.6 24.6 - - + +
414A PHE* 3.9 19.5 - - - +
415A LEU* 3.8 18.2 - - + -
421A PHE* 4.1 2.0 - - - -
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Residues in contact with VAL 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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315A LEU* 4.3 10.3 - - + -
321A ILE* 4.1 8.3 - - + -
325A LEU* 3.8 33.4 - - + -
349A TYR* 3.0 20.6 + - + +
350A MET* 3.0 7.8 + - - +
352A ALA* 1.3 75.1 - - - +
354A VAL* 1.3 66.7 - - - +
356A GLU* 2.9 5.9 + - - +
357A ILE* 2.9 47.5 + - + +
409A PHE* 4.7 3.8 - - + -
411A PRO* 4.0 24.0 - - + -
451A LEU* 4.4 8.1 - - + -
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Residues in contact with VAL 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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344A ARG* 5.2 4.0 - - - +
350A MET* 2.7 50.9 + - + +
351A ASP* 4.1 6.3 - - - +
353A VAL* 1.3 72.5 - - - +
355A HIS* 1.3 67.7 + - + +
357A ILE* 3.8 8.9 + - - +
358A GLN* 3.1 40.6 + - - +
444A ARG* 5.1 4.0 - - + +
447A LEU* 3.9 21.4 - - + +
448A PHE* 4.1 22.7 - - + +
451A LEU* 3.9 10.8 - - + -
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Residues in contact with HIS 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ARG* 5.0 7.4 - - - -
351A ASP* 2.6 45.0 + - - +
352A ALA 3.8 0.4 - - - +
353A VAL 3.1 0.4 - - - -
354A VAL* 1.3 82.3 - - + +
356A GLU* 1.3 60.6 + - - +
358A GLN* 3.1 2.7 + - - +
359A ARG* 3.0 26.3 + - - +
414A PHE* 3.7 25.4 - + + -
421A PHE* 3.4 27.0 - + - -
423A TYR* 6.1 2.6 - + - -
427A PHE* 3.4 44.5 - + + -
444A ARG* 3.4 22.6 + - - -
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Residues in contact with GLU 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 ALA 2.9 17.9 + - - +
353A VAL* 2.9 4.9 + - - +
355A HIS* 1.3 74.2 - - - +
357A ILE* 1.3 60.6 + - - +
359A ARG* 2.3 47.1 + - - -
360A PHE* 2.8 34.3 + - - +
408A LYS 3.6 1.2 - - - +
409A PHE* 3.4 26.0 - - + -
410A LYS 2.7 30.2 + - - +
411A PRO* 4.2 5.8 - - + -
413A HIS* 2.5 12.8 + - - +
414A PHE* 3.3 11.1 - - + -
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Residues in contact with ILE 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A THR* 3.7 35.2 - - + +
311A GLY* 3.7 29.4 - - - +
314A ILE* 4.4 9.4 - - + -
315A LEU* 5.1 2.9 - - + -
353A VAL* 2.9 33.0 + - + +
354A VAL* 3.8 7.0 - - - +
356A GLU* 1.3 79.6 - - - +
358A GLN* 1.3 61.5 + - - +
361A ILE* 3.2 30.9 + - + +
409A PHE* 3.5 23.1 - - + -
451A LEU* 4.1 18.8 - - + -
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Residues in contact with GLN 358 (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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307A THR* 4.2 9.4 - - + +
354A VAL* 3.1 32.1 + - - +
355A HIS* 3.1 9.0 + - - +
357A ILE* 1.3 78.4 - - - +
359A ARG* 1.3 63.2 + - - +
361A ILE* 3.9 8.4 - - - +
362A THR* 3.6 13.0 + - - -
363A LEU* 4.7 1.0 + - - +
397A LEU* 3.9 8.0 - - - +
427A PHE* 3.6 24.7 - - + -
429A PRO* 4.0 14.6 - - + +
430A PHE* 3.3 34.9 - - - -
444A ARG* 5.1 6.9 - - - +
447A LEU* 3.3 29.6 - - + +
500A HEM 4.9 3.4 - - + +
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Residues in contact with ARG 359 (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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355A HIS 3.0 16.1 + - - +
356A GLU* 2.3 45.7 + - - +
358A GLN* 1.3 75.9 - - - +
360A PHE* 1.3 91.1 + - - +
361A ILE 3.2 0.5 + - - -
362A THR* 3.3 22.3 + - - +
397A LEU* 3.2 44.9 + - + +
398A TYR* 3.5 11.2 - - - -
403A PHE* 3.9 29.4 - - + +
406A PRO* 2.6 30.1 + - - +
408A LYS 3.5 1.2 + - - -
413A HIS* 2.5 26.7 + - - -
414A PHE* 3.9 14.8 - - + -
427A PHE* 4.4 2.6 - - + -
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Residues in contact with PHE 360 (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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310A TYR* 5.1 1.6 - + - -
314A ILE* 3.8 11.9 - - + -
356A GLU 2.8 20.6 + - - +
357A ILE 4.2 2.0 - - - +
359A ARG* 1.3 94.1 - - - +
361A ILE* 1.3 73.8 + - + +
362A THR* 4.3 0.5 + - - +
398A TYR* 2.4 32.5 + - - -
407A GLU 3.5 22.9 - - - -
408A LYS* 4.1 2.7 - - - -
409A PHE* 3.7 36.8 - + + -
471A LEU* 4.1 46.0 - - + -
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Residues in contact with ILE 361 (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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307A THR* 4.1 30.7 - - + +
310A TYR* 3.6 48.7 - - + -
314A ILE* 3.8 19.3 - - + -
357A ILE* 3.2 22.0 + - + +
358A GLN* 3.9 6.5 - - - +
360A PHE* 1.3 81.2 - - + +
362A THR* 1.3 76.0 + - - +
363A LEU* 3.2 25.4 + - + +
480A CYS* 3.5 16.6 - - - +
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Residues in contact with THR 362 (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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358A GLN 3.6 2.5 + - - -
359A ARG 3.3 18.9 + - - +
360A PHE 4.3 0.6 + - - +
361A ILE* 1.3 83.3 + - - +
363A LEU* 1.3 65.6 + - - +
364A VAL 3.1 5.0 + - - -
365A PRO* 3.2 20.1 - - - +
393A LEU* 6.4 0.2 - - - -
394A ASP* 4.0 26.6 - - + +
397A LEU* 3.6 24.7 - - + -
398A TYR* 3.5 26.2 - - + -
429A PRO* 6.0 0.2 - - - -
480A CYS* 3.2 12.6 - - - -
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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