Contacts of the helix formed by residues 362 - 376 (chain E) in PDB entry 4DVQ
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 LEU 362 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343E GLU* 3.5 21.5 - - + +
344E SER* 3.4 29.2 - - - +
347E ALA* 4.5 1.8 - - + -
351E ILE* 3.9 15.7 - - + -
358E ALA* 3.3 38.3 + - + +
360E THR 3.4 0.6 - - - -
361E GLU* 1.3 85.7 - - - +
363E PRO* 1.3 59.8 - - - +
364E LEU 3.3 2.2 - - - -
365E LEU* 3.1 10.8 + - + -
366E ARG* 2.9 29.8 + - - +
461E LEU* 4.1 17.3 - - + -
465E HIS* 4.1 20.0 - - + +
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Residues in contact with PRO 363 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343E GLU* 3.1 13.5 - - - +
359E THR 5.9 0.2 - - - +
360E THR 3.9 11.4 - - - +
361E GLU 3.2 8.5 - - - +
362E LEU* 1.3 88.6 - - - +
364E LEU* 1.3 61.0 + - + +
366E ARG* 3.3 10.7 + - + +
367E ALA* 2.9 28.6 + - - +
429E LEU* 4.7 19.4 - - + +
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Residues in contact with LEU 364 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339E ILE* 3.5 32.3 - - + +
340E LEU* 3.2 18.8 - - + +
343E GLU* 3.2 24.9 + - + +
363E PRO* 1.3 78.9 - - + +
365E LEU* 1.3 57.2 + - - +
367E ALA* 3.3 5.2 + - - +
368E ALA* 2.9 22.9 + - - +
425E PRO* 3.8 21.7 - - + +
426E GLN* 3.8 35.2 - - + +
429E LEU* 4.0 19.3 - - + -
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Residues in contact with LEU 365 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330E LEU* 5.2 2.5 - - + -
340E LEU* 3.4 29.1 - - + +
343E GLU* 3.1 13.0 + - - +
344E SER* 4.1 8.7 - - - +
362E LEU* 3.1 13.3 + - + +
364E LEU* 1.3 72.5 - - - +
366E ARG* 1.3 66.7 + - - +
367E ALA 3.1 0.2 - - - -
368E ALA* 3.1 15.9 + - + +
369E LEU* 3.2 15.5 + - + +
461E LEU* 4.0 21.1 - - + +
464E LEU* 4.0 21.3 - - + -
465E HIS* 3.9 24.9 - - + +
468E LEU* 3.7 27.8 - - + -
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Residues in contact with ARG 366 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359E THR* 3.3 48.9 + - - +
362E LEU* 2.9 20.1 + - + +
363E PRO* 3.5 12.1 - - + +
365E LEU* 1.3 76.0 - - - +
367E ALA* 1.3 62.7 + - - +
369E LEU* 3.2 19.7 + - + +
370E LYS* 3.4 36.1 + - - +
453E ARG* 4.5 1.2 - - - +
457E GLU* 3.4 31.5 + - - +
461E LEU* 3.8 22.4 - - + +
603E SO4 3.2 30.6 + - - -
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Residues in contact with ALA 367 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363E PRO 2.9 17.9 + - - +
364E LEU* 3.4 9.4 - - - +
365E LEU 3.1 0.2 - - - -
366E ARG* 1.3 75.5 - - - +
368E ALA* 1.3 64.0 + - - +
370E LYS* 3.1 17.8 + - + +
371E GLU* 3.0 20.6 + - - +
425E PRO* 3.3 26.2 - - + +
428E TRP* 3.6 15.4 - - + -
429E LEU* 4.7 8.7 - - + -
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Residues in contact with ALA 368 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326E THR* 4.9 4.9 - - + -
340E LEU* 3.8 25.4 - - + -
364E LEU 2.9 13.2 + - - +
365E LEU* 3.3 14.1 - - + +
367E ALA* 1.3 75.2 - - - +
369E LEU* 1.3 59.4 + - + +
371E GLU* 3.2 2.5 + - - +
372E THR* 3.0 17.5 + - - -
423E TYR* 2.8 30.0 + - - +
425E PRO* 3.6 15.4 - - + +
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Residues in contact with LEU 369 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322E PRO* 5.4 2.0 - - + +
326E THR* 3.8 14.1 - - + +
365E LEU 3.2 12.5 + - - +
366E ARG* 3.2 11.3 + - + +
367E ALA 3.1 0.6 - - - -
368E ALA* 1.3 75.5 - - + +
370E LYS* 1.3 66.5 + - + +
372E THR* 3.1 5.7 + - - +
373E LEU* 3.0 31.3 + - + +
457E GLU* 4.5 11.0 - - + +
460E MET* 3.6 47.1 - - + -
461E LEU* 4.2 20.6 - - + +
464E LEU* 3.6 27.8 - - + -
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Residues in contact with LYS 370 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366E ARG* 3.7 42.7 + - - +
367E ALA* 3.1 10.5 + - + +
369E LEU* 1.3 76.1 - - - +
371E GLU* 1.3 57.2 + - - +
373E LEU* 3.4 2.8 + - - +
374E ARG* 2.9 29.5 + - - +
428E TRP* 3.7 43.1 - - + -
440E HIS* 3.4 50.8 + - + +
457E GLU* 6.0 0.2 + - - -
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Residues in contact with GLU 371 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367E ALA 3.0 12.1 + - - +
368E ALA* 3.3 14.4 - - - +
370E LYS* 1.3 76.2 - - - +
372E THR* 1.3 64.8 + - - +
374E ARG* 2.9 38.1 + - - +
375E LEU* 3.3 24.9 + - - +
423E TYR* 3.7 20.4 - - + -
424E ASN 2.6 45.0 + - - +
425E PRO* 4.2 2.0 - - + -
427E ARG* 2.9 18.8 + - - -
428E TRP* 3.0 18.7 + - - +
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Residues in contact with THR 372 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322E PRO* 3.3 35.2 - - + +
325E MET* 3.7 21.0 - - + -
326E THR* 2.7 21.7 + - - +
368E ALA 3.0 5.3 + - - -
369E LEU* 3.1 9.6 + - - -
371E GLU* 1.3 77.0 - - - +
373E LEU* 1.3 54.2 + - - +
376E TYR* 2.7 42.0 + - + +
423E TYR* 2.8 28.5 + - - -
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Residues in contact with LEU 373 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322E PRO* 4.0 31.9 - - + -
369E LEU* 3.0 22.7 + - + +
370E LYS 4.0 1.8 - - - +
372E THR* 1.3 76.4 - - - +
374E ARG* 1.3 64.0 + - - +
376E TYR 3.9 12.3 - - - +
377E PRO* 3.4 23.6 - - - +
378E VAL* 4.2 5.8 - - + +
407E LEU* 5.6 0.3 - - - +
440E HIS* 4.7 3.1 - - + -
442E PRO* 3.7 27.8 - - + +
443E PHE* 3.8 32.5 - - + -
460E MET* 4.7 10.1 - - + -
601E HEM 4.2 20.6 - - + -
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Residues in contact with ARG 374 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370E LYS 2.9 17.5 + - - +
371E GLU* 2.9 46.6 + - - +
372E THR 3.3 0.2 - - - -
373E LEU* 1.3 81.2 - - - +
375E LEU* 1.3 75.4 + - - +
377E PRO* 3.9 5.4 - - - +
407E LEU 4.0 5.9 - - - +
411E GLY* 3.1 49.7 + - - +
412E ARG* 4.3 3.5 + - - -
417E PHE* 3.8 29.6 - - + +
420E PRO* 2.9 32.1 + - - +
422E ARG 3.0 18.8 + - - -
427E ARG* 3.6 13.0 - - - +
428E TRP* 4.2 7.6 - - + -
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Residues in contact with LEU 375 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329E GLU* 4.3 2.9 - - - +
371E GLU 3.3 15.5 + - - +
374E ARG* 1.3 99.9 - - - +
376E TYR* 1.3 97.4 + - + +
377E PRO* 3.2 6.1 - - - +
408E TYR* 4.1 3.6 - - - -
412E ARG* 3.0 45.3 + - + +
420E PRO 3.3 25.1 - - - +
421E GLU* 4.9 8.7 - - - +
423E TYR* 4.0 27.6 - - + -
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Residues in contact with TYR 376 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322E PRO* 5.2 2.5 - - + +
325E MET* 3.7 37.0 - - + -
328E PHE* 4.8 4.3 - + - -
329E GLU* 2.5 41.2 + - + -
332E ARG* 3.5 10.6 + - - -
372E THR* 2.7 35.3 + - + +
373E LEU* 3.9 8.5 - - - +
375E LEU* 1.3 102.1 - - + +
377E PRO* 1.3 60.6 - - - +
378E VAL* 3.1 11.3 + - - +
412E ARG* 4.1 10.7 + - - -
480E ASP* 5.3 2.1 + - - -
481E ILE* 5.2 8.5 + - + -
483E MET* 3.9 42.9 - - + +
489E LEU* 4.6 3.3 - - - +
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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