Contacts of the helix formed by residues 384 - 397 (chain E) in PDB entry 6DWZ
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 PHE 384 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373E GLU* 4.0 33.7 - - + +
374E LEU* 4.9 6.5 - - + -
379E SER* 5.5 2.7 - - - -
380E PRO* 4.3 16.2 - - + -
381E SER 2.8 14.2 + - - +
383E CYS* 1.3 101.2 - - - +
385E VAL* 1.3 60.6 + - - +
387E PRO* 3.0 14.8 - - + +
388E SER* 2.4 41.1 + - - +
433E PHE* 5.6 1.1 - + - -
436E TYR* 3.8 25.8 - + - -
540E VAL* 6.0 0.4 - - + -
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Residues in contact with VAL 385 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E SER* 3.8 14.1 - - - +
374E LEU* 4.0 17.3 - - + -
381E SER 4.4 0.7 - - - +
382E LEU 2.9 24.0 + - - +
383E CYS 3.3 0.8 - - - -
384E PHE* 1.3 78.3 - - - +
386E VAL* 1.3 66.1 + - - +
388E SER* 3.2 6.9 - - - -
389E ILE* 3.1 21.5 + - + +
421E TRP* 3.9 27.4 - - + +
425E LEU* 4.2 10.5 - - + -
429E HIS* 3.4 30.5 - - + +
566E ALA* 4.0 12.3 - - + -
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Residues in contact with VAL 386 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382E LEU 4.8 0.2 + - - -
383E CYS 4.8 0.6 + - - +
385E VAL* 1.3 76.2 - - - +
387E PRO* 1.3 64.7 - - + +
389E ILE* 2.8 34.3 + - - +
390E LEU* 3.2 21.6 + - + +
425E LEU* 4.5 7.0 - - + -
429E HIS* 3.7 24.9 - - + +
430E TYR* 4.2 11.2 - - + -
433E PHE* 3.7 24.0 - - + -
442E MET* 3.7 25.8 - - + -
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Residues in contact with PRO 387 (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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383E CYS 3.7 0.7 - - - +
384E PHE* 3.0 32.8 - - + +
386E VAL* 1.3 88.4 - - + +
388E SER* 1.3 56.5 + - - +
390E LEU* 3.1 19.5 + - + +
391E LYS* 2.8 30.6 + - - +
433E PHE* 3.5 36.3 - - + -
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Residues in contact with SER 388 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370E ILE* 3.4 25.1 - - - +
373E GLU* 4.7 5.0 + - - -
374E LEU* 3.4 21.0 - - - +
384E PHE* 2.4 28.7 + - - +
385E VAL* 3.2 6.7 - - - -
387E PRO* 1.3 78.0 - - - +
389E ILE* 1.3 62.2 + - - +
391E LYS* 3.2 12.6 + - - +
392E VAL* 3.0 25.2 + - - +
421E TRP* 4.4 6.5 - - - -
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Residues in contact with ILE 389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385E VAL* 3.1 15.5 + - + +
386E VAL* 2.8 12.5 + - - +
388E SER* 1.3 75.0 - - - +
390E LEU* 1.3 60.8 + - + +
392E VAL* 2.6 37.7 + - - +
393E LYS* 3.2 26.9 + - - +
417E VAL* 3.7 15.5 - - + -
421E TRP* 3.5 44.4 - - + -
422E GLU* 3.9 19.1 - - + +
425E LEU* 3.9 24.7 - - + -
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Residues in contact with LEU 390 (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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386E VAL* 3.4 30.5 - - + +
387E PRO* 3.1 18.1 + - + +
389E ILE* 1.3 78.6 - - + +
391E LYS* 1.3 57.7 + - - +
393E LYS* 2.8 37.5 + - - +
394E GLU* 3.0 28.6 + - - +
422E GLU* 5.8 0.4 - - - +
433E PHE* 5.3 5.2 - - + -
441E HIS* 6.3 2.7 - - + -
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Residues in contact with LYS 391 (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 GLY 4.8 2.0 + - - -
369E ARG* 4.6 13.1 - - - +
370E ILE* 4.4 26.4 - - + +
373E GLU* 3.4 27.0 + - - -
387E PRO 2.8 16.5 + - - +
388E SER* 3.5 11.9 - - - +
390E LEU* 1.3 72.6 - - - +
392E VAL* 1.3 61.7 + - - +
394E GLU* 3.5 13.8 + - + +
395E ILE* 3.1 33.0 + - + +
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Residues in contact with VAL 392 (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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270E LEU* 4.8 3.4 - - + -
273E VAL* 6.1 0.2 - - + -
367E PHE* 4.3 18.8 - - + -
370E ILE* 3.9 17.5 - - + -
388E SER 3.0 17.8 + - - +
389E ILE* 2.6 23.8 + - - +
391E LYS* 1.3 72.1 - - - +
393E LYS* 1.3 55.0 + - - +
395E ILE* 3.1 22.9 - - - +
396E CYS* 3.1 11.4 + - - -
413E ILE* 4.0 12.6 - - + -
417E VAL* 3.6 30.5 - - + -
421E TRP* 4.2 17.7 - - + -
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Residues in contact with LYS 393 (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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389E ILE* 3.3 27.4 - - - +
390E LEU* 2.8 21.0 + - - +
392E VAL* 1.3 72.7 - - - +
394E GLU* 1.3 52.3 + - + +
395E ILE 2.9 4.5 - - - -
396E CYS 2.6 5.5 + - - +
397E SER* 2.3 39.1 + - - -
414E ILE* 4.2 25.0 + - + +
417E VAL* 4.1 12.3 - - + +
418E ARG* 5.0 6.5 - - - +
422E GLU* 2.4 32.3 + - - -
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Residues in contact with GLU 394 (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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390E LEU* 3.0 37.4 - - - +
391E LYS* 3.5 15.8 + - + +
393E LYS* 1.3 72.3 - - - +
395E ILE* 1.3 58.0 + - - +
397E SER* 3.2 23.3 + - - +
410E LYS* 5.4 0.2 + - - -
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Residues in contact with ILE 395 (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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362E ASN 5.8 0.4 - - - +
363E ILE* 4.4 27.3 - - + +
366E GLY* 5.1 15.3 - - - +
367E PHE* 3.6 32.5 - - + -
370E ILE* 5.7 3.1 - - + -
391E LYS* 3.1 24.1 + - + +
392E VAL* 3.1 16.8 - - - +
394E GLU* 1.3 79.6 - - - +
396E CYS* 1.3 61.5 + - - +
410E LYS* 3.1 23.4 + - - -
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Residues in contact with CYS 396 (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 ILE* 5.7 1.3 - - - -
367E PHE* 4.6 0.9 - - - -
392E VAL* 3.1 16.8 + - - +
393E LYS 2.6 9.4 + - - +
395E ILE* 1.3 81.4 - - - +
397E SER* 1.3 64.4 + - - -
398E PRO* 3.3 3.1 - - - +
410E LYS* 3.4 41.9 - - - +
413E ILE* 3.4 43.3 - - - -
414E ILE* 3.4 24.0 - - + +
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Residues in contact with SER 397 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393E LYS* 2.3 25.7 + - - -
394E GLU* 3.2 24.1 + - - +
395E ILE 3.4 0.4 - - - -
396E CYS* 1.3 65.9 - - - +
398E PRO* 1.3 77.2 + - - +
399E ASP* 4.5 0.3 - - - +
410E LYS* 3.1 15.9 + - - -
414E ILE* 5.1 2.2 - - - -
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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