Contacts of the helix formed by residues 366 - 379 (chain E) in PDB entry 6F0X
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 VAL 366 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349E GLN* 4.3 18.7 - - + +
350E LEU* 5.5 0.3 - - - +
351E LEU* 4.1 31.9 - - + -
364E ASN* 3.3 8.3 + - - +
365E ASN* 1.3 80.6 - - + +
367E SER* 1.3 63.5 + - - +
368E LYS 3.4 0.9 + - - -
369E LEU* 4.0 11.4 + - - +
370E SER* 4.1 10.0 + - - +
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Residues in contact with SER 367 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351E LEU* 5.4 1.3 - - - -
356E LEU* 5.0 1.3 - - - -
359E ILE* 3.6 21.3 - - - -
362E ILE 2.7 13.4 + - - -
363E GLU* 3.1 4.6 - - - -
364E ASN* 2.3 47.3 + - - -
366E VAL* 1.3 78.8 - - - +
368E LYS* 1.3 65.6 + - - +
369E LEU 3.4 0.2 - - - -
370E SER* 3.3 6.7 + - - -
371E LEU* 2.9 31.3 + - - +
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Residues in contact with LYS 368 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363E GLU* 2.9 26.2 - - - +
364E ASN 3.1 10.1 + - - +
365E ASN* 4.3 6.5 - - - +
366E VAL 3.4 1.8 - - - -
367E SER* 1.3 77.0 - - - +
369E LEU* 1.3 71.7 + - + +
371E LEU* 3.9 0.7 - - - +
372E LEU* 2.9 35.8 + - + +
408E GLU* 6.4 1.1 - - + -
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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
----------------------------------------------------------
348E GLN* 4.7 17.3 - - + +
349E GLN 5.7 1.8 - - - +
350E LEU* 4.1 18.4 - - + -
365E ASN 5.4 3.8 - - - +
366E VAL 4.0 7.3 + - - +
367E SER 3.4 0.4 - - - -
368E LYS* 1.3 85.0 - - + +
370E SER* 1.3 58.4 + - - +
372E LEU* 3.4 4.7 + - + +
373E LEU* 2.9 29.7 + - - +
407E ILE* 4.2 15.5 - - + -
408E GLU* 3.4 48.9 - - + +
411E LEU* 3.6 30.3 - - + +
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Residues in contact with SER 370 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328E PHE* 3.9 3.4 - - - -
350E LEU* 3.3 18.3 - - - +
351E LEU* 3.3 24.2 + - - +
356E LEU* 3.5 38.4 - - - +
366E VAL* 4.1 8.8 + - - +
367E SER* 3.3 4.4 + - - -
368E LYS 3.3 0.4 - - - -
369E LEU* 1.3 78.5 - - - +
371E LEU* 1.3 58.8 + - - +
373E LEU* 3.1 9.7 + - - +
374E ASN* 2.9 26.0 + - - +
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Residues in contact with LEU 371 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356E LEU* 4.3 18.4 - - + -
359E ILE* 4.5 4.0 - - + -
361E PHE* 4.0 37.5 - - + +
362E ILE 4.3 3.8 - - - +
363E GLU* 3.2 33.4 - - + +
367E SER* 2.9 34.0 + - - +
368E LYS 4.1 0.2 - - - +
370E SER* 1.3 72.4 - - - +
372E LEU* 1.3 66.6 + - - +
374E ASN* 3.1 13.6 + - - +
375E ASP* 3.0 28.6 + - - +
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Residues in contact with LEU 372 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368E LYS* 2.9 29.4 + - + +
369E LEU* 3.6 5.6 - - + +
371E LEU* 1.3 77.5 - - - +
373E LEU* 1.3 56.5 + - - +
375E ASP* 3.2 12.2 + - + +
376E ILE* 2.8 41.5 + - + +
411E LEU* 3.8 33.7 - - + -
412E GLN* 5.1 7.0 - - + +
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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
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328E PHE* 3.5 22.9 - - + -
331E TYR* 3.4 45.8 - - + -
332E LEU 4.4 2.9 - - - +
335E LEU* 3.6 26.7 - - + -
350E LEU* 4.3 12.8 - - + -
369E LEU 2.9 14.1 + - - +
370E SER* 3.1 10.3 + - - +
372E LEU* 1.3 77.1 - - - +
374E ASN* 1.3 57.5 + - - +
376E ILE* 3.1 22.7 + - + +
377E SER* 2.9 28.1 + - - -
411E LEU* 4.4 8.5 - - + +
414E LEU* 5.5 3.8 - - + -
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Residues in contact with ASN 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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324E ALA* 5.5 4.2 - - - +
328E PHE* 4.3 14.0 - - + +
353E LEU* 5.8 6.2 - - - +
356E LEU* 5.0 6.7 - - + +
361E PHE* 4.6 14.6 - - - -
370E SER 2.9 13.5 + - - +
371E LEU* 3.1 22.3 + - + +
373E LEU* 1.3 76.3 - - - +
375E ASP* 1.3 58.2 + - - +
377E SER* 3.1 8.6 + - - -
378E ARG* 2.9 61.9 + - - +
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Residues in contact with ASP 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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371E LEU* 3.0 17.5 + - - +
372E LEU* 3.7 14.8 - - + +
374E ASN* 1.3 78.2 - - - +
376E ILE* 1.3 57.2 + - - +
378E ARG* 3.3 26.8 + - - +
379E LYS* 2.9 39.4 + - + +
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Residues in contact with ILE 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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331E TYR* 3.5 27.1 - - + +
372E LEU* 2.8 42.1 + - + +
373E LEU* 3.2 27.6 - - + +
375E ASP* 1.3 75.0 - - - +
377E SER* 1.3 63.1 + - - +
379E LYS* 3.3 3.6 + - - +
380E SER* 2.1 34.4 + - - +
411E LEU* 4.1 26.5 - - + +
414E LEU* 5.3 9.9 - - + -
415E SER* 5.0 16.8 - - - +
418E VAL* 5.4 7.6 - - + -
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Residues in contact with SER 377 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324E ALA* 4.3 13.4 - - - +
327E ILE* 3.3 22.4 - - - +
328E PHE* 3.4 16.6 + - - +
331E TYR* 3.0 31.6 - - - -
373E LEU 2.9 9.9 + - - -
374E ASN* 3.4 11.7 - - - -
376E ILE* 1.3 74.8 - - - +
378E ARG* 1.3 57.7 + - - +
380E SER* 2.7 31.1 + - - -
381E GLU* 3.5 2.3 + - - -
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Residues in contact with ARG 378 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324E ALA* 5.5 9.4 - - + -
361E PHE* 5.1 11.3 - - - -
374E ASN* 2.9 48.7 + - - +
375E ASP* 3.3 30.0 + - - +
376E ILE 3.2 0.2 - - - -
377E SER* 1.3 76.7 - - - +
379E LYS* 1.3 62.1 + - + +
380E SER 3.1 4.3 + - - -
381E GLU* 3.5 21.1 + - - +
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Residues in contact with LYS 379 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375E ASP* 2.9 21.9 + - + +
376E ILE* 3.3 4.7 - - - +
378E ARG* 1.3 77.6 - - + +
380E SER* 1.3 56.1 + - - +
381E GLU* 3.5 3.4 - - - -
418E VAL* 4.6 1.4 - - - +
419E ASP* 5.5 2.8 - - - +
422E PHE* 3.0 26.9 - - - -
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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