Contacts of the helix formed by residues 418 - 431 (chain E) in PDB entry 6N0M
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 GLU 418 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257E ASP* 5.0 9.0 - - - +
414E ASN 5.5 0.7 - - - -
416E LEU 3.3 7.9 + - - +
417E LEU* 1.3 76.9 - - - +
419E ARG* 1.3 66.7 + - - +
420E ASN* 3.9 8.2 - - - +
421E LEU* 3.4 21.3 + - + +
422E LYS* 3.1 18.2 + - - +
442E LEU 4.4 2.1 - - - +
443E PHE* 3.3 9.0 - - - -
444E TRP* 2.8 50.9 + - + +
445E ARG 4.8 0.3 + - - -
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Residues in contact with ARG 419 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B MET 5.1 11.1 + - - -
381B HIS* 6.3 0.6 - - - +
382B SER* 5.2 4.8 + - - -
295E LEU* 4.0 28.7 - - + +
418E GLU* 1.3 75.2 - - - +
420E ASN* 1.3 70.3 + - - +
422E LYS* 2.9 13.5 + - + +
423E VAL* 2.9 40.7 + - + +
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Residues in contact with ASN 420 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418E GLU* 3.5 7.7 - - - +
419E ARG* 1.3 89.8 + - - +
421E LEU* 1.3 57.2 + - - +
423E VAL* 3.6 11.2 - - + +
424E TYR* 3.0 27.7 + - - +
439E MET* 4.7 3.3 - - - +
442E LEU* 3.6 40.8 + - + +
443E PHE* 3.5 24.7 - - + +
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Residues in contact with LEU 421 (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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393E ILE* 4.6 2.0 - - + -
417E LEU* 4.0 33.4 - - + -
418E GLU* 3.4 18.4 + - + +
419E ARG 3.1 0.2 - - - -
420E ASN* 1.3 77.0 - - - +
422E LYS* 1.3 59.5 + - - +
424E TYR* 4.3 1.3 - - + -
425E ILE* 2.8 57.0 + - + +
443E PHE* 3.4 42.5 - - + +
444E TRP* 3.4 34.3 - - + +
455E VAL* 4.2 11.9 - - + -
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Residues in contact with LYS 422 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290E GLU* 2.7 18.5 + - - -
293E GLU* 3.1 28.6 + - - -
295E LEU* 3.9 9.0 - - + -
396E TYR* 3.7 30.7 + - + +
413E VAL* 4.7 1.6 - - + -
414E ASN* 2.7 35.4 + - - +
417E LEU* 3.4 36.1 + - + +
418E GLU 3.1 9.6 + - - +
419E ARG* 2.9 11.7 + - + +
421E LEU* 1.3 74.1 - - - +
423E VAL* 1.3 58.9 + - - +
425E ILE* 3.8 5.6 - - - +
426E LYS* 2.8 33.4 + - - +
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Residues in contact with VAL 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295E LEU* 4.0 32.8 - - + +
419E ARG* 2.9 37.8 + - - +
420E ASN* 3.6 13.0 - - + +
422E LYS* 1.3 78.2 - - - +
424E TYR* 1.3 51.7 + - - +
426E LYS* 3.7 1.6 - - - +
427E THR* 2.7 48.5 + - - +
439E MET* 4.0 21.5 - - + -
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Residues in contact with TYR 424 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213E GLY 2.5 25.2 + - - -
420E ASN 3.0 15.9 + - - +
421E LEU* 3.7 4.0 - - + +
423E VAL* 1.3 77.7 - - - +
425E ILE* 1.3 60.6 + - - +
427E THR* 3.3 0.7 + - - -
428E VAL* 2.8 50.1 + - + +
435E THR* 3.7 26.9 - - + -
439E MET* 4.1 14.6 - - + +
440E TYR* 3.5 33.1 - + + -
443E PHE* 3.2 42.8 - + + -
452E LYS 4.9 0.4 - - - -
455E VAL* 4.5 13.5 - - + -
456E ASN* 2.5 26.4 + - - -
459E LEU* 5.7 1.1 - - + -
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Residues in contact with ILE 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393E ILE* 3.9 31.2 - - + -
396E TYR* 3.7 19.1 - - + -
397E ILE* 3.5 32.8 - - + -
417E LEU* 4.8 6.3 - - + -
421E LEU* 2.8 51.0 + - + +
422E LYS* 3.8 4.0 - - - +
424E TYR* 1.3 74.1 - - + +
426E LYS* 1.3 56.1 + - - +
429E ALA* 2.7 37.4 + - - +
455E VAL* 4.1 13.9 - - + -
459E LEU* 3.6 11.6 - - + +
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Residues in contact with LYS 426 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290E GLU 5.3 1.4 + - - -
291E LYS 5.0 5.9 + - - -
292E SER 5.3 0.4 + - - -
293E GLU 2.9 28.3 + - - -
294E SER* 4.0 5.8 - - - +
295E LEU* 4.0 27.1 - - + +
323E TYR* 4.1 27.5 + - - -
324E GLU* 5.1 4.3 - - - -
332E GLN 5.9 1.4 + - - -
396E TYR* 3.9 19.6 + - + +
400E VAL* 4.3 19.2 - - + +
422E LYS 2.8 21.6 + - - +
423E VAL* 3.7 4.0 - - - +
425E ILE* 1.3 74.6 - - - +
427E THR* 1.3 55.8 + - - +
429E ALA* 3.2 5.0 + - - -
430E CYS* 2.7 52.1 + - + +
431E TYR* 6.1 1.6 - - + -
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Residues in contact with THR 427 (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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295E LEU 5.0 6.8 + - - -
423E VAL* 2.7 29.2 + - - +
424E TYR 3.7 1.8 - - - -
426E LYS* 1.3 76.2 - - - +
428E VAL* 1.3 55.0 + - - +
430E CYS* 5.2 0.2 - - - -
431E TYR* 2.7 60.8 + - + +
434E LYS* 3.9 10.8 - - + +
435E THR* 3.9 9.2 - - - +
439E MET* 3.5 37.9 - - + +
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Residues in contact with VAL 428 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209E SER* 2.9 51.8 + - - +
213E GLY* 3.7 11.0 - - - +
424E TYR* 2.8 37.8 + - + +
427E THR* 1.3 71.5 - - - +
429E ALA* 1.3 60.5 + - - +
432E PRO* 3.4 12.1 - - - +
435E THR* 3.5 33.4 - - + +
456E ASN* 3.4 15.5 - - - +
459E LEU* 3.7 16.6 - - + -
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Residues in contact with ALA 429 (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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209E SER* 4.2 1.6 - - - -
397E ILE* 4.6 10.5 - - + -
400E VAL* 5.4 2.0 - - + -
401E PHE* 3.6 22.5 - - + -
425E ILE 2.7 24.2 + - - +
426E LYS* 3.6 5.2 - - - +
428E VAL* 1.3 74.9 - - - +
430E CYS* 1.3 60.5 + - - +
432E PRO* 4.5 0.4 - - - +
459E LEU* 3.6 23.7 - - + +
463E ARG* 3.2 31.8 + - + +
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Residues in contact with CYS 430 (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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123E HIS* 4.4 7.3 - - - -
168E HIS* 4.5 6.9 + - - -
323E TYR* 3.9 34.1 - - + +
400E VAL* 3.6 31.6 - - - -
401E PHE* 4.1 7.0 - - - -
426E LYS* 2.7 30.1 + - + +
429E ALA* 1.3 75.9 - - - +
431E TYR* 1.3 83.7 + - + +
432E PRO* 3.3 9.6 - - - +
433E GLU* 4.1 2.9 - - - +
463E ARG* 5.3 1.4 + - - +
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Residues in contact with TYR 431 (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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168E HIS* 6.0 1.3 - + - -
322E GLY* 3.4 10.9 - - - -
323E TYR* 3.0 27.9 + + + -
324E GLU* 2.6 52.5 + - + +
326E PHE* 5.0 4.3 - + - -
426E LYS* 5.3 2.0 - - + -
427E THR* 2.7 28.0 + - + +
430E CYS* 1.3 86.1 - - + +
432E PRO* 1.3 60.3 - - - +
433E GLU* 3.2 16.8 - - - -
434E LYS* 2.8 44.0 + - + -
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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