Contacts of the helix formed by residues 455 - 468 (chain B) in PDB entry 1B70
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 455 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A HIS* 3.7 28.9 - - + +
288A PRO* 4.1 20.0 - - + -
289A LYS* 4.7 14.4 - - + +
292A GLN* 5.9 1.3 - - - +
404B ILE* 3.6 9.0 - - - +
454B ARG* 1.3 92.3 - - + +
456B GLU* 1.3 65.8 + - - +
457B GLU* 3.2 13.7 - - + +
458B ASP* 2.9 18.4 + - - +
459B LEU* 3.4 17.7 + - - +
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Residues in contact with GLU 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B ILE* 3.7 11.1 - - + +
405B PRO* 3.2 26.4 - - + +
406B PHE* 3.5 11.8 - - + -
407B ARG* 2.7 54.1 + - - +
410B TYR* 3.4 30.2 - - + -
455B LEU* 1.3 74.6 - - - +
457B GLU* 1.3 67.6 + - - +
459B LEU* 2.9 26.3 + - - +
460B VAL* 3.0 7.8 + - - +
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Residues in contact with GLU 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A GLU* 4.0 26.0 - - + +
263A PRO* 4.9 0.2 - - - +
286A VAL 6.0 0.2 - - - +
287A HIS* 6.2 0.2 - - + -
288A PRO* 3.5 34.4 - - + +
407B ARG* 5.6 0.2 + - - -
410B TYR* 3.2 36.1 + - + +
414B LEU* 4.7 6.5 - - + -
455B LEU* 3.3 20.1 - - + +
456B GLU* 1.3 83.4 + - - +
458B ASP* 1.3 66.1 + - - +
460B VAL* 2.9 20.7 + - - +
461B GLU* 2.9 14.4 + - - +
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Residues in contact with ASP 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A GLU* 3.1 35.1 - - - +
287A HIS* 4.7 6.7 - - - -
351A MG 4.4 0.2 - - - -
452B ASP 3.2 21.9 - - - +
453B LEU* 3.9 12.6 - - + -
454B ARG* 3.1 13.0 + - - +
455B LEU* 2.9 38.4 + - - +
456B GLU 3.3 0.4 - - - -
457B GLU* 1.3 76.5 - - - +
459B LEU* 1.3 62.4 + - - +
461B GLU* 3.4 7.8 + - - +
462B GLU* 3.1 23.0 + - - +
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Residues in contact with LEU 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B ILE* 3.5 45.8 - - + -
406B PHE* 3.8 33.8 - - + -
428B LEU* 4.2 15.7 - - + +
433B CYS* 5.3 4.0 - - - -
444B VAL* 4.0 17.3 - - + -
453B LEU* 4.4 24.5 - - + -
455B LEU 3.4 6.8 + - - +
456B GLU* 2.9 13.9 + - - +
458B ASP* 1.3 78.5 - - - +
460B VAL* 1.3 62.1 + - - +
462B GLU* 3.2 20.3 - - + +
463B VAL* 3.5 11.3 + - - +
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Residues in contact with VAL 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A PRO* 4.6 2.2 - - + -
406B PHE* 3.9 14.4 - - + -
410B TYR* 4.7 12.8 - - + -
411B ALA* 3.9 30.3 - - + +
414B LEU* 4.3 13.7 - - + -
415B LEU* 3.9 33.9 - - + -
456B GLU 3.0 13.4 + - - +
457B GLU* 2.9 14.6 + - - +
459B LEU* 1.3 73.2 - - - +
461B GLU* 1.3 64.9 + - - +
462B GLU 2.8 6.6 + - - -
463B VAL* 3.0 16.0 + - + +
464B ALA* 3.1 9.9 + - - +
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Residues in contact with GLU 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A PRO* 5.2 3.4 - - - +
256A VAL 4.4 4.8 - - - +
257A TYR* 6.0 0.3 - - - -
262A GLU* 2.6 42.7 - - - +
263A PRO* 3.2 23.1 - - + +
264A GLY* 3.0 30.7 + - - +
351A MG 2.7 7.8 - - - -
163B ASN* 4.5 6.9 + - - -
457B GLU 2.9 6.9 + - - +
458B ASP 3.5 2.7 - - - +
460B VAL* 1.3 76.1 - - - +
462B GLU* 1.3 68.2 + - - +
464B ALA* 3.3 3.2 - - - +
465B ARG* 3.0 34.5 + - - +
469B TYR* 3.3 10.9 + - - +
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Residues in contact with GLU 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A MG 3.0 25.3 - - - -
427B ILE* 4.8 0.7 - - - -
428B LEU* 4.5 7.4 - - + -
431B LEU* 3.8 18.7 - - + +
450B ARG* 3.0 23.8 + - - -
453B LEU* 3.8 14.6 - - + -
458B ASP 3.1 13.9 - - - +
459B LEU* 3.2 13.7 - - + +
460B VAL 2.8 1.2 + - - -
461B GLU* 1.3 79.8 - - - +
463B VAL* 1.3 66.8 + - - +
464B ALA 3.0 1.1 - - - -
465B ARG* 2.4 37.6 + - - +
466B ILE* 3.0 27.2 + - - +
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Residues in contact with VAL 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B PHE* 4.4 7.9 - - + -
411B ALA* 5.5 2.7 - - + -
415B LEU* 5.2 3.1 - - + -
419B TYR* 4.0 19.7 - - + -
424B GLN* 4.0 39.3 - - + +
427B ILE* 4.2 15.2 - - + +
428B LEU* 4.2 17.5 - - + -
459B LEU 3.5 11.9 + - - +
460B VAL* 3.0 7.5 + - + +
462B GLU* 1.3 76.2 - - - +
464B ALA* 1.3 52.8 + - - +
466B ILE* 3.4 0.9 + - - +
467B GLN* 2.7 57.0 + - + +
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Residues in contact with ALA 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A PRO* 4.9 1.3 - - + -
415B LEU* 4.1 29.5 - - + +
419B TYR* 5.0 2.7 - - - -
460B VAL 3.1 11.0 + - - +
461B GLU* 3.3 13.9 - - - +
463B VAL* 1.3 76.9 - - - +
465B ARG* 1.3 53.3 + - - +
467B GLN* 3.1 4.6 + - - +
468B GLY* 2.6 39.3 + - - +
469B TYR* 3.7 19.7 - - + -
472B ILE* 5.0 4.5 - - + -
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Residues in contact with ARG 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A PRO* 4.0 21.8 - - + -
27B GLY 3.9 16.1 - - - +
28B LEU* 3.2 36.9 + - + +
30B PHE* 4.3 0.2 - - - -
164B ARG* 2.8 19.5 - - - +
176B ASP* 2.2 35.3 + - - -
180B LEU* 4.8 2.4 - - - +
431B LEU* 4.6 7.7 - - - +
450B ARG* 3.7 10.9 - - - +
461B GLU* 3.0 21.7 + - - +
462B GLU* 2.4 60.9 + - - +
464B ALA* 1.3 78.0 - - - +
466B ILE* 1.3 66.0 + - + +
468B GLY* 3.4 10.7 + - - -
469B TYR* 3.6 12.3 - - + +
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Residues in contact with ILE 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU* 3.8 24.2 - - + -
176B ASP* 4.3 0.4 - - - +
179B ALA* 3.4 42.6 - - + +
180B LEU* 3.8 21.4 - - + +
427B ILE* 3.5 41.1 - - + -
431B LEU* 4.3 12.3 - - + -
462B GLU 3.0 19.7 + - - +
463B VAL 3.8 2.7 - - - +
465B ARG* 1.3 80.6 - - + +
467B GLN* 1.3 64.5 + - - +
468B GLY* 4.6 0.2 - - - -
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Residues in contact with GLN 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B TYR* 3.2 51.1 - - + +
423B GLU* 2.9 37.5 + - - +
424B GLN 5.7 0.2 - - - +
427B ILE* 3.7 19.1 - - + +
463B VAL* 2.7 32.2 + - + +
464B ALA 3.7 1.1 - - - +
466B ILE* 1.3 76.2 - - - +
468B GLY* 1.3 59.8 + - - +
470B GLU* 4.1 2.3 - - - +
471B THR* 3.1 21.4 - - + +
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Residues in contact with GLY 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B GLY 5.9 0.4 - - - -
419B TYR* 4.2 1.9 + - - -
464B ALA 2.6 17.1 + - - +
465B ARG 3.7 9.0 - - - -
466B ILE 3.2 2.6 - - - -
467B GLN* 1.3 74.4 - - - +
469B TYR* 1.3 65.3 + - - -
470B GLU* 3.0 17.9 - - - -
471B THR* 2.7 25.6 + - - -
472B ILE* 4.0 1.2 + - - +
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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