Contacts of the helix formed by residues 457 - 468 (chain B) in PDB entry 5M64
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 ILE 457 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158B CYS* 3.7 31.2 + - + +
161B LEU* 5.5 3.8 - - + -
413B LEU* 4.8 13.0 - - + -
416B LYS 4.8 6.1 - - - +
417B ILE* 4.7 17.5 - - + -
419B GLU* 4.3 19.5 - - - +
420B TYR* 5.5 7.9 - - + -
454B ASN 5.2 2.2 - - - +
455B GLU* 3.3 27.2 + - - +
456B ASN* 1.3 72.8 - - - +
458B GLY* 1.3 63.6 + - - +
459B SER 3.2 1.8 - - - -
460B LYS* 2.8 24.3 + - + +
461B MET* 2.9 37.0 + - + +
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Residues in contact with GLY 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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134B ARG* 4.5 10.3 - - - -
158B CYS 4.1 5.3 + - - -
160B GLY 3.2 27.2 + - - +
161B LEU* 6.1 0.2 - - - -
162B PRO* 5.0 3.7 - - - +
456B ASN* 3.5 5.5 + - - -
457B ILE* 1.3 79.4 - - - +
459B SER* 1.3 56.9 + - - +
461B MET* 3.5 6.2 + - - +
462B GLN* 2.8 31.8 + - - +
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Residues in contact with SER 459 (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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134B ARG* 4.9 1.6 - - - +
456B ASN* 3.3 33.1 + - - -
457B ILE 3.2 0.4 - - - -
458B GLY* 1.3 75.7 - - - +
460B LYS* 1.3 58.5 + - - +
462B GLN* 3.7 14.6 + - - +
463B TYR* 2.9 27.7 + - - +
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Residues in contact with LYS 460 (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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416B LYS* 3.6 28.7 - - - +
419B GLU* 5.0 14.5 + - - +
454B ASN* 5.8 3.4 - - - +
456B ASN 4.4 7.3 + - - +
457B ILE* 2.8 20.2 + - + +
459B SER* 1.3 75.8 - - - +
461B MET* 1.3 68.7 + - + +
463B TYR* 3.1 14.6 + - + +
464B PHE* 3.0 21.5 + - - +
471B VAL* 3.9 21.9 - - + +
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Residues in contact with MET 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU* 4.3 9.4 - - + -
162B PRO* 4.4 9.9 - - + -
409B TYR* 3.9 25.4 - - + +
412B ILE* 4.2 12.8 - - + +
413B LEU* 3.6 27.1 - - + -
416B LYS* 3.7 42.8 - - + -
457B ILE* 2.9 32.9 + - + +
458B GLY* 3.9 4.0 - - - +
460B LYS* 1.3 84.2 - - + +
462B GLN* 1.3 62.7 + - - +
464B PHE* 3.2 8.5 + - + +
465B LEU* 3.1 31.7 + - - +
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Residues in contact with GLN 462 (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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132B SER* 4.5 14.2 + - - +
134B ARG* 5.6 4.2 + - - -
162B PRO* 5.2 5.7 - - + +
196B VAL* 3.7 24.8 - - + +
197B ASN* 3.0 31.4 + - - +
201B LYS* 4.6 1.0 + - - -
458B GLY 2.8 17.9 + - - +
459B SER* 3.7 14.5 + - - +
460B LYS 3.3 0.2 - - - -
461B MET* 1.3 76.0 - - - +
463B TYR* 1.3 58.2 + - - +
465B LEU* 4.2 4.5 - - - +
466B SER* 3.0 31.6 + - - -
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Residues in contact with TYR 463 (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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459B SER 2.9 19.0 + - - +
460B LYS* 3.1 13.9 + - + +
462B GLN* 1.3 75.9 - - - +
464B PHE* 1.3 67.4 + - - +
466B SER* 4.3 5.2 - - - -
467B THR* 3.0 47.5 + - - +
469B ASN* 4.6 13.3 + - - -
471B VAL* 4.7 25.4 - - + -
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Residues in contact with PHE 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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203B ILE* 4.5 18.2 - - + -
408B LEU* 5.4 2.2 - - + -
409B TYR* 4.8 10.1 - + - -
412B ILE* 3.5 33.9 - - + -
416B LYS* 6.2 1.8 - - + -
460B LYS 3.0 12.3 + - - +
461B MET* 3.2 13.7 + - + +
463B TYR* 1.3 80.5 - - - +
465B LEU* 1.3 86.8 + - + +
468B GLY* 2.9 47.0 + - - -
469B ASN 3.2 26.2 - - - +
470B LEU* 3.5 28.3 - - + -
471B VAL* 5.6 6.3 - - + +
484B TYR* 4.1 11.0 - + + -
485B THR* 4.9 0.4 - - - +
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Residues in contact with LEU 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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162B PRO* 5.2 4.9 - - + -
194B PHE* 3.9 28.7 - - + -
196B VAL* 4.8 5.6 - - + -
201B LYS* 3.1 39.8 - - + +
202B LEU 5.9 0.2 - - - -
203B ILE* 4.6 16.6 - - + +
409B TYR* 3.8 26.2 - - + +
461B MET 3.1 28.6 + - - +
462B GLN* 4.2 2.9 - - - +
464B PHE* 1.3 101.1 - - + +
466B SER* 1.3 63.1 + - - +
485B THR* 3.5 27.3 - - - +
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Residues in contact with SER 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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196B VAL* 5.2 0.7 - - - -
197B ASN* 4.6 15.7 + - - -
201B LYS* 3.3 12.8 - - - +
462B GLN* 3.0 21.9 + - - -
463B TYR* 3.8 7.6 - - - -
464B PHE 3.3 0.2 - - - -
465B LEU* 1.3 80.3 - - - +
467B THR* 1.3 66.9 + - - +
485B THR* 5.0 1.4 - - - +
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Residues in contact with THR 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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463B TYR* 3.0 41.3 + - - +
466B SER* 1.3 81.3 + - - +
468B GLY* 1.3 58.1 + - - +
469B ASN* 3.3 31.8 + - - +
485B THR* 4.8 2.1 - - - +
4R G 4.3 20.9 + - - +
5R U 4.2 27.3 + - - +
6R A 5.7 0.3 - - - +
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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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464B PHE* 2.9 21.1 + - - -
466B SER 3.6 0.6 - - - -
467B THR* 1.3 78.2 - - - +
469B ASN* 1.3 63.5 + - - +
483B GLY 5.4 2.0 - - - -
484B TYR* 3.3 32.2 - - - +
485B THR* 3.7 22.2 - - - -
5R U 5.2 5.2 - - - -
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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