Contacts of the helix formed by residues 461 - 476 (chain B) in PDB entry 2ETM
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 SER 461 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458B ASN* 3.0 6.4 + - - +
460B THR* 1.3 78.6 - - - +
462B ASP* 1.3 53.1 + - - +
463B SER* 3.2 20.3 + - - -
464B VAL* 2.9 25.2 + - - +
465B ARG* 2.7 34.6 + - - +
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Residues in contact with ASP 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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460B THR 3.7 5.5 + - - +
461B SER* 1.3 71.3 + - - +
463B SER* 1.3 62.6 + - - +
465B ARG* 2.9 39.7 + - - +
466B GLU* 3.0 24.6 + - - +
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Residues in contact with SER 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B SER* 3.2 11.9 + - - -
462B ASP* 1.3 79.1 - - - +
464B VAL* 1.3 66.7 + - - +
466B GLU* 3.3 7.0 + - - +
467B LYS* 2.6 48.4 + - - +
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Residues in contact with VAL 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B PHE* 3.9 25.6 - - + -
456B CYS* 4.1 5.6 - - - -
458B ASN* 3.7 35.7 - - + +
461B SER* 2.9 30.4 + - - +
463B SER* 1.3 83.2 + - - +
465B ARG* 1.3 66.9 + - - +
466B GLU 3.1 0.2 + - - -
467B LYS* 3.2 10.5 + - - +
468B PHE* 3.1 20.8 + - - +
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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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459B CYS* 3.7 30.4 + - - +
460B THR 4.4 4.0 + - - -
461B SER 2.7 13.6 + - - +
462B ASP* 2.9 41.1 + - - +
464B VAL* 1.3 73.2 - - - +
466B GLU* 1.3 58.3 + - - +
468B PHE* 3.5 1.9 + - - +
469B LEU* 3.1 48.5 + - + +
491B THR* 4.6 9.5 + - - -
493B ASN* 4.7 4.5 + - - +
495B VAL* 4.0 24.9 - - + -
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Residues in contact with GLU 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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462B ASP 3.0 17.6 + - - +
463B SER* 3.7 7.5 - - - +
464B VAL 3.1 0.2 - - - -
465B ARG* 1.3 81.1 - - - +
467B LYS* 1.3 58.8 + - + +
469B LEU* 3.7 4.8 + - - +
470B GLN* 3.1 24.9 + - - +
473B LEU* 5.9 0.9 - - - +
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Residues in contact with LYS 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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433B PHE* 4.0 21.8 - - + -
463B SER* 2.6 55.0 + - - +
464B VAL* 3.4 10.3 - - - +
466B GLU* 1.3 75.8 - - + +
468B PHE* 1.3 63.1 + - - +
470B GLN* 3.1 38.5 + - - +
471B GLU* 4.3 0.9 + - - +
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Residues in contact with PHE 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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433B PHE* 3.7 38.8 - + + -
454B LYS* 3.6 36.8 - - + -
455B THR 3.9 9.9 - - - -
456B CYS* 3.8 23.8 - - + -
459B CYS* 3.9 2.2 - - - -
464B VAL 3.1 14.8 + - - +
465B ARG 3.7 2.9 - - - +
466B GLU 3.2 0.2 - - - -
467B LYS* 1.3 75.8 - - - +
469B LEU* 1.3 72.5 + - + +
470B GLN 3.1 5.4 + - - -
471B GLU* 3.4 13.6 + - - +
495B VAL* 3.5 32.3 - - + -
497B ILE* 3.2 44.5 - - + +
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Residues in contact with LEU 469 (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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465B ARG* 3.1 40.8 + - + +
466B GLU* 4.2 4.9 - - - +
468B PHE* 1.3 85.4 - - + +
470B GLN* 1.3 63.5 + - - +
471B GLU 3.1 2.9 - - - -
472B ALA* 3.0 15.8 + - + +
473B LEU* 3.2 21.7 + - + +
489B VAL* 4.8 14.4 - - + -
491B THR* 4.3 20.6 - - + -
495B VAL* 3.5 26.2 - - + -
497B ILE* 4.1 12.6 - - + -
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Residues in contact with GLN 470 (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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433B PHE* 6.2 0.2 - - - -
466B GLU 3.1 16.2 + - - +
467B LYS* 3.1 32.7 + - - +
469B LEU* 1.3 77.3 - - - +
471B GLU* 1.3 60.7 + - - +
473B LEU* 3.4 12.4 + - - +
474B THR* 3.1 32.1 + - - +
565B PHE 4.3 2.2 + - - -
566B GLY* 3.3 40.2 + - - -
567B LEU* 5.4 2.6 - - - +
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Residues in contact with GLU 471 (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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454B LYS* 2.7 41.2 + - - +
467B LYS 5.3 0.4 - - - +
468B PHE* 3.4 14.1 + - - +
469B LEU 3.1 0.6 - - - -
470B GLN* 1.3 82.7 - - - +
472B ALA* 1.3 56.9 + - - +
474B THR* 3.5 2.6 + - - -
475B MET* 3.0 34.7 + - - +
497B ILE* 4.2 6.0 - - + +
499B MET* 3.3 26.1 - - + +
564B ASP* 4.4 5.4 + - - +
565B PHE* 3.6 28.9 + - - +
566B GLY* 3.7 22.9 + - - +
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Residues in contact with ALA 472 (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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469B LEU* 3.0 12.5 + - + +
471B GLU* 1.3 76.9 - - - +
473B LEU* 1.3 60.2 + - + +
474B THR 3.1 1.6 - - - -
475B MET* 4.5 0.4 - - - -
476B ARG* 2.8 28.3 + - - +
486B LEU* 3.3 26.3 - - + +
489B VAL* 3.5 32.3 - - + -
497B ILE* 4.2 11.5 - - + +
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Residues in contact with LEU 473 (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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413B ARG* 3.6 32.5 - - + +
466B GLU 5.9 0.7 - - - +
469B LEU* 3.2 17.5 + - + +
470B GLN* 3.8 12.6 - - - +
472B ALA* 1.3 80.1 - - + +
474B THR* 1.3 62.1 + - - +
476B ARG* 3.6 26.1 - - - +
477B GLN* 3.8 14.3 + - - +
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Residues in contact with THR 474 (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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470B GLN* 3.1 22.7 + - - +
471B GLU 3.6 4.5 - - - -
472B ALA 3.1 0.4 - - - -
473B LEU* 1.3 78.1 - - - +
475B MET* 1.3 63.2 + - - +
476B ARG 3.4 0.3 + - - -
477B GLN* 3.1 25.2 + - - +
478B PHE* 3.4 17.2 - - + -
542B PHE* 3.7 30.3 - - + -
565B PHE* 3.9 25.8 + - + +
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Residues in contact with MET 475 (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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471B GLU* 3.0 28.5 + - - +
472B ALA 3.2 3.6 + - - +
474B THR* 1.3 71.5 - - - +
476B ARG* 1.3 62.0 - - - +
477B GLN 3.1 6.6 + - - -
478B PHE* 3.1 28.6 + - + +
483B ILE* 6.2 0.2 - - + -
484B VAL* 3.0 41.8 - - + +
485B LYS 4.1 6.3 - - - -
486B LEU* 4.0 20.1 + - + +
499B MET* 3.4 47.6 - - + +
563B GLY* 6.1 0.2 - - - -
565B PHE* 3.7 30.7 - - + -
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Residues in contact with ARG 476 (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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413B ARG* 4.0 25.5 - - - +
414B ASP* 2.5 44.1 + - - -
415B TYR* 3.4 35.5 + - + -
472B ALA 2.8 17.1 + - - +
473B LEU* 3.6 19.4 - - - +
474B THR 3.2 0.4 - - - -
475B MET* 1.3 75.7 - - - +
477B GLN* 1.3 61.3 + - + +
478B PHE 3.4 4.5 + - - +
486B LEU* 4.1 9.8 - - + +
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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