Contacts of the helix formed by residues 457 - 470 (chain B) in PDB entry 5EMQ
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 CYS 457 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440B CYS* 3.4 7.2 - - + +
443B CYS* 3.9 4.3 - - - -
445B ASP* 4.4 9.9 - - + +
446B GLU 3.3 24.9 - - - +
447B ALA* 3.9 0.2 - - - +
448B SER* 3.9 3.8 - - - +
451B HIS* 4.6 0.2 - - - -
456B THR* 1.3 82.2 + - - +
458B GLY* 1.3 63.5 + - - +
459B SER* 3.1 26.5 - - - +
460B CYS 3.3 6.6 + - - -
461B LYS* 3.1 18.4 + - - +
489B ARG* 4.1 2.7 - - - -
601B ZN 2.4 35.2 - - - -
14C T 6.1 0.2 - - - +
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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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448B SER* 3.5 18.3 + - - -
457B CYS* 1.3 73.0 - - - +
459B SER* 1.3 61.6 + - - +
461B LYS* 3.2 13.4 + - - +
462B VAL* 3.1 25.1 + - - +
14C T 3.7 17.1 + - - +
15C T 6.3 1.8 - - - -
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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
----------------------------------------------------------
457B CYS* 3.1 18.5 - - - +
458B GLY* 1.3 76.5 - - - +
460B CYS* 1.3 56.6 + - - +
462B VAL* 3.2 10.9 - - - +
463B PHE* 2.9 28.1 + - - +
489B ARG* 3.1 21.2 + - - -
496B ARG* 3.9 3.6 + - - -
13C G 3.4 49.1 + - - -
14C T 4.0 6.8 + - - -
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Residues in contact with CYS 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B CYS* 4.1 6.1 - - - -
442B VAL* 3.8 29.4 - - + -
443B CYS* 3.9 4.0 - - - -
456B THR* 4.2 6.7 - - + -
457B CYS* 3.3 6.3 + - - +
458B GLY 3.3 0.2 - - - -
459B SER* 1.3 78.7 + - - +
461B LYS* 1.3 61.2 + - - +
463B PHE* 3.7 3.7 - - - +
464B PHE* 2.9 31.9 + - - +
496B ARG* 3.1 27.6 - - - +
500B CYS* 4.6 2.9 - - - -
505B MET* 4.5 2.5 - - + +
601B ZN 2.3 35.4 - - - -
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Residues in contact with LYS 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B HIS* 3.4 37.7 - - + +
452B TYR* 3.5 30.5 + - + -
456B THR* 4.1 4.6 + - - -
457B CYS 3.1 13.4 + - - +
458B GLY* 3.3 13.7 - - - +
460B CYS* 1.3 79.5 - - - +
462B VAL* 1.3 80.5 + - - +
464B PHE* 3.4 1.7 + - - +
465B LYS* 3.3 14.9 + - - +
505B MET* 5.3 1.3 - - - -
15C T 5.1 1.6 + - - -
4D A 3.8 28.7 - - - +
5D G 3.0 40.7 + - - -
6D A 4.6 0.8 - - - +
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Residues in contact with VAL 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B GLY 3.1 11.4 + - - +
459B SER* 3.2 15.5 - - - +
461B LYS* 1.3 99.1 - - - +
463B PHE* 1.3 61.5 + - - +
465B LYS* 3.5 6.0 + - - +
466B ARG* 2.8 49.7 + - - +
12C T 5.9 0.7 - - + -
13C G 4.0 18.2 - - + +
14C T 3.6 32.1 - - + +
15C T 5.2 0.2 - - - +
5D G 5.6 0.7 - - + +
6D A 4.4 9.2 - - - +
7D A 5.0 2.2 - - - +
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Residues in contact with PHE 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 19.3 + - - +
460B CYS* 3.7 4.0 - - - +
461B LYS 3.3 0.2 - - - -
462B VAL* 1.3 78.3 - - + +
464B PHE* 1.3 55.0 + - - +
466B ARG* 3.2 10.0 + - + +
467B ALA* 2.7 37.5 + - + +
474B TYR* 4.0 20.9 - + - -
489B ARG 6.0 0.2 - - - -
493B PRO* 3.6 28.7 - - + -
496B ARG* 3.3 52.0 - - + +
497B TYR* 3.7 18.4 - + + -
500B CYS* 4.2 6.7 - - - -
12C T 3.7 33.4 - - - -
13C G 5.1 0.2 - - - +
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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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452B TYR* 3.9 18.2 - + + -
460B CYS 2.9 18.3 + - - +
461B LYS 3.8 2.7 - - - +
463B PHE* 1.3 83.1 - - - +
465B LYS* 1.3 65.7 + - - +
467B ALA* 2.8 15.8 + - - +
468B VAL* 2.9 39.8 + - + +
497B TYR* 4.1 12.3 - + - -
500B CYS* 3.6 22.9 - - + -
501B LEU* 4.1 12.8 - - + -
505B MET* 3.4 45.3 - - + -
506B ASN* 3.7 16.2 - - - -
507B LEU* 3.5 26.5 - - + -
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Residues in contact with LYS 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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452B TYR* 3.5 25.6 - - + +
461B LYS 3.3 12.9 + - - +
462B VAL* 3.8 6.7 - - - +
464B PHE* 1.3 83.3 - - - +
466B ARG* 1.3 66.8 + - - +
468B VAL* 3.4 6.1 - - - +
469B GLU* 3.0 60.3 + - + +
507B LEU* 4.2 12.3 - - + +
5D G 3.3 47.7 + - + +
6D A 4.9 5.6 - - - +
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Residues in contact with ARG 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 VAL* 2.8 36.7 + - - +
463B PHE* 3.4 9.0 - - + +
465B LYS* 1.3 81.3 - - - +
467B ALA* 1.3 56.9 + - - +
469B GLU* 3.9 2.5 - - - +
470B GLY* 2.9 30.1 + - - -
474B TYR* 5.3 1.8 - - - +
12C T 3.1 40.8 + - + +
13C G 2.7 46.2 + - - -
7D A 4.0 12.1 + - - +
8D C 5.0 2.4 - - - +
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Residues in contact with ALA 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 PHE* 2.7 22.7 + - + +
464B PHE 2.8 9.9 + - - +
466B ARG* 1.3 72.3 - - - +
468B VAL* 1.3 60.1 + - - +
469B GLU 3.1 1.3 + - - -
470B GLY* 3.5 8.1 + - - +
472B HIS* 3.1 32.1 + - - +
474B TYR* 3.9 23.1 + - + +
497B TYR* 3.5 27.8 - - + -
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Residues in contact with VAL 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B PHE* 2.9 55.2 + - + +
465B LYS* 3.4 13.0 - - - +
467B ALA* 1.3 71.2 - - - +
469B GLU* 1.3 63.7 + - + +
472B HIS* 5.3 0.2 - - - -
497B TYR* 3.7 20.2 - - + +
501B LEU* 5.6 0.2 - - + -
507B LEU* 3.6 38.7 - - + +
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Residues in contact with GLU 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 LYS* 3.0 54.1 + - + +
466B ARG* 4.0 2.7 - - - +
467B ALA 3.1 0.2 - - - -
468B VAL* 1.3 85.2 - - + +
470B GLY* 1.3 67.5 + - - +
507B LEU* 3.4 18.3 - - - +
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Residues in contact with GLY 470 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B ARG 2.9 17.7 + - - -
467B ALA* 3.5 7.2 + - - +
469B GLU* 1.3 85.8 - - - +
471B GLN* 1.3 69.1 + - - +
472B HIS* 3.6 4.2 - - - -
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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