Contacts of the helix formed by residues 473 - 484 (chain B) in PDB entry 5E6C
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 473 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472A ASN* 4.7 5.2 - - + +
457B CYS* 3.9 16.8 - - - -
458B ALA 4.8 0.7 - - - -
463B CYS* 3.8 17.0 - - + -
465B ILE* 3.9 5.2 - - + +
469B ARG 4.1 1.2 + - - -
470B ARG 3.9 5.9 + - - -
471B LYS 3.3 1.0 - - - -
472B ASN* 1.3 81.5 - - + +
474B PRO* 1.3 69.2 - - - +
475B ALA* 3.1 5.6 - - - -
476B CYS* 3.4 15.0 - - + -
477B ARG* 2.9 21.8 + - - +
601B ZN 2.3 37.9 - - - -
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Residues in contact with PRO 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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472A ASN* 4.4 14.8 - - - +
444B PHE* 3.4 23.9 - - + -
455B TYR* 3.4 37.2 - - + -
456B LEU 5.8 0.4 - - - +
470B ARG 5.2 0.7 - - - +
471B LYS 4.1 8.7 - - - +
472B ASN 3.7 7.0 - - - +
473B CYS* 1.3 86.0 - - - +
475B ALA* 1.3 53.3 + - - +
477B ARG* 4.1 1.8 - - + -
478B TYR* 2.7 37.9 + - - +
14C A 5.0 10.1 - - - +
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Residues in contact with ALA 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B TYR* 3.5 31.9 - - + +
456B LEU 3.9 1.6 - - - -
457B CYS* 3.7 29.8 - - + +
461B ASN* 5.0 4.7 - - - +
473B CYS* 3.1 5.7 - - - -
474B PRO* 1.3 79.8 - - - +
476B CYS* 1.3 59.4 + - - +
478B TYR* 3.8 2.7 - - - +
479B ARG* 3.0 29.0 + - - +
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Residues in contact with CYS 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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457B CYS* 3.8 1.3 - - - -
461B ASN* 3.5 26.9 - - - -
463B CYS* 3.3 28.7 - - + +
465B ILE* 4.1 8.5 - - + -
473B CYS* 3.2 7.9 + - - +
475B ALA* 1.3 79.7 - - - +
477B ARG* 1.3 57.9 + - - +
479B ARG* 3.3 18.5 + - - +
480B LYS* 2.9 32.7 + - - +
601B ZN 2.3 35.4 - - - -
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Residues in contact with ARG 477 (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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423B VAL* 4.1 14.4 - - + +
440B SER* 3.0 28.7 + - - -
441B CYS* 3.4 28.1 - - - +
444B PHE* 3.5 45.9 - - + +
465B ILE* 3.8 18.0 - - + +
470B ARG* 3.3 46.0 + - - +
471B LYS* 4.5 4.2 - - - +
473B CYS 2.9 17.1 + - - +
474B PRO* 3.6 3.6 - - + +
476B CYS* 1.3 77.6 - - - +
478B TYR* 1.3 62.2 + - - +
480B LYS* 3.3 5.5 + - - +
481B CYS* 3.0 25.7 + - - -
14C A 5.9 0.4 + - - -
15C C 3.2 18.8 + - - -
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Residues in contact with TYR 478 (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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444B PHE* 3.6 12.7 - + + -
445B PHE* 3.8 30.1 - + - -
448B ALA* 3.9 27.9 + - + -
449B VAL* 3.8 22.1 - - + +
453B HIS 4.7 12.8 - - - -
455B TYR* 4.3 16.8 - + + -
474B PRO 2.7 21.9 + - - +
475B ALA* 3.8 4.3 - - - +
477B ARG* 1.3 71.8 - - - +
479B ARG* 1.3 64.2 + - - +
481B CYS* 2.9 15.7 + - - +
482B LEU* 3.0 37.3 + - + +
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Residues in contact with ARG 479 (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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461B ASN* 3.2 36.7 + - - +
462B ASP* 3.9 7.5 - - - +
463B CYS 4.3 3.4 + - - +
475B ALA 3.0 16.1 + - - +
476B CYS* 3.7 31.8 + - - +
478B TYR* 1.3 77.7 - - - +
480B LYS* 1.3 71.5 + - - +
482B LEU* 3.4 10.4 + - + +
483B GLN* 3.0 64.3 + - + +
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Residues in contact with LYS 480 (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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422B LEU 4.3 10.3 + - - +
423B VAL* 2.8 41.6 + - + +
425B SER* 5.6 3.0 + - - -
463B CYS 5.4 2.0 - - - +
465B ILE* 3.8 34.2 + - + +
476B CYS 2.9 16.5 + - - +
477B ARG* 3.7 4.9 - - - +
478B TYR 3.2 0.2 - - - -
479B ARG* 1.3 90.2 - - - +
481B CYS* 1.3 66.5 + - - +
483B GLN* 4.0 8.8 - - - +
484B ALA* 3.1 25.3 + - - +
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Residues in contact with CYS 481 (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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423B VAL* 4.1 16.8 - - - -
441B CYS* 4.6 5.4 - - - -
444B PHE* 4.2 17.5 - - - -
445B PHE* 3.4 35.0 - - + -
477B ARG 3.0 20.4 + - - -
478B TYR* 2.9 9.5 + - - +
480B LYS* 1.3 77.0 - - - +
482B LEU* 1.3 60.6 + - - +
484B ALA* 3.3 7.6 + - - +
485B GLY 3.4 0.2 + - - -
486B MET* 3.1 47.9 + - - +
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Residues in contact with LEU 482 (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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445B PHE* 4.0 20.9 - - + -
449B VAL* 5.8 0.2 - - + -
478B TYR* 3.0 45.6 + - + +
479B ARG* 3.8 11.0 - - - +
481B CYS* 1.3 75.4 - - - +
483B GLN* 1.3 60.7 + - + +
485B GLY* 3.0 20.3 + - - -
486B MET 4.1 11.8 - - - +
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Residues in contact with GLN 483 (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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479B ARG* 3.0 61.5 + - + +
480B LYS* 4.0 8.5 - - - +
481B CYS 3.4 0.2 - - - -
482B LEU* 1.3 78.0 - - + +
484B ALA* 1.3 59.6 + - - +
485B GLY* 3.1 1.6 + - - -
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Residues in contact with ALA 484 (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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422B LEU* 4.9 14.7 - - + +
423B VAL* 4.8 7.2 - - + -
435B VAL* 3.2 33.8 - - + +
480B LYS 3.1 17.9 + - - +
481B CYS* 3.6 7.9 - - - +
482B LEU 3.1 0.4 - - - -
483B GLN* 1.3 77.9 - - - +
485B GLY* 1.3 58.2 + - - +
486B MET 3.6 0.4 - - - -
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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