Contacts of the helix formed by residues 452 - 461 (chain A) in PDB entry 5WIU
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 ASN 452 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A LEU* 4.7 0.3 - - - +
70A ASN* 5.9 0.2 + - - -
392A ALA* 3.8 25.3 + - - +
395A VAL* 4.0 21.6 - - + +
448A TYR* 2.9 14.7 + - + +
450A VAL 3.7 0.4 - - - -
451A PHE* 1.3 80.5 - - - +
453A ALA* 1.3 60.5 + - - +
454A GLU* 3.1 13.6 + - - +
455A PHE* 3.0 44.4 + - + -
456A ARG* 2.9 31.4 + - - +
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Residues in contact with ALA 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A PHE 4.1 1.6 + - - -
452A ASN* 1.3 75.0 - - - +
454A GLU* 1.3 58.5 + - - +
456A ARG* 3.5 8.3 - - - +
457A ASN* 2.8 32.8 + - - +
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Residues in contact with GLU 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ALA* 4.5 16.8 - - + +
65A LEU* 3.6 21.1 - - + -
452A ASN* 3.1 9.1 + - - +
453A ALA* 1.3 78.6 - - - +
455A PHE* 1.3 63.8 + - - +
457A ASN* 3.8 4.2 - - - +
458A VAL* 2.9 28.7 + - + +
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Residues in contact with PHE 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A VAL* 4.4 16.4 - - + -
58A SER* 4.6 0.9 - - - -
59A VAL* 4.0 24.2 - - + -
65A LEU* 3.8 25.4 - - + -
70A ASN* 3.8 29.6 - - - -
73A ILE* 4.2 22.9 - - + -
395A VAL* 6.6 0.2 - - + -
448A TYR* 3.7 37.7 - + + +
449A THR* 4.5 2.2 - - - +
452A ASN* 3.0 28.2 + - + +
454A GLU* 1.3 76.2 - - - +
456A ARG* 1.3 53.8 + - - +
458A VAL* 3.2 4.2 + - - +
459A PHE* 2.8 36.1 + - - +
1209A OLA 3.9 26.4 - - + +
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Residues in contact with ARG 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A THR 3.2 28.2 + - - +
450A VAL 4.0 13.5 - - - -
452A ASN 2.9 17.7 + - - +
453A ALA* 3.5 9.0 - - - +
455A PHE* 1.3 77.7 - - - +
457A ASN* 1.3 57.4 + - - +
459A PHE* 3.4 5.9 + - - +
460A ARG* 2.7 34.2 + - + +
1209A OLA 4.1 20.2 - - - +
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Residues in contact with ASN 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A ALA 2.8 20.3 + - - +
454A GLU* 3.9 5.2 - - - +
456A ARG* 1.3 70.1 - - - +
458A VAL* 1.3 65.4 + - + +
460A ARG* 3.9 7.6 - - - +
461A LYS* 3.3 25.7 + - - +
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Residues in contact with VAL 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A SER* 4.1 17.0 - - - +
61A THR* 5.5 2.2 - - - +
62A GLU* 4.3 15.7 - - + -
64A ALA* 5.8 4.9 - - + -
65A LEU* 3.9 21.8 - - + -
454A GLU* 2.9 21.9 + - + +
455A PHE 3.6 4.5 - - - +
457A ASN* 1.3 77.1 - - + +
459A PHE* 1.3 62.0 + - - +
461A LYS* 3.1 28.4 - - + +
1209A OLA 4.0 16.2 - - + +
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Residues in contact with PHE 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A THR* 3.5 26.2 - - + -
455A PHE 2.8 17.6 + - - +
456A ARG 3.4 4.0 - - - +
458A VAL* 1.3 72.8 - - - +
460A ARG* 1.3 61.9 + - - +
461A LYS 2.8 19.0 + - - +
462A ALA* 3.0 22.7 + - + +
1209A OLA 3.9 84.1 - - + +
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Residues in contact with ARG 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456A ARG* 2.7 24.0 + - + +
457A ASN* 3.5 9.4 + - - +
459A PHE* 1.3 79.1 - - + +
461A LYS* 1.3 56.2 + - - +
462A ALA* 3.1 9.4 + - - +
1209A OLA 5.8 1.3 - - - +
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Residues in contact with LYS 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457A ASN 3.3 12.1 + - - +
458A VAL* 3.1 25.3 - - + +
459A PHE 2.8 10.0 + - - +
460A ARG* 1.3 70.8 - - - +
462A ALA* 1.3 66.8 + - - +
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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