Contacts of the helix formed by residues 447 - 455 (chain A) in PDB entry 2WSL
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 GLY 447 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A PHE* 3.9 12.5 - - - -
443A GLU 3.2 3.4 + - - -
444A PHE 3.3 1.4 + - - -
445A VAL 3.2 4.8 - - - -
446A PHE* 1.3 78.9 - - - +
448A LEU* 1.3 65.3 + - - +
449A PRO 3.3 2.9 - - - -
450A LEU* 3.0 29.0 + - - +
451A GLU 4.1 1.0 + - - -
464A SER* 3.4 16.6 - - - -
468A VAL* 3.9 11.2 - - - -
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Residues in contact with LEU 448 (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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126A HIS* 3.6 52.7 - - + +
127A VAL* 4.2 15.9 - - + +
129A ASP 4.7 1.8 - - - +
132A PHE* 3.5 31.9 - - + -
443A GLU* 3.0 16.6 + - + +
446A PHE* 4.0 19.7 - - + -
447A GLY* 1.3 77.5 - - - +
449A PRO* 1.4 65.0 - - + +
450A LEU 3.1 0.2 - - - -
451A GLU* 3.1 27.2 + - - +
454A ASP* 4.2 4.7 - - - +
456A TYR* 3.9 22.4 - - + +
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Residues in contact with PRO 449 (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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443A GLU 3.3 13.7 - - - +
444A PHE* 3.9 17.5 - - + -
447A GLY 3.4 3.6 - - - -
448A LEU* 1.4 88.8 - - + +
450A LEU* 1.3 61.1 + - - -
451A GLU 3.1 6.7 + - - +
452A ARG* 5.3 0.5 - - - -
456A TYR* 3.4 46.0 - - + +
460A GLU 3.8 22.9 - - - +
461A GLU* 3.5 20.5 + - - +
464A SER* 3.5 16.4 - - - +
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Residues in contact with LEU 450 (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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21A PHE* 3.6 24.0 - - + -
132A PHE* 5.2 2.5 - - + +
136A VAL* 3.9 33.4 - - + -
447A GLY* 3.0 29.9 + - - +
449A PRO* 1.3 76.8 - - - +
451A GLU* 1.3 58.0 + - - +
452A ARG* 3.2 13.5 + - - +
461A GLU* 3.4 38.4 - - + +
464A SER* 4.1 2.5 - - - +
465A ARG* 3.6 29.2 - - + +
468A VAL* 4.4 11.7 - - + -
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Residues in contact with GLU 451 (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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21A PHE* 3.7 24.9 - - + -
132A PHE* 4.5 18.3 - - + -
448A LEU 3.1 15.0 + - - +
449A PRO* 4.0 5.1 - - - +
450A LEU* 1.3 76.8 - - - +
452A ARG* 1.3 65.0 + - - +
453A ARG* 3.2 36.7 - - + +
454A ASP* 3.2 32.3 + - + +
455A GLN 4.8 0.2 + - - -
456A TYR* 4.8 2.1 + - - +
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Residues in contact with ARG 452 (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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21A PHE* 5.1 0.2 - - - -
449A PRO 5.3 0.9 - - - +
450A LEU 3.2 7.5 + - - +
451A GLU* 1.3 70.3 + - - +
453A ARG* 1.3 57.7 + - + +
454A ASP 2.9 11.7 + - - -
455A GLN* 3.8 7.8 + - - -
456A TYR 5.6 1.2 - - - +
458A LYS* 3.4 16.8 - - - +
461A GLU* 2.8 44.4 + - - +
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Residues in contact with ARG 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 GLU* 3.2 26.6 - - + +
452A ARG* 1.3 75.7 - - + +
454A ASP* 1.3 59.7 + - - +
455A GLN* 3.6 11.6 + - - +
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Residues in contact with ASP 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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126A HIS* 5.1 11.0 - - - -
427A LYS* 3.3 29.4 + - - -
448A LEU* 4.2 7.3 - - - +
451A GLU* 3.2 30.5 - - + +
452A ARG 2.9 2.6 + - - -
453A ARG* 1.3 79.5 - - - +
455A GLN* 1.3 72.1 + - - +
456A TYR* 3.3 29.7 + - + -
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Residues in contact with GLN 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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426A SER* 4.2 3.5 + - - -
427A LYS* 4.1 14.9 - - + +
452A ARG 3.8 7.1 + - - -
453A ARG 3.6 13.1 - - - +
454A ASP* 1.3 78.9 - - - +
456A TYR* 1.3 65.6 + - - +
457A THR* 4.0 1.2 + - - +
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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