Contacts of the helix formed by residues 439 - 445 (chain W) in PDB entry 5IY8
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 ASP 439 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244W ILE* 3.8 4.3 - - - -
413W GLY 5.4 0.5 + - - +
437W CYS* 3.6 13.9 - - - -
438W MET* 1.3 85.5 - - + +
440W ALA* 1.3 64.0 + - - +
441W SER* 2.6 41.9 + - - +
442W LEU* 4.3 6.9 + - - +
443W ALA* 4.7 1.0 + - - +
636W ARG* 2.9 29.1 + - + +
639W TYR* 3.7 33.3 - - + -
640W LEU* 4.5 4.9 - - - +
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Residues in contact with ALA 440 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240W ASP* 3.4 34.1 - - - +
243W CYS* 4.3 5.2 - - + -
244W ILE* 3.4 17.9 - - + +
439W ASP* 1.3 72.9 - - - +
441W SER* 1.3 65.2 + - - +
442W LEU 3.3 0.9 - - - -
443W ALA* 3.0 10.8 + - - +
444W ILE* 2.9 40.0 + - + +
636W ARG* 3.2 8.1 - - - +
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Residues in contact with SER 441 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439W ASP* 2.6 23.5 + - - +
440W ALA* 1.3 75.5 - - - +
442W LEU* 1.4 63.6 + - - +
444W ILE* 3.2 25.7 - - - +
445W LYS* 3.3 27.3 - - - +
470W ILE 5.2 9.0 - - - -
471W LEU 5.7 1.6 - - - -
472W ASP* 5.8 5.2 - - - -
639W TYR* 4.5 9.9 + - - -
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Residues in contact with LEU 442 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247W MET* 6.4 0.9 - - + -
410W TYR* 4.6 13.9 - - + +
412W LYS* 3.4 43.3 - - + +
413W GLY* 3.8 15.9 - - - +
439W ASP 4.3 4.8 + - - +
440W ALA 3.3 0.8 - - - -
441W SER* 1.4 81.2 + - - +
443W ALA* 1.4 60.4 + - - +
445W LYS* 3.3 30.7 + - + +
446W PRO* 4.3 2.8 - - - +
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Residues in contact with ALA 443 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213W LEU 4.2 4.9 - - - +
215W PRO* 3.6 15.2 - - - +
243W CYS* 3.4 22.2 - - - -
247W MET* 3.9 36.1 - - + -
437W CYS* 4.4 7.6 - - - -
439W ASP 4.8 0.4 + - - -
440W ALA* 3.0 15.4 + - - +
442W LEU* 1.4 76.4 - - - +
444W ILE* 1.3 56.4 + - - +
446W PRO* 3.3 16.8 - - - +
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Residues in contact with ILE 444 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213W LEU* 5.4 8.1 - - + -
239W ILE* 5.1 16.6 - - + +
240W ASP* 5.6 0.7 - - - -
243W CYS* 3.7 26.7 - - + -
440W ALA* 2.9 25.0 + - + +
441W SER* 3.2 24.2 - - - +
443W ALA* 1.3 69.8 - - - +
445W LYS* 1.3 67.4 + - + +
446W PRO* 3.3 4.7 - - - -
447W VAL* 3.0 32.5 + - + +
448W PHE 4.5 0.3 + - - -
470W ILE* 4.6 10.1 - - + +
471W LEU* 3.9 42.8 - - + +
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Residues in contact with LYS 445 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441W SER* 3.3 32.1 + - - +
442W LEU* 3.3 28.0 - - + +
444W ILE* 1.3 79.7 - - + +
446W PRO* 1.4 68.1 - - + +
447W VAL 3.2 1.4 + - - -
448W PHE* 3.2 22.8 + - - +
449W GLU* 3.7 6.0 + - - +
471W LEU 4.4 13.3 + - - -
472W ASP* 4.8 11.3 + - - +
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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