Contacts of the helix formed by residues 68 - 78 (chain Y) in PDB entry 2W4V
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 68 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24Y PHE* 4.1 1.3 - - - -
33Y GLY* 2.7 31.3 + - - -
34Y PHE* 5.5 0.4 - - - +
66Y PRO* 3.3 10.2 + - + +
67Y LEU* 1.3 79.4 - - - +
69Y PHE* 1.3 61.0 + - - +
70Y THR* 2.6 37.8 + - - +
71Y MET 3.5 1.6 + - - +
72Y PHE* 3.4 15.9 + - - +
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Residues in contact with PHE 69 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Y ILE* 4.4 3.6 - - + -
20Y MET* 3.4 12.1 - - + -
21Y LYS* 3.1 55.0 - - + +
24Y PHE* 3.5 37.2 - + + -
68Y ASN* 1.3 80.1 - - - +
70Y THR* 1.3 62.6 + - + +
72Y PHE* 3.8 10.1 - + - -
73Y LEU* 3.1 49.7 + - + +
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Residues in contact with THR 70 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68Y ASN* 2.6 28.0 + - - +
69Y PHE* 1.3 82.4 - - + +
71Y MET* 1.3 68.1 + - - +
72Y PHE 2.8 10.5 + - - -
73Y LEU* 3.2 5.6 + - - +
74Y SER* 2.7 31.1 + - - -
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Residues in contact with MET 71 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Y ALA* 4.5 2.7 - - + -
64Y PRO* 3.5 27.1 - - + -
65Y GLY* 2.8 49.8 - - - +
66Y PRO* 3.2 16.8 - - + +
67Y LEU* 3.8 11.6 - - + +
68Y ASN 3.5 1.4 + - - +
70Y THR* 1.3 85.1 + - - +
72Y PHE* 1.3 56.7 + - - +
74Y SER* 3.4 11.6 - - - +
75Y ILE* 2.9 35.1 + - + +
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Residues in contact with PHE 72 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826C TRP* 2.2 56.5 - + - -
830C TYR* 4.8 12.6 - + - -
20Y MET* 3.9 42.0 - - + -
23Y ALA* 5.4 0.9 - - + -
24Y PHE* 4.0 27.1 - + + -
27Y ILE* 5.5 8.7 - - + -
35Y VAL* 5.2 1.3 - - + -
67Y LEU* 3.9 5.6 - - + +
68Y ASN 3.4 16.8 + - - +
69Y PHE* 3.7 21.8 - + - +
70Y THR 2.8 1.0 + - - -
71Y MET* 1.3 74.6 - - - +
73Y LEU* 1.3 69.5 + - - +
74Y SER 2.8 11.8 + - - -
75Y ILE* 2.4 32.4 + - - +
76Y PHE* 3.1 5.5 + - - +
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Residues in contact with LEU 73 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Y ILE* 4.8 16.2 - - + -
20Y MET* 2.5 54.3 - - + -
69Y PHE* 3.1 46.2 + - + +
70Y THR* 3.2 4.4 + - - +
72Y PHE* 1.3 81.3 - - + +
74Y SER* 1.3 56.6 + - - +
76Y PHE* 4.0 1.1 - - + -
77Y SER* 3.0 32.5 + - - -
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Residues in contact with SER 74 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70Y THR* 2.7 24.3 + - - -
71Y MET* 3.4 14.4 - - - +
72Y PHE 2.8 1.4 + - - -
73Y LEU* 1.3 76.5 - - - +
75Y ILE* 1.3 59.5 + - - -
77Y SER* 2.7 16.5 + - - -
78Y ASP* 2.2 29.8 + - - +
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Residues in contact with ILE 75 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824C TRP* 5.1 7.1 - - + +
826C TRP* 3.4 37.0 - - + -
62Y GLU* 4.0 24.7 - - + +
63Y ALA* 4.4 11.0 - - + -
64Y PRO* 5.4 2.7 - - + -
67Y LEU* 4.9 1.6 - - + -
71Y MET* 2.9 18.2 - - + +
72Y PHE* 2.4 38.5 + - - +
74Y SER* 1.3 76.3 - - - +
76Y PHE* 1.3 63.6 - - - +
78Y ASP* 3.4 8.0 + - - +
79Y LYS* 3.2 30.1 + - - +
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Residues in contact with PHE 76 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826C TRP* 3.9 29.2 - + - +
827C TRP* 3.8 37.9 - + - -
830C TYR* 4.9 19.7 - + - -
16Y GLN* 6.0 4.7 - - + -
20Y MET* 3.0 46.9 - - + -
72Y PHE 3.1 10.8 + - - +
73Y LEU* 4.1 0.9 - - + +
75Y ILE* 1.3 82.3 - - - +
77Y SER* 1.3 66.6 + - - +
79Y LYS* 3.2 28.6 + - - +
80Y LEU* 3.3 25.1 + - + +
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Residues in contact with SER 77 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73Y LEU* 3.0 18.2 + - - -
74Y SER* 2.7 22.7 + - - -
76Y PHE* 1.3 78.3 - - - +
78Y ASP* 1.3 61.9 + - - +
79Y LYS 3.0 9.2 + - - -
80Y LEU* 3.7 5.5 + - - +
81Y SER* 3.4 22.3 + - - -
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Residues in contact with ASP 78 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74Y SER* 2.2 34.0 + - - +
75Y ILE* 3.8 9.6 - - - +
76Y PHE 3.3 0.2 - - - -
77Y SER* 1.3 83.0 + - - +
79Y LYS* 1.3 61.2 + - - +
81Y SER* 3.1 19.4 + - - +
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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