Contacts of the helix formed by residues 56 - 65 (chain A) in PDB entry 5W4A
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 SER 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A LYS 3.8 1.6 + - - -
55A PRO* 1.3 76.6 - - - +
57A VAL* 1.3 65.6 + - - +
58A ASP* 3.5 9.2 + - - +
59A ASP* 2.9 36.4 + - - +
60A ILE* 3.1 24.3 + - - +
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Residues in contact with VAL 57 (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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56A SER* 1.3 72.9 - - - +
58A ASP* 1.3 60.5 + - - +
60A ILE* 3.1 7.0 + - + +
61A VAL* 2.9 36.4 + - + +
87A ASP* 5.3 12.1 - - + +
88A PHE* 3.8 34.5 - - + -
91A GLU* 6.4 0.9 - - + -
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Residues in contact with ASP 58 (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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56A SER* 3.2 7.7 + - - +
57A VAL* 1.3 81.3 - - - +
59A ASP* 1.3 59.4 + - - +
61A VAL* 3.2 6.1 + - - +
62A GLN* 2.8 68.5 + - - +
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Residues in contact with ASP 59 (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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41A ASN* 4.9 7.0 + - - +
42A SER* 3.8 18.3 - - - -
43A PHE* 4.4 8.6 - - + +
53A LYS* 5.5 1.2 + - - -
55A PRO* 3.7 14.8 - - + +
56A SER* 2.9 45.2 + - - +
58A ASP* 1.3 78.2 - - - +
60A ILE* 1.3 62.9 + - - +
62A GLN* 3.6 5.4 + - - +
63A ILE* 3.3 27.0 + - - +
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Residues in contact with ILE 60 (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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19A PHE* 5.9 0.4 - - + -
43A PHE* 3.9 34.5 - - + -
55A PRO* 4.2 16.6 - - + +
56A SER 3.1 18.6 + - - +
57A VAL* 3.5 5.4 - - - +
59A ASP* 1.3 75.4 - - - +
61A VAL* 1.3 66.2 + - - +
63A ILE* 3.2 4.2 + - - +
64A LEU* 3.0 40.7 + - + +
84A LEU* 4.1 15.3 - - + -
88A PHE* 4.2 22.0 - - + -
178A ILE* 4.0 26.5 - - + -
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Residues in contact with VAL 61 (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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57A VAL* 2.9 34.2 + - + +
58A ASP* 3.8 7.6 - - - +
60A ILE* 1.3 75.7 - - + +
62A GLN* 1.3 69.5 + - - +
64A LEU* 3.2 6.0 + - - +
65A PHE* 2.8 33.8 + - + +
81A LEU* 4.7 4.3 - - + -
88A PHE* 4.5 12.8 - - + -
91A GLU* 3.7 42.8 - - + +
95A ARG* 3.8 13.0 - - - +
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Residues in contact with GLN 62 (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 ASN* 4.6 0.3 + - - -
41A ASN* 6.2 0.9 - - - +
58A ASP* 2.8 52.6 + - - +
59A ASP* 4.0 5.8 - - - +
60A ILE 3.2 0.4 - - - -
61A VAL* 1.3 88.5 - - - +
63A ILE* 1.3 62.0 + - + +
65A PHE 3.5 9.3 - - - +
66A PRO* 3.4 25.6 - - - +
67A SER 5.9 0.3 + - - -
95A ARG* 5.6 2.2 + - - +
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ASN* 2.9 40.3 + - + +
22A LEU* 3.9 30.5 - - + +
25A TYR* 4.6 20.2 - - + -
41A ASN* 3.6 35.7 - - - +
43A PHE* 3.8 26.0 - - + -
59A ASP 3.3 11.8 + - - +
60A ILE 3.2 7.6 + - - +
62A GLN* 1.3 78.7 - - + +
64A LEU* 1.3 66.8 + - + +
66A PRO* 3.4 2.1 - - - +
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Residues in contact with LEU 64 (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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18A PHE 4.1 12.6 - - - +
19A PHE* 4.1 16.2 - - + -
20A PRO* 6.2 0.4 - - + -
21A ASN* 5.4 1.7 - - + +
43A PHE* 4.9 4.5 - - + -
60A ILE* 3.0 38.3 + - + +
61A VAL* 3.2 0.9 + - - -
63A ILE* 1.3 82.1 - - + +
65A PHE* 1.3 71.0 + - + +
66A PRO* 3.4 6.3 - - - +
73A THR* 4.2 7.3 - - - +
77A SER* 2.7 31.3 + - - +
80A THR* 3.9 34.1 - - + -
81A LEU* 4.0 25.4 - - + -
84A LEU* 4.3 1.8 - - + -
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Residues in contact with PHE 65 (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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61A VAL* 2.8 26.3 + - + +
62A GLN* 3.5 15.0 - - - +
64A LEU* 1.3 88.5 - - + +
66A PRO* 1.3 68.6 - - - +
67A SER* 3.6 1.2 + - - -
69A SER* 3.8 5.6 - - - +
73A THR 5.5 0.2 - - - -
74A ILE* 3.6 32.1 - - + -
77A SER* 3.4 25.1 - - - -
78A MSE 4.0 1.8 - - + -
81A LEU* 3.7 38.6 - - + -
91A GLU* 4.7 2.2 - - + -
95A ARG* 3.5 60.9 + - + +
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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