Contacts of the helix formed by residues 58 - 65 (chain A) in PDB entry 1EX0
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 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A PHE* 3.6 43.5 - - - +
55A GLU* 3.0 20.4 + - - +
56A ARG 4.2 0.2 - - - +
57A TRP* 1.3 110.6 - - + +
59A THR* 1.3 88.7 + - - +
60A ASN 3.4 1.3 + - - -
61A LYS 3.7 2.0 + - - -
62A VAL* 3.1 26.3 + - - +
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Residues in contact with THR 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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53A PHE* 6.3 0.7 - - - -
58A ASP* 1.3 84.7 + - - +
60A ASN* 1.3 70.7 + - - +
62A VAL* 4.8 1.6 - - - -
63A ASP* 2.8 51.2 + - + +
83A TYR* 4.2 28.7 - - + -
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Residues in contact with ASN 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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52A LEU 2.9 19.6 + - - -
53A PHE* 3.4 18.9 + - - +
58A ASP* 3.4 1.4 - - - -
59A THR* 1.3 79.3 - - - +
61A LYS* 1.3 59.4 + - + +
63A ASP* 5.1 0.4 - - - -
64A HIS* 2.9 39.5 + - + +
74A LEU* 4.0 18.4 - - + +
75A ILE 5.3 0.7 - - - -
76A VAL* 5.1 0.2 - - + -
82A PHE* 3.4 18.0 - - + +
83A TYR* 2.9 55.8 + - - +
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Residues in contact with LYS 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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53A PHE 5.1 0.4 + - - -
54A LYS* 3.2 30.1 + - - +
55A GLU 4.3 9.1 + - - +
56A ARG* 4.0 23.2 - - + +
58A ASP 3.7 2.6 + - - -
59A THR 3.4 0.2 - - - -
60A ASN* 1.3 76.4 - - - +
62A VAL* 1.3 60.8 + - - +
65A HIS* 2.8 27.4 + - - -
66A THR* 3.0 35.3 + - - +
67A ASP* 3.5 14.2 + - + +
69A TYR 4.9 1.4 + - - -
71A ASN 3.0 22.2 + - - -
72A ASN* 4.4 1.2 - - - +
73A LYS 2.9 28.1 + - - +
74A LEU* 4.2 6.5 - - + +
75A ILE* 4.1 25.2 - - - +
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Residues in contact with VAL 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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56A ARG 3.6 15.9 - - - +
57A TRP* 3.6 13.5 - - - +
58A ASP 3.1 20.1 + - - +
59A THR* 4.1 2.5 - - - +
61A LYS* 1.3 79.7 - - - +
63A ASP* 1.3 71.1 + - - +
65A HIS* 3.3 17.0 + - - -
67A ASP* 3.9 20.0 - - - +
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Residues in contact with ASP 63 (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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59A THR* 2.8 43.6 + - + +
60A ASN* 4.1 1.6 - - - +
62A VAL* 1.3 85.3 - - - +
64A HIS* 1.3 61.6 + - + +
65A HIS* 3.2 17.5 - - - -
80A GLN* 3.0 25.3 + - - +
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Residues in contact with HIS 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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60A ASN* 2.9 34.4 + - - +
61A LYS 3.1 0.2 + - - -
63A ASP* 1.3 79.0 - - + +
65A HIS* 1.4 62.5 + - - +
66A THR* 3.3 18.3 + - + +
75A ILE 4.3 0.9 - - - +
76A VAL* 3.4 21.0 - - + +
77A ARG* 2.8 68.7 + - - +
80A GLN* 3.4 41.3 + - + +
81A SER 2.6 30.6 + - - -
82A PHE* 3.7 4.5 - - + +
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Residues in contact with HIS 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 LYS 2.8 6.3 + - - -
62A VAL 3.7 10.7 + - - -
63A ASP* 3.2 16.7 + - - -
64A HIS* 1.4 88.6 + - - +
66A THR* 1.3 57.6 + - - +
67A ASP* 3.6 9.4 - - - -
68A LYS* 5.3 2.4 - - - +
69A TYR* 4.7 0.7 - - - -
77A ARG* 2.9 20.5 + - - -
80A GLN* 5.2 3.4 + - - -
187A TRP* 3.2 73.3 + + + +
198A GLU* 4.4 7.1 + - - -
206A LEU* 4.0 12.1 - - + +
230A PHE* 5.4 1.0 - - - -
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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