Contacts of the strand formed by residues 54 - 59 (chain A) in PDB entry 2EC8
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 ILE 54 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 5.5 2.5 - - + -
48A VAL* 4.2 15.0 - - + -
53A GLU* 1.3 72.3 - - - +
55A ARG* 1.3 60.6 + - - +
56A LEU* 4.1 22.7 - - + -
82A TRP* 3.0 14.6 - - + +
83A ILE* 3.2 1.7 - - - -
84A THR* 2.7 43.0 + - - +
87A ALA* 3.7 28.5 - - + -
91A ASN* 4.1 14.4 - - + -
95A TYR* 4.0 17.3 - - - +
109A VAL* 4.0 33.4 - - + -
111A VAL* 5.4 1.3 - - + -
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Residues in contact with ARG 55 (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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40A HIS 4.3 0.5 - - - +
41A PRO* 4.2 10.0 - - - +
46A LEU* 5.7 3.6 - - - +
53A GLU* 2.6 48.1 + - - +
54A ILE* 1.3 73.4 - - - +
56A LEU* 1.3 66.5 + - - +
57A LEU* 4.2 1.9 + - + -
81A GLU* 3.7 23.9 + - + +
82A TRP 3.3 2.9 - - - -
83A ILE* 4.1 18.9 - - + +
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 5.3 0.7 - - + -
40A HIS 3.8 1.3 - - - +
41A PRO* 4.1 18.4 - - + -
46A LEU* 4.6 16.6 - - + -
54A ILE* 4.1 10.8 - - + -
55A ARG* 1.3 80.8 - - - +
57A LEU* 1.3 61.9 + - - +
66A TRP* 4.0 13.7 - - + -
81A GLU* 3.2 7.7 - - - +
82A TRP* 2.6 51.1 + - + +
95A TYR* 3.6 48.5 - - + -
107A ILE* 3.7 21.8 - - + -
109A VAL* 4.3 5.8 - - + -
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Residues in contact with LEU 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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13A VAL* 5.3 10.5 - - + -
38A SER 3.9 0.2 - - - +
39A ILE* 3.2 4.2 - - - +
40A HIS* 2.6 68.3 + - + +
55A ARG* 4.2 1.5 + - + -
56A LEU* 1.3 76.0 - - - +
58A CYS* 1.3 74.2 + - - +
59A THR* 4.1 15.7 + - - +
66A TRP* 4.0 4.0 - - - -
80A ASN* 3.9 16.2 - - - +
81A GLU* 4.3 23.1 - - + +
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Residues in contact with CYS 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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37A PRO* 3.8 13.7 - - - -
38A SER 3.3 14.4 - - - -
39A ILE* 4.5 0.4 - - - +
57A LEU* 1.3 75.3 - - - +
59A THR* 1.3 63.7 + - - +
60A ASP* 4.0 1.8 + - - -
63A PHE* 3.8 9.4 - - + +
66A TRP* 3.6 11.6 - - + +
80A ASN* 3.0 43.5 + - - +
97A CYS* 2.1 48.7 - - - -
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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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37A PRO* 4.1 0.2 - - - +
38A SER* 2.8 46.0 + - - -
40A HIS* 4.7 7.7 - - - -
57A LEU* 4.1 18.4 + - - +
58A CYS* 1.3 72.3 + - - +
60A ASP* 1.3 63.9 + - - +
61A PRO* 5.5 2.5 - - + -
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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