Contacts of the strand formed by residues 43 - 48 (chain A) in PDB entry 2E9I
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 MET 43 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ILE* 3.6 54.1 - - + -
38A ILE* 3.4 15.9 - - + +
39A ASN 3.1 28.0 - - - +
40A SER* 2.5 26.4 + - - +
41A SER 4.3 2.3 - - - +
42A ASP* 1.3 76.0 - - - +
44A SER* 1.3 65.4 - - - +
59A ILE* 4.4 14.9 - - + +
67A HIS* 3.9 14.4 - - + +
83A VAL* 5.0 12.6 - - + -
84A LYS 3.8 5.8 - - - +
85A TYR* 4.1 15.3 - - + +
90A VAL* 5.8 3.6 - - - -
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Residues in contact with SER 44 (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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42A ASP 5.3 0.7 - - - -
43A MET* 1.3 79.3 - - - +
45A ALA* 1.3 60.8 + - - +
46A HIS* 3.8 21.1 + - - -
59A ILE* 5.1 1.3 - - - -
82A SER 3.2 15.1 + - - +
83A VAL* 3.5 4.9 - - - +
84A LYS* 3.2 33.9 + - - +
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Residues in contact with ALA 45 (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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44A SER* 1.3 71.7 - - - +
46A HIS* 1.3 74.7 + - - +
56A GLU* 4.3 0.2 - - - +
57A ALA* 3.0 45.7 + - + +
59A ILE* 4.2 22.7 - - + +
69A VAL* 4.5 10.1 - - + -
81A VAL* 5.5 2.5 - - + -
82A SER 4.0 2.0 - - - -
83A VAL* 4.7 14.8 - - + -
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Residues in contact with HIS 46 (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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44A SER* 3.8 24.9 + - - -
45A ALA* 1.3 95.8 + - - +
47A VAL* 1.3 63.6 + - - +
48A THR* 3.8 1.1 + - - +
54A VAL* 4.0 17.3 - - + -
55A THR 3.0 23.1 - - - +
56A GLU* 3.8 25.0 + - + +
57A ALA* 4.6 0.6 - - - +
81A VAL* 4.8 2.1 - - - +
82A SER* 2.9 45.6 + - - +
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Residues in contact with VAL 47 (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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46A HIS* 1.3 73.4 - - - +
48A THR* 1.3 71.7 + - - +
49A SER 4.0 0.2 + - - -
53A ARG 3.9 0.7 - - - +
54A VAL* 3.6 2.1 - - - -
55A THR* 2.8 50.8 + - - +
56A GLU* 5.1 1.3 - - - +
57A ALA* 5.0 7.4 - - + -
71A PHE* 3.3 46.4 - - + -
73A PRO* 5.5 2.0 - - + -
75A GLU* 4.5 10.2 - - - +
79A HIS* 4.8 13.7 - - + -
80A THR 3.7 13.2 - - - +
81A VAL* 4.2 12.6 - - + +
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Residues in contact with THR 48 (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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46A HIS* 4.2 1.9 + - - +
47A VAL* 1.3 75.2 - - - +
49A SER* 1.3 73.6 + - - +
50A PRO 4.2 0.2 - - - -
52A GLY* 5.5 2.9 - - - -
53A ARG 3.6 8.5 - - - +
54A VAL* 4.4 18.1 - - + +
75A GLU* 4.2 2.2 - - - +
78A VAL 4.3 0.9 - - - +
79A HIS* 4.3 3.3 - - - -
80A THR* 2.8 43.0 + - - -
82A SER* 3.4 21.8 + - - -
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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