Contacts of the strand formed by residues 25 - 30 (chain E) in PDB entry 2I3T
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 LEU 25 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E ILE* 3.7 2.3 - - - -
20E ILE* 2.9 45.8 + - + -
23E LYS* 3.0 31.8 - - + +
24E SER* 1.3 78.6 - - - +
26E LEU* 1.3 61.7 + - - +
27E LEU* 5.7 0.4 - - + -
37E VAL* 4.2 13.7 - - + -
38E TYR 3.3 15.5 - - - +
39E LYS* 4.0 16.8 - - + -
40E PHE* 3.4 10.5 - - - -
50E LEU* 4.1 15.0 - - + -
70E LEU* 3.8 26.2 - - + -
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Residues in contact with LEU 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E ILE* 3.9 17.5 - - + -
17E ILE* 4.4 3.1 - - + -
18E LYS 3.7 4.7 - - - +
19E ILE* 3.8 26.9 - - + -
25E LEU* 1.3 79.1 - - - +
27E LEU* 1.3 63.1 + - - +
28E ILE* 4.4 10.5 - - + -
36E THR 3.6 2.1 - - - +
37E VAL* 3.4 6.4 - - - +
38E TYR* 2.9 45.4 + - + +
40E PHE* 4.4 5.2 - - + -
47E VAL* 4.7 0.4 - - + -
306E ILE* 4.6 7.4 - - + -
308E CYS* 3.7 36.6 - - + -
335E ILE* 3.9 22.4 - - + -
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Residues in contact with LEU 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ASP 3.9 0.2 - - - +
17E ILE* 3.4 1.7 - - - -
18E LYS* 2.8 40.9 + - + +
20E ILE* 3.8 26.7 - - + -
25E LEU* 5.7 0.4 - - + -
26E LEU* 1.3 74.2 - - - +
28E ILE* 1.3 67.8 + - - +
35E LEU* 4.5 4.9 - - + -
36E THR 3.9 0.9 - - - -
37E VAL* 3.7 25.4 - - + -
62E CYS* 3.9 22.1 - - - -
63E ASN 4.6 1.8 - - - +
64E PHE* 4.1 16.4 - - + -
72E ILE* 3.7 48.9 - - + -
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Residues in contact with ILE 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E PRO* 4.8 2.9 - - + -
14E ILE* 4.1 15.3 - - + -
16E ASP 3.5 11.7 - - - +
17E ILE* 4.3 11.0 - - + -
26E LEU* 4.4 13.5 - - + -
27E LEU* 1.3 81.7 - - - +
29E THR* 1.3 68.2 + - - +
35E LEU* 3.4 4.9 - - - +
36E THR* 2.9 52.7 + - + +
38E TYR* 3.9 19.3 - - + -
308E CYS* 4.5 4.5 - - - -
333E ILE* 3.3 50.5 - - + -
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Residues in contact with THR 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E ILE* 3.7 6.1 - - - +
15E SER* 2.9 43.2 + - - -
16E ASP* 3.1 26.7 + - - +
28E ILE* 1.3 74.2 - - - +
30E SER* 1.3 61.1 + - - +
34E SER 3.4 2.9 - - - -
35E LEU* 3.7 16.4 - - + -
59E LEU* 3.9 17.9 - - + -
61E CYS* 3.8 10.4 - - - +
62E CYS* 3.6 30.7 - - + -
74E VAL* 4.1 6.1 - - + -
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Residues in contact with SER 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E PRO* 3.5 22.0 - - - +
12E ASP* 3.4 13.0 + - - +
13E TYR 3.1 13.6 + - - -
14E ILE* 4.9 2.0 - - - -
29E THR* 1.3 75.4 - - - +
31E TRP* 1.3 67.6 + - - +
32E ASP* 3.0 28.0 + - - -
33E GLY* 3.4 4.7 + - - -
34E SER* 3.0 15.3 + - - -
59E LEU* 3.1 29.3 + - - +
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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