Contacts of the strand formed by residues 24 - 27 (chain E) in PDB entry 2Y1T
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 24 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3E ILE* 5.5 1.3 - - + -
15E ILE* 3.3 34.1 - - + -
16E ASN 4.3 8.5 - - - +
17E LYS* 4.1 32.5 - - + -
18E MET 5.2 0.7 - - - +
22E ASP 3.7 9.6 - - - +
23E TRP* 1.3 76.1 - - - +
25E ASP* 1.3 66.4 + - - +
26E LEU 3.7 0.2 + - - -
110E GLN* 3.2 1.8 - - - -
111E PHE* 2.8 70.8 + - + +
117F MET* 3.9 19.5 - - + -
120F VAL* 5.2 6.5 - - + -
122F LEU* 5.0 5.8 - - + -
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Residues in contact with ASP 25 (chain E).
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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15E ILE* 3.5 24.4 - - - +
16E ASN 5.5 1.2 + - - -
23E TRP 4.2 4.5 + - - +
24E ILE* 1.3 74.8 - - - +
26E LEU* 1.3 62.0 + - - +
27E ARG* 4.7 1.5 + - - +
61E ARG* 3.4 20.0 + - - +
107E ARG* 2.8 49.8 + - + +
109E CYS 3.4 5.6 - - - +
110E GLN* 3.6 19.4 - - - +
143E DUD 5.3 0.3 + - - -
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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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15E ILE* 3.9 22.0 - - + -
24E ILE 4.3 0.9 - - - +
25E ASP* 1.3 80.0 - - - +
27E ARG* 1.3 64.6 + - - +
44E LEU* 3.9 23.3 - - + +
46E VAL* 4.3 10.8 - - + -
48E MET* 4.3 10.1 - - + -
58E VAL* 5.2 1.8 - - + -
90E TRP* 3.6 31.2 - - + -
107E ARG* 3.4 4.0 - - - -
108E ILE* 3.1 23.7 + - - +
109E CYS* 2.9 28.4 + - - +
111E PHE* 3.7 37.5 - - + +
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Residues in contact with ARG 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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12E GLN* 5.2 0.7 - - - +
13E THR* 4.0 45.7 + - - +
14E ARG 4.5 2.2 + - - -
15E ILE* 4.0 18.3 - - + +
16E ASN* 5.7 2.6 + - - -
25E ASP 4.7 0.6 + - - +
26E LEU* 1.3 81.6 - - - +
28E ALA* 1.3 66.5 + - - +
44E LEU* 3.2 31.0 + - - +
105E GLY* 2.8 49.4 + - - +
106E ASP 3.1 4.3 - - - +
107E ARG* 3.4 37.7 - - + +
108E ILE 4.6 0.2 - - - +
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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