Contacts of the strand formed by residues 89 - 96 (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 PHE 89 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E LYS* 3.9 22.7 - - + -
7E TYR 4.4 2.0 - - - -
8E LEU* 3.6 52.7 - - + -
43E PRO* 6.5 0.4 - - + -
45E GLY* 3.7 6.5 - - - +
46E VAL 3.3 24.5 - - - +
47E ALA* 3.6 15.5 - - + -
83E TYR* 2.7 23.7 + - - -
86E ASP 3.7 16.6 - - - -
87E ASN* 3.1 27.4 + - - +
88E ASP* 1.3 76.8 - - - +
90E TRP* 1.3 63.3 + - - +
91E PHE* 3.2 28.7 - - + -
144E DUD 4.0 0.2 - - - +
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Residues in contact with TRP 90 (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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26E LEU* 3.6 25.6 - - + -
43E PRO* 3.8 0.9 - - - +
44E LEU* 2.9 35.4 + - + +
45E GLY 4.2 1.4 + - - -
46E VAL* 2.8 26.0 + - + +
47E ALA* 4.2 1.1 - - - -
48E MET* 3.5 58.7 + - + +
50E LEU* 4.3 5.8 - - + -
56E ALA* 3.4 23.1 - - + -
58E VAL* 3.9 22.2 - - + -
79E ILE* 3.8 32.7 - - + +
83E TYR* 3.9 10.8 - + - -
88E ASP 3.6 12.6 - - - -
89E PHE* 1.3 75.9 - - - +
91E PHE* 1.3 66.1 + - - +
111E PHE* 3.9 11.9 - + - -
144E DUD 3.4 8.5 - - + +
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Residues in contact with PHE 91 (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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41E LEU* 4.1 41.3 - - + -
42E VAL 3.3 6.1 - - - +
43E PRO* 3.6 34.8 - - + -
44E LEU* 4.0 9.0 - - - +
58E VAL* 5.5 3.1 - - - +
83E TYR* 4.6 4.9 - - - -
89E PHE* 3.2 37.0 - - + -
90E TRP* 1.3 73.6 - - - +
92E PHE* 1.3 59.8 + - - +
93E PRO* 4.1 0.4 - - - -
144E DUD 2.9 39.4 + - + +
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Residues in contact with PHE 92 (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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41E LEU* 4.5 0.7 - - - -
42E VAL* 2.8 42.4 + - + +
44E LEU* 4.0 11.4 - - + +
58E VAL* 4.9 2.7 - - + -
60E PRO* 4.1 13.9 - - + -
64E THR* 4.6 2.7 - - + -
70E VAL* 4.0 19.1 - - + -
71E ILE 4.6 0.2 - - - -
72E GLN* 3.1 51.1 - - + -
91E PHE* 1.3 72.5 - - - +
93E PRO* 1.3 60.8 - - - +
94E ALA* 3.2 31.3 + - + -
102E ILE* 5.4 0.7 - - + -
108E ILE* 3.7 35.4 - - + -
109E CYS* 3.5 27.1 - - + -
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Residues in contact with PRO 93 (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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62D SER 5.5 4.9 - - - +
39E PHE* 3.7 17.7 - - + -
40E LYS 4.0 0.2 - - - +
41E LEU* 3.7 18.2 - - + -
72E GLN* 3.3 17.7 - - + +
73E THR* 3.0 35.1 + - - +
74E ASN* 3.3 34.5 - - + +
91E PHE 3.8 2.5 - - - +
92E PHE* 1.3 82.2 - - - +
94E ALA* 1.3 56.5 + - - +
144E DUD 3.7 18.8 - - + +
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Residues in contact with ALA 94 (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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34E ILE* 3.8 21.1 - - + +
38E GLU 4.0 0.7 - - - +
39E PHE* 3.2 7.6 - - - -
40E LYS 2.9 42.7 + - - +
42E VAL* 4.0 5.4 - - + -
70E VAL* 4.2 10.5 - - + -
71E ILE 3.5 5.4 - - - -
92E PHE* 3.2 23.3 + - + -
93E PRO* 1.3 73.2 - - - +
95E TYR* 1.3 57.8 + - - +
96E ALA 4.1 0.4 + - - -
102E ILE* 5.0 0.7 - - + -
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Residues in contact with TYR 95 (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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36D LYS* 4.8 2.4 + - - -
65D TYR* 3.2 31.9 - + - -
97D LEU* 3.8 42.0 + - + +
37E ASP* 3.3 45.0 + - - +
38E GLU 3.5 10.8 - - - -
39E PHE* 4.3 3.8 - - + -
70E VAL* 3.2 5.2 - - - -
71E ILE* 3.0 40.0 + - + +
73E THR* 3.4 19.0 - - + +
94E ALA* 1.3 73.4 - - - +
96E ALA* 1.3 76.6 + - - +
97E LEU* 3.6 23.7 + - + -
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Residues in contact with ALA 96 (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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34E ILE* 3.5 31.8 - - + +
35E LYS 3.6 8.3 - - - +
37E ASP* 2.8 31.5 + - - -
38E GLU 2.8 10.5 + - - -
69E GLY 3.8 2.9 - - - -
70E VAL* 4.1 4.0 - - + -
94E ALA 4.1 0.8 + - - -
95E TYR* 1.3 77.2 - - - +
97E LEU* 1.3 60.5 + - - +
98E ARG 3.4 18.4 - - - +
100E THR* 4.1 8.3 - - + -
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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