Contacts of the strand formed by residues 29 - 37 (chain E) in PDB entry 1U3H
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 29 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2E GLN 4.4 16.6 - - - -
3E VAL* 5.0 2.2 - - + -
24E TYR* 3.7 26.7 + + + -
26E ASN* 2.9 47.1 + - + +
27E SER 3.3 7.0 - - - +
28E ALA* 1.3 79.3 - - - +
30E ASP* 1.3 59.8 + - - +
32E PHE* 3.6 27.4 - - + -
51E SER* 4.1 6.6 + - - -
68E LYS* 5.9 1.0 - - - -
92E ALA* 3.9 18.8 - - + -
93E SER* 3.1 28.9 - - - +
98E ALA* 3.3 15.7 - - + -
103E TYR 5.6 0.2 - - - -
105E ARG* 3.8 28.3 - - + -
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Residues in contact with ASP 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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28E ALA 4.3 3.1 - - - +
29E PHE* 1.3 74.4 - - - +
31E TYR* 1.3 62.3 + - - +
32E PHE* 3.5 7.8 - - - -
50E LEU* 3.2 19.1 - - - +
51E SER* 2.7 42.0 + - - +
93E SER* 2.9 14.9 + - - +
98E ALA 3.3 4.3 - - - +
99E ASN* 3.3 24.8 + - + -
73H ALA* 6.0 0.3 - - - +
74H GLU* 6.0 0.7 - - - +
77H THR* 3.7 29.6 + - + +
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Residues in contact with TYR 31 (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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30E ASP* 1.3 84.5 + - - +
32E PHE* 1.3 65.1 + - - +
33E PRO* 3.5 38.5 - - + +
45E LEU* 4.6 2.8 - - - +
48E SER* 3.5 28.4 + - - -
49E ILE 3.7 8.5 - - - -
50E LEU* 4.0 19.3 - - + -
92E ALA* 3.1 5.9 - - - +
93E SER* 3.0 40.7 + - - +
104E GLN* 4.3 0.7 - - - -
99F GLY 4.0 3.6 - - - -
100F GLY* 3.3 40.2 - - - +
104F TYR 3.9 7.9 - - - -
105F GLU* 3.6 22.3 + - - +
70H ARG* 3.7 16.6 + - - -
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Residues in contact with PHE 32 (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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24E TYR* 3.1 40.4 - + - -
29E PHE* 3.6 18.8 - - + -
30E ASP* 3.5 26.7 - - - -
31E TYR* 1.3 76.7 - - - +
33E PRO* 1.3 64.6 - - - +
34E TRP* 3.6 12.7 - - - -
48E SER* 3.7 0.8 - - - -
49E ILE* 3.0 35.3 + - + +
51E SER* 4.2 3.6 - - - -
66E PHE* 3.3 29.4 - + - -
73E LEU* 3.6 30.3 - - + -
90E CYS* 5.3 1.1 - - - -
91E ALA 3.2 8.3 - - - +
92E ALA* 3.7 22.0 - - + -
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Residues in contact with PRO 33 (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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31E TYR* 3.5 47.3 - - + +
32E PHE* 1.3 87.8 - - - +
34E TRP* 1.3 61.2 + - - +
35E TYR* 3.7 25.7 - - + +
45E LEU* 3.9 6.7 - - + -
48E SER* 3.5 13.0 - - - -
90E CYS* 4.1 0.2 - - - -
91E ALA* 3.0 38.5 + - + +
92E ALA* 4.3 0.9 - - - +
104E GLN* 3.7 12.3 - - - +
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Residues in contact with TRP 34 (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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5E GLN* 3.8 14.6 - - - -
20E LEU* 3.3 34.1 - - + -
21E ASN 4.3 0.7 - - - -
22E CYS* 3.7 13.5 - - + -
32E PHE 3.6 9.0 - - - -
33E PRO* 1.3 73.6 - - - +
35E TYR* 1.3 55.9 + - - +
45E LEU* 3.5 1.9 - - - +
46E LEU* 2.7 36.7 + - + +
47E ILE* 3.1 21.4 + - + +
64E ILE* 3.5 34.7 - - + +
73E LEU* 4.1 20.7 - - + +
74E SER 4.4 0.2 - - - -
75E LEU* 3.9 39.9 - - + -
88E TYR* 4.4 9.6 - - + -
89E PHE 3.3 16.6 - - - -
90E CYS* 3.5 34.0 - - + -
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Residues in contact with TYR 35 (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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33E PRO* 3.7 34.3 - - + +
34E TRP* 1.3 80.3 - - - +
36E GLN* 1.3 60.6 + - - +
43E PRO* 3.9 13.7 - - + -
44E ALA* 3.0 7.4 - - - +
45E LEU* 3.6 24.5 - - + -
46E LEU* 4.7 0.9 - - - -
87E THR 3.8 0.3 - - - +
88E TYR* 3.3 9.5 - - - +
89E PHE* 2.9 41.7 + - + +
91E ALA* 4.3 0.7 - - + -
104E GLN* 2.9 24.1 + - - -
106E PHE* 3.8 20.9 - + + -
105F GLU* 4.0 3.5 - - - -
106F GLN* 3.1 43.7 + - - +
108F PHE* 3.5 24.0 - + - -
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Residues in contact with GLN 36 (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 TRP 4.3 0.2 + - - -
35E TYR* 1.3 73.4 - - - +
37E GLN* 1.3 63.2 + - - +
38E PHE* 3.0 46.2 - - + -
42E GLY 4.2 0.9 - - - +
43E PRO* 3.5 0.7 - - - +
44E ALA* 2.5 47.4 + - + +
46E LEU* 4.3 23.6 - - + +
62E PHE* 5.0 5.0 - - - -
84E ASP* 5.1 2.6 - - - +
86E ALA* 4.8 0.7 - - + -
88E TYR* 3.1 40.9 + - + -
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Residues in contact with GLN 37 (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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36E GLN* 1.3 76.8 - - - +
38E PHE* 1.3 59.0 + - - +
39E PRO* 4.0 4.4 - - + +
41E GLU 3.3 27.5 + - - +
42E GLY 4.0 4.9 - - - +
43E PRO* 3.8 23.8 - - + +
86E ALA* 2.5 29.4 - - - +
87E THR* 2.9 29.9 + - - +
89E PHE* 3.2 12.4 - - + -
37F GLN* 2.8 44.3 - - - +
91F PHE* 3.4 14.3 - - - -
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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