Contacts of the strand formed by residues 42 - 50 (chain E) in PDB entry 3UTS
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 GLY 42 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88D LEU* 5.9 1.8 - - - -
102D GLY 4.9 9.6 - - - -
103D SER* 4.9 9.6 + - - -
36E ARG 3.4 9.4 - - - +
37E GLN* 3.5 22.6 - - - -
38E THR* 3.0 11.9 + - - -
39E MET 4.3 4.0 + - - -
41E ARG* 1.3 81.2 - - - +
43E LEU* 1.3 63.6 + - - -
44E GLU* 3.6 5.0 + - - +
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Residues in contact with LEU 43 (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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44D PRO* 4.0 26.5 - - + -
88D LEU* 4.4 13.4 - - + +
101D PHE* 3.5 66.0 + - + +
102D GLY 5.0 0.4 + - - -
35E TYR* 3.5 32.5 - - + -
36E ARG 3.4 15.5 - - - +
37E GLN* 4.0 21.9 - - + +
41E ARG 4.9 1.0 - - - +
42E GLY* 1.3 71.6 - - - -
44E GLU* 1.3 61.6 + - - +
91E PHE* 4.2 10.1 - - + -
107E PHE* 5.0 5.8 - - + -
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Residues in contact with GLU 44 (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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35E TYR* 3.1 7.7 - - - -
36E ARG* 2.8 74.2 + - + +
41E ARG* 2.8 46.2 + - + +
42E GLY 4.2 5.8 - - - +
43E LEU* 1.3 79.8 - - - +
45E LEU* 1.3 64.3 + - - +
46E LEU* 3.5 4.6 + - + +
59E GLY 5.4 2.7 - - - +
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Residues in contact with LEU 45 (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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98D LYS* 3.8 49.2 - - + +
99D LEU 4.5 10.7 + - - +
101D PHE* 5.5 0.4 - - - -
33E PHE* 4.0 12.1 - - + -
34E TRP 3.3 17.9 - - - +
35E TYR* 3.5 34.8 - - + -
43E LEU 4.3 0.2 - - - -
44E GLU* 1.3 73.6 - - - +
46E LEU* 1.3 63.9 + - - +
47E ILE* 3.5 21.3 - - - +
48E TYR* 4.0 19.3 - - + -
56E ASP* 4.8 3.4 - - - +
59E GLY* 3.4 19.2 - - - +
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Residues in contact with LEU 46 (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* 2.6 24.6 + - + +
35E TYR 4.8 0.4 - - - -
36E ARG* 4.0 38.8 - - + +
44E GLU* 3.5 4.2 + - + +
45E LEU* 1.3 76.9 - - - +
47E ILE* 1.3 61.9 + - + +
56E ASP 4.2 0.2 - - - +
57E ASP* 3.8 3.1 - - - -
59E GLY* 3.5 22.6 + - - +
60E MET* 3.2 51.8 + - + +
61E PRO* 4.4 3.1 - - + -
65E PHE* 4.6 4.9 - - + -
77E LEU* 4.2 14.1 - - + -
90E TYR* 4.1 30.7 - - + -
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Residues in contact with ILE 47 (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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32E LEU 4.1 0.2 - - - +
33E PHE* 3.5 0.3 - - - -
34E TRP* 2.9 55.7 + - + -
45E LEU* 3.5 8.7 - - - +
46E LEU* 1.3 81.7 - - + +
48E TYR* 1.3 80.2 + - - +
49E PHE* 3.8 23.6 - - + -
54E PRO* 4.0 15.7 - - + -
56E ASP 3.2 17.3 - - - +
57E ASP* 3.9 16.8 - - + -
60E MET* 4.3 10.5 - - + -
67E ALA* 4.0 21.1 - - + +
77E LEU* 5.7 0.4 - - + -
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Residues in contact with TYR 48 (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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65A ARG* 5.7 1.0 - - - -
5C PRO* 4.9 2.4 - - - +
96D SER* 3.5 24.8 + - - -
97D TYR* 3.4 45.0 + + + -
98D LYS 4.0 1.3 - - - -
31E TYR* 4.3 8.3 - + - -
32E LEU 3.1 6.7 - - - +
33E PHE* 3.3 36.1 - + + -
45E LEU* 4.0 15.5 - - + -
47E ILE* 1.3 80.8 - - - +
49E PHE* 1.3 74.5 + - - +
54E PRO* 3.8 1.9 - - - +
55E ILE* 2.9 56.1 + - + +
56E ASP* 3.1 28.0 + - + +
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Residues in contact with PHE 49 (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 4.6 0.2 - - - -
31E TYR* 3.2 5.9 - - - -
32E LEU* 2.7 39.2 + - + +
34E TRP* 4.2 3.6 - + - -
47E ILE* 3.8 32.1 - - + -
48E TYR* 1.3 87.2 - - - +
50E ASN* 1.3 61.4 + - - +
52E ASN* 3.5 19.7 - - - +
53E VAL 3.4 4.9 - - - +
54E PRO* 3.4 38.4 - - + -
67E ALA* 4.0 2.9 - - + -
68E LYS* 3.6 33.9 - - - -
69E MET* 4.0 28.5 - - + -
75E SER* 3.9 15.3 - - - -
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Residues in contact with ASN 50 (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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72A GLN* 5.8 6.3 - - - +
6C ASP* 4.1 7.7 + - - +
30E ASP* 3.1 17.4 - - - +
31E TYR* 3.5 37.7 + - + -
49E PHE* 1.3 75.9 - - - +
51E ASN* 1.3 85.2 + - - +
52E ASN 3.0 0.9 + - - -
53E VAL* 3.0 26.0 + - - +
55E ILE* 3.6 21.0 - - + +
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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