Contacts of the strand formed by residues 41 - 47 (chain B) in PDB entry 1UNN
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 THR 41 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B GLN 3.4 2.9 - - - +
37B VAL* 3.5 1.7 - - - +
38B ALA* 2.9 33.3 + - - -
39B ASP* 3.3 9.3 + - - -
40B GLY* 1.4 80.8 + - - +
42B LEU* 1.3 75.8 + - - +
43B SER* 3.9 9.3 + - - +
56B ARG* 3.8 28.9 - - + +
57B VAL 3.5 8.5 - - - +
58B ALA* 5.0 2.5 - - - -
59B LEU* 3.9 5.6 - - - +
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B PHE* 3.6 33.7 - - + -
10B LEU* 3.6 31.2 - - + -
35B LEU* 4.2 2.7 - - + -
36B GLN 3.3 20.2 - - - +
37B VAL* 3.8 15.7 - - + -
41B THR* 1.3 74.7 - - - +
43B SER* 1.3 69.8 + - - +
44B LEU* 3.9 20.8 - - + +
55B ALA 3.7 0.5 - - - +
56B ARG* 3.4 1.4 - - - -
57B VAL* 2.7 47.9 + - + +
59B LEU* 3.8 19.1 - - + +
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Residues in contact with SER 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU 3.4 1.3 - - - +
35B LEU* 3.2 5.2 - - - -
36B GLN* 2.8 54.2 + - - +
41B THR* 3.9 4.9 + - - +
42B LEU* 1.3 76.5 - - - +
44B LEU* 1.3 64.4 + - - +
45B THR* 5.0 0.2 - - - -
54B VAL* 4.5 4.0 - - - -
55B ALA 3.2 7.0 - - - -
56B ARG* 2.5 41.2 + - - -
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 4.8 4.5 - - + -
13B PRO* 4.4 10.8 - - + +
14B LEU* 4.6 18.8 - - + -
17B VAL* 3.3 24.8 - - + +
33B LEU* 5.2 1.6 - - + -
34B LEU 3.1 3.6 - - - -
35B LEU* 3.8 28.3 - - + -
42B LEU* 3.9 21.3 - - + +
43B SER* 1.3 82.4 - - - +
45B THR* 1.4 61.7 + - - +
54B VAL* 3.1 3.8 - - - -
55B ALA* 2.8 38.0 + - + +
57B VAL* 3.7 30.5 - - + -
75B PHE* 5.4 1.3 - - + -
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Residues in contact with THR 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 4.8 0.2 - - - +
33B LEU* 3.2 9.8 - - - +
34B LEU* 2.8 46.7 + - + +
36B GLN* 4.3 7.6 + - - -
44B LEU* 1.4 74.0 + - - +
46B GLY* 1.4 64.3 + - - +
52B GLU* 3.6 24.9 - - + +
53B MET 3.2 11.0 - - - +
54B VAL* 3.4 22.5 - - + +
116B PHE* 3.5 25.5 - - + -
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Residues in contact with GLY 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 3.2 25.2 + - - +
20B PRO* 3.8 3.3 - - - +
21B LEU* 3.7 12.3 - - - -
32B ASN 4.6 0.7 - - - -
33B LEU* 3.8 5.6 - - - -
45B THR* 1.4 73.1 - - - +
47B THR* 1.4 60.9 + - - -
52B GLU* 3.1 6.1 - - - +
53B MET 2.8 32.8 + - - -
116B PHE* 4.4 1.6 - - - -
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Residues in contact with THR 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PRO* 4.2 5.6 - - - +
21B LEU* 3.5 8.2 - - - +
30B LEU* 3.6 30.5 - - + +
32B ASN 5.0 0.8 + - - -
46B GLY* 1.4 76.6 - - - -
48B ASP* 1.4 59.7 + - - +
49B LEU* 3.0 15.9 + - - +
51B MET 2.8 19.6 + - - -
52B GLU* 3.7 11.0 - - - +
116B PHE* 3.7 26.9 - - + -
117B PRO* 3.9 25.8 - - + -
119B LEU* 3.8 8.1 - - - +
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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