Contacts of the strand formed by residues 34 - 41 (chain F) in PDB entry 1NUE
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 ARG 34 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F ARG* 3.2 4.9 - - - +
32F GLY 3.9 1.5 + - - +
33F PHE* 1.3 73.2 - - - +
35F LEU* 1.3 61.5 + - - +
36F VAL* 3.4 12.8 + - - +
78F TRP* 3.4 5.6 - - - -
79F GLU* 2.8 83.3 + - + +
140F VAL 2.7 24.9 + - - -
141F ASP* 3.1 21.6 + - - +
142F TYR* 3.3 65.0 + - + +
143F LYS* 4.9 0.2 - - - +
144F SER* 3.8 25.1 - - - +
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Residues in contact with LEU 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C VAL* 5.8 2.2 - - + -
21C VAL* 5.0 14.6 - - + -
40C PHE* 3.4 27.2 - - + -
74C VAL* 5.1 0.4 - - + -
25F ILE* 5.4 1.6 - - + -
33F PHE 4.0 0.2 + - - -
34F ARG* 1.3 71.6 - - - +
36F VAL* 1.3 58.1 + - - +
37F ALA 3.4 25.1 - - - +
38F MET* 3.9 29.2 - - + -
76F MET* 4.1 7.9 - - + -
77F VAL 3.7 8.1 - - - +
78F TRP* 3.6 45.0 - - + +
142F TYR* 2.6 38.7 + - - +
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Residues in contact with VAL 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C PHE* 3.6 11.3 - - - -
6F ARG* 3.9 22.2 - - - +
34F ARG* 3.5 24.9 - - - +
35F LEU* 1.3 77.7 - - - +
37F ALA* 1.3 57.7 + - - +
77F VAL* 2.8 21.7 + - + +
78F TRP 4.4 0.4 - - - -
79F GLU* 3.6 26.2 - - + +
139F LEU* 3.8 29.2 - - + -
140F VAL* 2.9 42.0 + - - +
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Residues in contact with ALA 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C PHE* 4.0 6.1 - - - -
35F LEU* 3.4 6.5 - - - +
36F VAL* 1.3 81.3 - - - +
38F MET* 1.3 67.1 + - - +
76F MET* 3.2 2.3 - - - -
77F VAL* 3.0 28.9 + - + -
134F PHE* 3.7 17.0 - - + -
138F GLU 3.4 20.0 - - - +
139F LEU* 3.5 22.4 - - + -
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Residues in contact with MET 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C VAL* 4.6 8.3 - - + -
38C MET* 3.8 24.9 - - + -
39C LYS* 3.3 3.0 - - - +
40C PHE* 3.0 40.1 + - + +
74C VAL* 3.8 32.8 - - + -
25F ILE* 3.8 24.9 - - + -
35F LEU* 3.9 23.8 - - + -
37F ALA* 1.3 78.1 - - - +
39F LYS* 1.3 66.7 + - - +
74F VAL* 4.1 7.6 - - + -
75F ALA 3.1 7.2 - - - +
76F MET* 3.8 22.2 - - + +
134F PHE* 3.8 3.8 - - - -
138F GLU 5.1 0.6 + - - -
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Residues in contact with LYS 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C MET* 3.3 11.2 - - - +
39C LYS* 4.8 4.9 - - + -
38F MET* 1.3 79.3 - - - +
40F PHE* 1.3 62.2 + - - +
41F LEU* 4.0 26.2 - - + +
73F VAL 3.7 0.3 - - - +
74F VAL* 3.6 3.5 - - - +
75F ALA* 2.8 38.1 + - + +
133F TRP* 2.8 31.6 + - - -
134F PHE* 3.7 21.1 - - + -
135F LYS* 5.5 2.8 - - - +
138F GLU* 2.9 31.3 + - - +
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Residues in contact with PHE 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LEU* 3.4 44.4 - - + -
36C VAL 3.8 24.5 - - - -
37C ALA* 4.0 3.8 - - - -
38C MET* 3.0 30.8 + - + +
138C GLU* 4.3 8.5 - - - +
140C VAL* 4.0 15.5 - - + +
142C TYR* 3.9 7.4 - + - -
16F VAL* 4.0 15.9 - - + -
39F LYS* 1.3 75.8 - - - +
41F LEU* 1.3 62.6 + - - +
72F PRO* 3.3 36.3 - - + -
73F VAL 3.3 12.1 - - - -
74F VAL* 3.7 18.4 - - + -
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Residues in contact with LEU 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C VAL* 3.9 9.0 - - - -
39F LYS* 4.0 32.8 - - + +
40F PHE* 1.3 80.8 - - - +
42F ARG* 1.3 61.0 + - - +
43F ALA* 3.8 17.4 + - + +
47F HIS* 5.6 3.6 - - + +
72F PRO* 4.0 6.1 - - - -
73F VAL* 2.7 46.8 + - + +
75F ALA* 4.2 5.4 - - + -
133F TRP* 4.1 32.8 - - + -
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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