Contacts of the strand formed by residues 34 - 41 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E ARG* 3.5 16.8 - - - +
32E GLY 4.0 0.8 + - - +
33E PHE* 1.3 71.9 - - - +
35E LEU* 1.3 63.8 + - - +
36E VAL* 3.5 10.7 + - - +
78E TRP* 3.3 4.8 - - - -
79E GLU* 2.8 81.2 + - + +
140E VAL 3.1 17.6 + - - -
141E ASP* 5.0 3.0 + - - +
142E TYR* 3.1 75.6 + - + +
143E LYS* 4.8 0.7 - - - +
144E SER* 3.9 26.0 - - - +
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Residues in contact with LEU 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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16B VAL* 5.8 2.7 - - + -
21B VAL* 5.1 13.5 - - + -
40B PHE* 3.5 27.9 - - + -
74B VAL* 5.2 0.7 - - + -
25E ILE* 5.5 1.3 - - + -
29E GLU* 6.2 0.2 - - + -
34E ARG* 1.3 72.5 - - - +
36E VAL* 1.3 57.9 + - - +
37E ALA 3.4 24.2 - - - +
38E MET* 3.9 29.4 - - + -
76E MET* 4.1 7.0 - - + -
77E VAL 3.6 9.0 - - - +
78E TRP* 3.6 45.3 - - + +
142E TYR* 2.7 39.9 + - - +
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Residues in contact with VAL 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE* 3.7 3.5 - - - -
6E ARG* 3.2 33.7 - - - +
34E ARG* 3.7 17.3 - - - +
35E LEU* 1.3 75.5 - - - +
37E ALA* 1.3 57.2 + - - +
77E VAL* 2.8 22.5 + - + +
78E TRP 4.4 1.3 - - - -
79E GLU* 3.6 23.1 - - + +
139E LEU* 3.7 27.4 - - + -
140E VAL* 2.9 48.7 + - - +
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Residues in contact with ALA 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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40B PHE* 4.1 5.4 - - - -
35E LEU* 3.4 7.5 - - - +
36E VAL* 1.3 79.5 - - - +
38E MET* 1.3 66.4 + - - +
76E MET* 3.1 2.1 - - - -
77E VAL* 2.9 30.8 + - + -
134E PHE* 3.5 27.6 - - + -
138E GLU 3.5 16.6 - - - +
139E LEU* 3.9 14.6 - - + -
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Residues in contact with MET 38 (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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21B VAL* 4.5 9.4 - - + -
38B MET* 3.9 24.7 - - + -
39B LYS* 3.4 2.9 - - - +
40B PHE* 3.2 38.5 + - + +
74B VAL* 3.9 32.5 - - + -
25E ILE* 3.9 22.9 - - + -
35E LEU* 3.9 23.8 - - + -
37E ALA* 1.3 79.6 - - - +
39E LYS* 1.3 67.4 + - - +
74E VAL* 4.1 7.0 - - + -
75E ALA 3.1 12.8 - - - +
76E MET* 3.9 15.5 - - + +
134E PHE* 3.8 3.2 - - - -
138E GLU 5.1 0.4 + - - -
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Residues in contact with LYS 39 (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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38B MET* 3.4 11.2 - - - +
39B LYS* 4.9 5.2 - - + -
38E MET* 1.3 78.7 - - - +
40E PHE* 1.3 62.5 + - - +
41E LEU* 4.1 24.1 - - + +
73E VAL 3.8 0.3 - - - +
74E VAL* 3.6 4.0 - - - +
75E ALA* 2.9 35.1 + - + +
133E TRP* 2.8 31.2 + - - -
134E PHE* 3.7 20.4 - - + +
135E LYS* 4.7 2.4 - - - +
138E GLU* 2.8 36.2 + - - +
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Residues in contact with PHE 40 (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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35B LEU* 3.3 45.1 - - + -
36B VAL 3.7 24.9 - - - -
37B ALA* 4.0 3.6 - - - -
38B MET* 3.1 30.4 + - + +
138B GLU* 4.4 8.5 - - - +
140B VAL* 4.0 16.6 - - + +
142B TYR* 3.8 7.4 - + - -
16E VAL* 4.1 13.0 - - + -
39E LYS* 1.3 74.8 - - - +
41E LEU* 1.3 63.3 + - - +
72E PRO* 3.5 35.2 - - + -
73E VAL 3.4 13.9 - - - -
74E VAL* 3.7 18.8 - - + -
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Residues in contact with LEU 41 (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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140B VAL* 4.0 8.7 - - - -
39E LYS* 4.1 31.9 - - + +
40E PHE* 1.3 80.2 - - - +
42E ARG* 1.3 61.5 + - - +
43E ALA* 3.7 17.9 + - + +
47E HIS* 5.2 4.5 - - + +
72E PRO* 4.0 5.4 - - - -
73E VAL* 2.8 39.6 + - + +
75E ALA* 4.2 6.5 - - + -
133E 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