Contacts of the strand formed by residues 39 - 43 (chain D) in PDB entry 1NR4
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 ILE 39 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D TRP* 3.7 25.4 - - + -
28D TYR 3.6 4.5 - - - +
29D GLN* 3.5 25.4 - - + +
37D ASP 3.7 0.6 + - - -
38D ALA* 1.3 72.6 - - - +
40D VAL* 1.3 60.9 + - - +
41D PHE* 3.8 31.6 - - + -
49D ILE 3.6 0.2 - - - +
51D SER* 2.7 40.5 + - - +
53D PRO* 4.0 24.7 - - + +
58D VAL* 3.8 15.0 - - + -
59D LYS* 6.5 0.2 - - + -
62D VAL* 3.8 16.6 - - + -
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Residues in contact with VAL 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C GLU* 3.9 28.0 - - + +
28C TYR* 4.3 0.4 - - - +
27D TRP* 3.2 4.1 - - - -
28D TYR* 2.8 78.8 + - + +
30D THR* 4.1 14.8 - - + -
38D ALA* 4.2 0.7 - - + +
39D ILE* 1.3 76.1 - - - +
41D PHE* 1.3 64.9 + - - +
42D VAL 3.9 0.3 + - - -
48D ALA* 3.7 25.4 - - + -
49D ILE 3.6 7.6 - - - +
50D CYS* 4.2 5.2 - - + +
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Residues in contact with PHE 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ILE* 4.0 16.8 - - + -
24D LEU* 3.7 26.9 - - + -
26D THR 3.4 2.2 - - - -
27D TRP* 3.9 11.7 - - + -
39D ILE* 3.8 13.9 - - + -
40D VAL* 1.3 72.9 - - - +
42D VAL* 1.3 61.2 + - - +
43D THR* 4.0 1.2 + - + -
47D ARG 3.8 0.2 - - - +
48D ALA* 3.1 6.2 - - - -
49D ILE* 2.9 39.6 + - + +
51D SER* 3.5 26.2 - - - -
58D VAL* 3.7 39.0 - - + -
61D ALA* 3.8 21.1 - - + -
62D VAL* 4.0 17.5 - - + -
65D LEU* 4.0 13.5 - - + -
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Residues in contact with VAL 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C THR* 5.5 4.5 - - + -
27C TRP 5.0 1.8 - - - +
28C TYR* 3.9 40.6 - - + -
42C VAL* 4.7 7.0 - - + -
24D LEU* 4.1 1.6 - - - -
25D LYS* 2.8 40.8 + - - +
26D THR* 2.8 25.9 + - - +
28D TYR* 4.0 24.9 - - + -
41D PHE* 1.3 75.4 - - - +
43D THR* 1.3 69.3 + - - +
46D GLY 4.8 0.7 - - - -
47D ARG 3.4 10.5 - - - +
48D ALA* 4.9 0.9 - - + -
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Residues in contact with THR 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ILE* 5.0 7.6 - - + -
23D LYS* 3.0 22.2 - - + +
24D LEU* 4.5 4.7 - - + +
25D LYS* 3.0 15.9 + - - -
41D PHE 4.8 1.3 - - - +
42D VAL* 1.3 75.9 - - - +
44D VAL* 1.3 63.4 + - - +
45D GLN* 3.4 16.0 + - - +
46D GLY* 3.0 11.8 + - - -
47D ARG* 2.8 41.0 + - + +
49D ILE* 3.9 30.5 - - + -
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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