Contacts of the helix formed by residues 37 - 46 (chain F) in PDB entry 1NJI
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 ALA 37 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25F MET* 2.9 28.3 - - + +
27F ILE* 3.3 32.3 - - + -
35F ALA 2.6 6.9 + - - +
36F ASN* 1.3 79.5 - - - +
38F GLU* 1.3 64.8 + - - +
40F ILE* 2.8 32.1 - - + +
71F ALA* 6.4 0.7 - - + -
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Residues in contact with GLU 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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25F MET* 4.7 0.4 - - - -
35F ALA 2.9 19.0 + - - +
37F ALA* 1.3 75.4 - - - +
39F ASP* 1.3 57.9 + - - +
41F LEU* 2.7 31.4 + - - +
42F GLY 2.8 11.3 + - - -
48F MET* 5.9 1.2 - - - +
49F PRO* 3.5 36.4 - - + +
51F ARG* 2.6 53.2 + - - -
71F ALA* 3.9 22.6 - - + +
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Residues in contact with ASP 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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36F ASN* 2.6 30.0 - - - +
38F GLU* 1.3 80.0 - - - +
40F ILE* 1.3 64.0 + - + +
42F GLY* 3.2 9.9 + - - -
43F GLU* 3.3 25.2 + - - +
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Residues in contact with ILE 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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25F MET* 3.4 28.7 - - + -
36F ASN 5.5 1.8 - - - +
37F ALA* 2.8 28.9 + - + +
39F ASP* 1.3 75.7 - - + +
41F LEU* 1.3 61.4 + - + +
43F GLU* 3.3 13.8 + - - +
44F ILE* 2.8 33.1 + - - +
128F LEU* 5.3 6.5 - - + -
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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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23F VAL* 3.5 45.3 - - + +
25F MET* 3.2 43.1 - - + -
37F ALA 4.8 0.2 - - - +
38F GLU* 2.7 16.6 + - - +
40F ILE* 1.3 79.1 - - - +
42F GLY* 1.3 54.4 + - - +
44F ILE* 2.9 23.3 - - + +
45F THR* 2.6 27.5 + - - -
49F PRO* 4.4 2.7 - - + -
71F ALA* 4.1 30.5 - - + +
73F VAL* 4.2 12.8 - - + -
128F LEU* 4.6 9.0 - - + -
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Residues in contact with GLY 42 (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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38F GLU 2.8 11.8 + - - -
39F ASP* 3.2 4.7 + - - -
40F ILE 3.2 0.2 - - - -
41F LEU* 1.3 77.6 - - - +
43F GLU* 1.3 55.7 + - - +
46F GLY* 2.7 33.1 + - - -
47F GLN 3.7 18.7 + - - -
48F MET* 5.4 0.2 - - - -
49F PRO* 4.3 7.7 - - - +
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Residues in contact with GLU 43 (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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39F ASP* 3.3 20.5 + - - +
40F ILE* 3.9 15.5 - - - +
41F LEU 3.2 0.4 - - - -
42F GLY* 1.3 76.4 - - - +
44F ILE* 1.3 64.3 + - - +
45F THR 3.2 1.4 + - - -
46F GLY* 4.3 3.0 + - - -
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Residues in contact with ILE 44 (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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23F VAL* 5.7 0.4 - - + -
40F ILE* 2.8 18.6 + - + +
41F LEU* 2.9 39.5 - - + +
43F GLU* 1.3 77.3 - - - +
45F THR* 1.3 65.8 + - + +
83F PHE* 3.2 38.4 - - + -
128F LEU* 4.2 26.5 - - + -
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Residues in contact with THR 45 (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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23F VAL* 3.3 33.9 - - + -
41F LEU 2.6 20.1 + - - +
43F GLU 4.4 1.8 - - - -
44F ILE* 1.3 86.4 - - + +
46F GLY* 1.3 64.6 + - - +
47F GLN 3.5 15.1 + - - -
73F VAL* 3.7 6.2 - - + +
75F LEU* 3.6 36.1 - - + +
79F MET* 4.7 12.8 - - - +
83F PHE* 3.9 12.2 - - + +
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Residues in contact with GLY 46 (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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42F GLY 2.7 21.0 + - - -
43F GLU 4.3 2.2 + - - -
45F THR* 1.3 74.5 + - - +
47F GLN* 1.3 63.2 + - - +
79F MET* 3.9 13.6 - - - +
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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