Contacts of the strand formed by residues 37 - 46 (chain F) in PDB entry 6NQN
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 LYS 37 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLN* 4.2 20.8 + - - +
31F GLY* 3.2 1.8 - - - -
32F LYS* 2.8 38.2 + - + +
35F GLU* 3.4 38.4 + - + +
36F GLY* 1.3 83.3 - - - +
38F GLN* 1.3 61.2 + - - +
68F PHE* 3.7 4.5 - - - -
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Residues in contact with GLN 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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10F ILE* 3.3 25.5 - - + +
30F LEU 3.4 13.2 - - - +
31F GLY* 3.8 2.9 - - - -
37F LYS* 1.3 77.8 - - - +
39F SER* 1.3 62.4 + - - +
40F MET* 3.7 15.8 - - - +
63F KZ4 3.8 34.9 - - + +
65F ASN* 4.2 6.8 + - - +
68F PHE* 3.6 37.4 - - + +
116F TYR* 4.2 4.2 + - - -
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Residues in contact with SER 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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10F ILE* 4.7 1.7 - - - +
29F GLY* 3.2 1.4 - - - -
30F LEU* 2.9 49.5 + - - +
38F GLN* 1.3 78.1 - - - +
40F MET* 1.3 65.9 + - - +
63F KZ4 6.1 1.1 - - - -
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Residues in contact with MET 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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10F ILE* 3.9 15.0 - - + -
12F LEU* 3.8 20.6 - - + -
27F GLY* 5.6 0.7 - - - -
28F VAL 3.3 15.0 - - - +
29F GLY* 3.7 5.4 - - - -
30F LEU* 6.0 0.2 - - - -
38F GLN* 3.7 22.4 - - - +
39F SER* 1.3 79.9 - - - +
41F ASP* 1.3 69.1 + - - +
42F LEU* 4.1 20.4 + - + +
61F PHE* 3.5 43.5 - - - +
63F KZ4 3.7 11.9 - - - -
116F TYR* 4.5 0.4 - - + -
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Residues in contact with ASP 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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202A LYS* 4.6 16.8 + - - -
26F GLU 4.0 0.2 - - - +
27F GLY* 3.2 3.1 - - - -
28F VAL* 2.8 44.2 + - + +
40F MET* 1.3 78.7 - - - +
42F LEU* 1.3 62.1 + - - +
43F LYS* 4.3 6.6 + - + +
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Residues in contact with LEU 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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12F LEU* 3.9 12.3 - - + -
25F ILE* 3.4 10.3 - - + -
26F GLU 3.4 3.8 - - - +
27F GLY* 4.1 2.0 - - - -
40F MET* 4.1 23.7 + - + +
41F ASP* 1.3 75.6 - - - +
43F LYS* 1.3 72.4 + - - +
54F TYR* 3.5 21.9 + - + +
58F THR* 6.1 0.9 - - + -
61F PHE* 3.3 63.3 - - + -
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Residues in contact with LYS 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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25F ILE* 4.0 4.0 - - - -
26F GLU 2.7 36.0 + - - +
41F ASP* 5.3 6.7 - - + +
42F LEU* 1.3 83.1 - - - +
44F VAL* 1.3 66.0 + - - +
45F LYS* 3.4 31.6 + - - +
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Residues in contact with VAL 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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24F ALA 3.6 6.7 - - - +
25F ILE* 3.6 20.0 - - + -
43F LYS* 1.3 70.8 - - - +
45F LYS* 1.3 61.8 + - - +
46F GLU 3.3 25.1 - - - +
48F GLY* 3.9 22.4 - - - +
50F LEU* 3.7 29.6 - - + -
54F TYR* 4.3 10.1 - - + +
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Residues in contact with LYS 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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13F ARG* 4.6 8.7 - - - +
24F ALA 2.8 10.8 + - - +
26F GLU* 3.4 47.7 + - + +
43F LYS* 3.5 40.2 - - + +
44F VAL* 1.3 76.5 - - - +
46F GLU* 1.3 72.2 + - + +
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Residues in contact with GLU 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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13F ARG* 3.0 23.5 + - - -
15F GLU* 5.9 0.2 - - - +
23F PHE* 3.3 6.6 - - - +
24F ALA* 3.0 44.3 + - + +
44F VAL* 3.3 10.8 - - - +
45F LYS* 1.3 85.1 - - + +
47F GLY* 1.3 63.9 + - - +
48F GLY 3.3 3.4 - - - -
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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