Contacts of the strand formed by residues 21 - 29 (chain F) in PDB entry 3M4D
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 21 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E LYS 5.6 0.7 - - - -
47E ASN* 3.3 36.8 - - + +
19F THR* 3.9 15.9 - - - +
20F VAL* 1.3 75.9 - - - +
22F THR* 1.3 61.4 + - - +
40F TYR* 4.8 0.4 - - - -
41F SER* 3.4 1.0 - - - -
42F PHE* 2.8 42.2 + - + +
288F LYS 5.4 4.0 + - - +
289F GLU* 3.5 48.1 + - + +
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Residues in contact with THR 22 (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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12E THR 3.9 15.9 - - - +
13E ASP 5.3 2.5 - - - +
14E ILE* 4.1 6.5 - - + +
45E ASP* 5.1 1.9 + - - -
47E ASN* 2.9 10.4 + - - +
48E HIS* 2.6 34.7 + - - +
49E ASN* 2.9 22.2 + - - +
20F VAL* 3.9 13.7 - - + +
21F LYS* 1.3 80.0 - - - +
23F GLY* 1.3 60.5 + - - +
39F PHE* 4.3 4.5 - - - -
40F TYR* 3.1 16.3 + - - -
41F SER* 3.5 24.9 - - - +
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Residues in contact with GLY 23 (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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48E HIS* 3.5 7.9 - - - -
49E ASN* 3.0 18.2 - - - -
22F THR* 1.3 78.5 - - - +
24F ASP* 1.3 60.4 + - - -
39F PHE* 3.3 8.5 - - - -
40F TYR* 2.9 46.6 + - - -
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Residues in contact with ASP 24 (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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14E ILE* 4.1 3.1 - - - +
48E HIS* 2.7 29.0 + - - +
49E ASN* 2.7 13.9 + - - +
50E LYS* 3.0 19.5 + - + +
52E LEU* 4.2 8.1 - - - +
99E SER* 3.3 8.4 + - - +
231E VAL* 5.9 0.2 - - - +
233E THR* 4.1 17.5 - - + +
23F GLY* 1.3 72.6 - - - -
25F LEU* 1.3 74.7 + - - +
26F VAL* 5.3 1.3 - - + -
37F LYS* 2.6 39.8 + - + +
38F VAL 3.3 2.2 - - - -
39F PHE* 3.7 11.9 - - - -
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Residues in contact with LEU 25 (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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49E ASN* 3.5 16.6 - - - +
50E LYS* 4.1 8.1 - - - +
24F ASP* 1.3 92.3 + - - +
26F VAL* 1.3 61.7 + - - +
27F THR* 4.3 1.5 + - - -
36F LYS 3.8 1.0 - - - +
37F LYS* 3.4 2.6 - - - +
38F VAL* 2.9 40.1 + - + +
40F TYR* 4.2 7.6 - - + -
282F TYR* 3.7 37.7 + - + -
291F MET* 3.6 37.9 - - + +
292F THR* 4.1 5.4 - - - +
293F ASN* 4.2 19.1 - - - +
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Residues in contact with VAL 26 (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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50E LYS* 4.4 6.2 - - - +
97E GLN* 3.2 29.9 + - - +
98E ILE 3.7 6.7 - - - +
99E SER* 3.9 24.0 - - - -
162E ASP* 3.8 14.8 - - + -
233E THR* 4.7 5.8 - - - +
24F ASP* 5.3 2.2 - - + -
25F LEU* 1.3 78.6 - - - +
27F THR* 1.3 69.5 + - - +
35F HIS* 3.4 30.7 - - + +
36F LYS 3.4 4.3 - - - +
37F LYS* 3.6 22.2 - - + -
293F ASN* 4.8 3.3 + - - +
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Residues in contact with THR 27 (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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97E GLN* 4.9 1.1 - - - +
26F VAL* 1.3 80.5 + - - +
28F TYR* 1.3 70.2 + - - +
29F ASP* 5.4 1.8 - - + -
34F MET 3.7 1.0 - - - +
35F HIS* 3.9 0.3 - - - -
36F LYS* 2.8 49.1 + - - +
280F GLU* 2.9 40.3 + - - +
282F TYR* 4.3 3.1 + - - -
293F ASN* 3.3 9.7 + - - -
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Residues in contact with TYR 28 (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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160E PRO 3.7 7.6 + - - -
161E THR* 3.4 48.1 - - + +
162E ASP* 3.4 35.4 + - + +
27F THR* 1.3 80.6 - - - +
29F ASP* 1.3 64.4 + - - +
30F LYS* 3.5 47.0 + - + +
33F GLY* 3.8 15.4 - - - -
34F MET 3.3 28.3 - - - -
35F HIS* 3.7 4.7 - - + -
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Residues in contact with ASP 29 (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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27F THR* 4.0 3.0 + - + +
28F TYR* 1.3 71.5 - - - +
30F LYS* 1.3 57.9 + - - +
31F GLU* 3.2 10.0 + - - +
32F ASN* 3.0 38.0 + - - -
33F GLY* 2.8 25.8 + - - -
34F MET* 2.9 26.5 + - + +
36F LYS* 4.7 5.6 - - - +
278F SER* 2.7 29.0 + - - +
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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