Contacts of the strand formed by residues 35 - 40 (chain F) in PDB entry 4R2G
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 35 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280E ASN* 2.7 47.1 + - - +
281E ALA* 3.8 13.9 - - - +
455E THR* 3.2 25.9 + - - -
456E ARG 3.2 19.5 + - - -
457E ASP* 3.9 13.7 + - - +
27F HIS* 3.8 23.0 + - + +
28F TRP 4.0 4.3 - - - -
29F LYS* 4.2 10.1 - - + -
33F GLN 3.5 0.4 + - - -
34F ILE* 1.3 72.4 - - - +
36F ILE* 1.3 59.9 + - - +
47F GLY* 3.2 31.4 - - - -
48F PRO* 3.5 12.5 - - + +
49F SER 3.8 5.5 + - - -
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Residues in contact with ILE 36 (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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28F TRP* 2.7 23.2 + - + +
29F LYS 3.8 3.1 - - - -
30F ASN* 3.8 35.4 - - + +
34F ILE 4.0 2.9 - - - +
35F LYS* 1.3 71.9 - - - +
37F LEU* 1.3 69.1 + - + +
46F LYS* 3.8 3.6 - - - +
47F GLY* 2.9 20.9 + - - +
49F SER* 3.4 30.9 + - - +
51F LEU* 3.7 29.2 - - + -
52F ASN* 5.5 2.1 + - - -
55F ALA* 4.2 12.5 - - + +
69F LEU* 4.2 17.0 - - + -
82F TYR* 4.1 8.7 - - + -
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Residues in contact with LEU 37 (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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26F PHE* 3.9 21.8 - - + -
27F HIS* 3.8 6.5 - - - -
28F TRP* 2.8 36.0 + - + +
35F LYS* 3.7 1.2 - - - +
36F ILE* 1.3 91.5 - - + +
38F GLY* 1.3 62.3 + - - +
44F LEU* 3.8 17.5 - - + -
45F THR 3.6 13.7 - - - +
46F LYS* 4.7 7.4 - - + -
47F GLY 4.1 2.9 - - - +
55F ALA* 4.1 5.4 - - + -
56F ASP* 3.4 44.2 - - - +
57F SER* 4.0 10.1 - - - +
68F PRO 5.0 0.4 - - - +
69F LEU* 3.9 10.3 - - + -
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Residues in contact with GLY 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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26F PHE* 3.3 18.8 - - - -
27F HIS* 4.0 10.4 + - - -
37F LEU* 1.3 78.8 - - - +
39F ASN* 1.3 59.6 + - - -
44F LEU* 3.3 12.0 - - - +
45F THR* 2.9 40.3 + - - +
47F GLY 5.2 0.2 - - - +
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Residues in contact with ASN 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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23F SER* 3.9 11.7 + - - -
24F ILE 3.0 23.6 + - - -
25F GLN* 2.6 29.4 + - - -
26F PHE* 2.6 54.6 + - + +
27F HIS* 4.8 2.3 + - - -
38F GLY* 1.3 73.2 - - - -
40F GLN* 1.3 55.8 + - - +
41F GLY 3.8 14.6 + - - +
43F PHE 3.2 3.6 - - - -
45F THR* 3.7 0.6 + - - -
62F TRP* 3.4 23.0 - - + -
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Residues in contact with GLN 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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281E ALA 4.7 5.9 + - - -
283E THR* 3.4 24.8 + - - -
455E THR* 5.3 6.5 - - - +
471E GLY* 6.3 0.2 - - - -
472E GLY* 3.5 30.8 - - - +
474E ASP* 3.8 13.7 + - - +
477E ASP* 3.9 12.3 - - - +
25F GLN* 3.6 15.6 + - - +
27F HIS* 4.7 13.7 - - - -
39F ASN* 1.3 73.8 + - - +
41F GLY* 1.3 60.7 + - - +
42F SER 3.2 0.2 + - - -
43F PHE* 2.9 37.0 + - + +
45F THR* 3.6 27.6 - - + +
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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