Contacts of the strand formed by residues 28 - 36 (chain F) in PDB entry 3IT8
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 GLN 28 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F HIS* 3.4 3.7 - - - -
25F TYR 2.8 40.1 + - - +
26F ASN 3.3 0.2 - - - -
27F ASP* 1.3 104.1 - - - +
29F LEU* 1.3 66.0 + - - +
30F VAL* 3.3 2.6 + - - +
50F TRP* 4.2 21.0 - - + +
177F LYS 4.7 2.4 + - - -
178F ILE* 3.6 37.7 - - + +
179F PRO* 4.0 15.2 - - - +
208F TYR* 4.0 4.2 + - - +
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Residues in contact with LEU 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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22F TYR* 3.9 19.3 - - + -
23F ASP 3.7 4.0 - - - +
24F HIS* 3.4 30.2 + - + +
27F ASP 3.8 2.6 + - - -
28F GLN* 1.3 73.4 - - - +
30F VAL* 1.3 63.9 + - - +
31F THR 3.6 23.6 - - - +
32F LYS* 4.6 7.4 - - + -
46F PHE* 3.6 44.5 - - + -
48F ALA* 3.6 15.1 - - - +
50F TRP* 5.0 0.7 + - - -
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Residues in contact with VAL 30 (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 ASP* 2.7 26.4 + - - +
25F TYR* 3.8 23.3 - - + +
28F GLN 3.5 13.7 - - - +
29F LEU* 1.3 74.8 - - - +
31F THR* 1.3 67.8 + - - +
46F PHE* 4.3 2.5 - - - -
47F ARG* 3.3 4.0 - - - -
48F ALA* 2.9 27.1 + - + -
50F TRP* 3.9 15.7 - - + -
51F PHE* 3.5 42.2 - - + -
170F TYR* 4.0 11.2 - - + -
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Residues in contact with THR 31 (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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21F PHE* 3.6 3.1 - - + +
22F TYR* 3.4 5.5 - - - -
23F ASP* 2.9 31.9 + - - -
29F LEU* 3.6 7.2 - - - +
30F VAL* 1.3 86.9 + - - +
32F LYS* 1.3 64.4 + - - +
33F ILE* 3.9 20.9 - - + -
44F VAL* 4.5 2.0 - - + -
46F PHE* 3.3 9.4 - - - +
47F ARG* 2.3 41.0 + - - +
64F TYR* 3.0 29.4 + - + -
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Residues in contact with LYS 32 (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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20F VAL* 4.5 13.2 - - + -
21F PHE 3.3 4.9 - - - +
22F TYR* 3.6 40.9 + - + -
29F LEU* 4.6 6.5 - - + -
31F THR* 1.3 74.8 - - - +
33F ILE* 1.3 70.8 + - - +
34F SER* 5.0 0.7 - - - -
44F VAL* 3.5 1.9 - - - +
45F ASN* 2.8 49.9 + - + +
46F PHE* 3.1 27.1 + - + +
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Residues in contact with ILE 33 (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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20F VAL* 3.1 5.7 - - - +
21F PHE* 2.7 48.1 + - + +
31F THR* 3.9 12.1 - - + -
32F LYS* 1.3 82.2 - - - +
34F SER* 1.3 64.6 + - - +
42F GLY* 4.2 1.6 - - - -
43F ASN 3.2 17.9 - - - +
44F VAL* 3.9 16.2 - - + -
45F ASN* 3.7 2.2 - - - +
63F ASP* 3.6 38.4 - - + +
64F TYR* 3.8 17.9 - - + -
66F PHE* 3.6 31.8 - - + -
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Residues in contact with SER 34 (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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19F GLY 3.1 11.2 - - - -
20F VAL* 4.0 11.2 - - - -
32F LYS* 5.0 1.6 - - - -
33F ILE* 1.3 76.1 - - - +
35F TYR* 1.3 65.8 + - - +
36F ASN 3.4 0.7 + - - -
42F GLY* 3.3 0.2 - - - -
43F ASN* 2.9 29.0 + - - +
45F ASN* 2.4 35.5 + - - -
66F PHE* 4.1 5.4 - - - -
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Residues in contact with TYR 35 (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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18F ASP* 4.7 3.1 - - - +
19F GLY 2.9 17.6 + - - +
34F SER* 1.3 71.6 - - - +
36F ASN* 1.3 66.6 + - - +
37F HIS* 3.5 41.8 + + - +
40F ARG* 3.1 55.1 + - - +
41F HIS* 3.5 13.2 - - - -
42F GLY 4.3 0.2 - - - -
66F PHE* 3.8 9.9 - + + -
67F ASN* 5.4 1.1 - - - -
70F TYR* 3.4 66.8 - + + -
74F LYS* 6.0 0.4 + - - -
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Residues in contact with ASN 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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34F SER 3.4 2.0 + - - -
35F TYR* 1.3 72.3 - - - +
37F HIS* 1.3 54.6 + - - +
38F GLU* 2.8 16.4 + - - +
39F THR* 2.6 41.9 + - - -
40F ARG* 2.6 37.1 + - - -
41F HIS 2.9 16.4 + - - +
43F ASN* 2.9 33.5 - - - +
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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