Contacts of the strand formed by residues 28 - 36 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J HIS* 3.4 3.8 - - - -
25J TYR* 2.7 39.6 + - + +
26J ASN 3.2 0.4 - - - -
27J ASP* 1.3 104.1 - - - +
29J LEU* 1.3 65.7 + - - +
30J VAL* 3.3 2.8 + - - +
50J TRP* 4.2 21.7 - - + +
177J LYS 4.8 2.4 + - - -
178J ILE* 3.6 37.6 - - + +
179J PRO* 4.1 15.3 - - - +
208J TYR* 4.1 3.8 + - - +
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Residues in contact with LEU 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J TYR* 3.9 18.6 - - + -
23J ASP 3.7 6.3 - - - +
24J HIS* 3.5 28.0 + - + +
27J ASP 3.8 2.6 + - - -
28J GLN* 1.3 73.2 - - - +
30J VAL* 1.3 61.5 + - - +
31J THR 3.5 24.2 - - - +
32J LYS* 4.6 7.9 - - + -
46J PHE* 3.6 49.7 - - + -
48J ALA* 3.6 9.2 - - - +
50J TRP* 5.1 0.7 + - - -
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Residues in contact with VAL 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J ASP* 2.7 27.3 + - - +
25J TYR* 3.8 23.3 - - + +
28J GLN 3.6 14.1 - - - +
29J LEU* 1.3 75.3 - - - +
31J THR* 1.3 66.9 + - - +
46J PHE* 4.3 2.0 - - - -
47J ARG* 3.3 5.0 - - - -
48J ALA* 2.9 27.9 + - + -
50J TRP* 3.9 15.9 - - + -
51J PHE* 3.5 41.1 - - + -
170J TYR* 4.0 11.0 - - + -
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Residues in contact with THR 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J PHE* 3.7 3.5 - - + +
22J TYR* 3.5 5.0 - - - -
23J ASP* 3.0 31.7 + - - -
29J LEU* 3.5 8.6 - - - +
30J VAL* 1.3 84.1 + - - +
32J LYS* 1.3 64.5 + - - +
33J ILE* 3.8 21.5 - - + -
44J VAL* 4.4 2.0 - - + -
46J PHE 3.3 9.0 - - - +
47J ARG* 2.3 41.3 + - - +
64J TYR* 2.9 29.9 + - + -
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Residues in contact with LYS 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J VAL* 4.5 12.8 - - - +
21J PHE 3.3 4.7 - - - +
22J TYR* 3.6 42.8 + - + -
29J LEU* 4.6 7.0 - - + -
31J THR* 1.3 75.9 - - - +
33J ILE* 1.3 71.2 + - - +
34J SER* 5.0 1.3 - - - -
44J VAL* 3.5 1.6 - - - -
45J ASN* 2.8 50.3 + - + +
46J PHE* 3.0 25.0 + - + +
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Residues in contact with ILE 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J VAL* 3.1 5.7 - - - +
21J PHE* 2.8 44.2 + - + +
31J THR* 3.8 12.3 - - + -
32J LYS* 1.3 80.9 - - - +
34J SER* 1.3 64.3 + - - +
42J GLY* 4.2 1.6 - - - -
43J ASN 3.2 21.1 - - - +
44J VAL* 3.9 15.7 - - + -
45J ASN* 3.7 1.8 - - - +
63J ASP* 3.6 38.4 - - + +
64J TYR* 3.8 18.2 - - + -
66J PHE* 3.6 30.2 - - + -
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Residues in contact with SER 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J GLY 3.1 11.0 - - - -
20J VAL* 4.0 11.2 - - - -
32J LYS* 5.0 2.0 - - - -
33J ILE* 1.3 75.2 - - - +
35J TYR* 1.3 65.4 + - - +
36J ASN 3.4 1.2 + - - -
42J GLY* 3.3 0.2 - - - -
43J ASN* 2.9 30.1 + - - +
45J ASN* 2.4 34.1 + - - -
66J PHE* 4.1 4.5 - - - -
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Residues in contact with TYR 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J ASP* 4.7 3.1 - - - +
19J GLY 2.9 18.0 + - - +
34J SER* 1.3 72.8 - - - +
36J ASN* 1.3 67.2 + - - +
37J HIS* 3.5 40.2 + + - -
40J ARG* 3.2 54.9 + - - +
41J HIS* 3.5 13.7 - - - -
66J PHE* 3.8 9.7 - + + -
67J ASN* 5.4 1.8 - - - -
70J TYR* 3.4 65.7 - + + -
74J LYS* 6.0 0.2 + - - -
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Residues in contact with ASN 36 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34J SER 3.4 2.4 + - - +
35J TYR* 1.3 71.9 - - - +
37J HIS* 1.3 52.9 + - - +
38J GLU* 2.8 15.6 + - - +
39J THR* 2.6 42.3 + - - -
40J ARG* 2.6 36.7 + - - -
41J HIS 2.9 16.0 + - - +
43J ASN* 2.9 33.1 - - - +
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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