Contacts of the strand formed by residues 17 - 25 (chain J) in PDB entry 3SHD
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 17 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13J HIS* 3.2 8.5 + - - -
14J ALA 2.9 33.4 + - - +
15J GLU 4.0 7.4 - - - +
16J GLY* 1.3 88.5 - - - +
18J PHE* 1.3 65.0 + - - +
91J ILE* 4.5 7.2 - - + -
106J TRP* 3.9 28.1 + - + -
107J VAL 3.3 10.5 - - - +
108J SER* 3.5 25.8 - - - +
111J GLU* 3.5 21.8 + - - -
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Residues in contact with PHE 18 (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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11J VAL* 3.7 23.8 - - + -
12J VAL 3.6 2.2 - - - +
13J HIS* 3.5 40.2 - + + -
16J GLY 4.6 4.0 - - - -
17J LYS* 1.3 74.9 - - - +
19J LEU* 1.3 66.1 + - - +
20J VAL* 3.3 8.0 + - - +
105J ARG 3.5 0.3 - - - +
106J TRP* 3.6 3.4 - - - -
107J VAL* 2.5 34.5 + - - +
109J ALA* 3.4 45.8 - - + -
112J ILE* 3.9 16.6 - - + -
127J ILE* 3.5 21.3 - - + -
130J TYR* 3.7 25.4 - + - -
131J GLN* 5.2 2.2 - - - -
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Residues in contact with LEU 19 (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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11J VAL* 5.8 0.2 - - - -
12J VAL* 3.1 31.8 + - + +
18J PHE* 1.3 71.8 - - - +
20J VAL* 1.3 65.1 + - - +
33J GLN* 4.6 6.1 - - - +
34J PRO* 3.7 17.0 - - + +
52J LEU* 4.1 8.7 - - + -
56J THR* 3.7 28.3 - - + +
58J ILE* 3.8 25.4 - - + -
94J THR* 4.2 4.0 - - + -
104J CYS* 3.9 23.6 - - + -
105J ARG 3.8 4.3 - - - +
106J TRP* 3.3 47.3 - - + +
112J ILE* 5.7 0.5 - - - +
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Residues in contact with VAL 20 (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 PHE 3.8 7.9 - - - +
19J LEU* 1.3 76.0 - - - +
21J VAL* 1.3 63.8 + - - +
31J TRP* 3.5 32.8 - - + -
32J ASN 2.7 27.4 - - - +
33J GLN* 4.9 1.6 - - + +
34J PRO* 4.6 1.8 - - - -
104J CYS* 3.3 7.8 - - - +
105J ARG* 3.1 55.9 + - + +
107J VAL* 4.1 16.2 - - + -
112J ILE* 4.6 14.4 - - + -
123J VAL* 5.2 3.4 - - + -
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Residues in contact with VAL 21 (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* 1.3 78.4 - - - +
22J GLU* 1.3 58.9 + - - +
23J GLU* 3.8 22.0 - - + +
30J LEU 3.5 1.4 - - - +
31J TRP* 3.3 12.5 - - - -
32J ASN* 2.9 39.5 + - + +
33J GLN 4.0 10.3 - - - +
34J PRO* 4.2 12.8 - - + -
55J GLU* 3.9 25.6 - - - +
56J THR* 3.8 29.2 - - + -
101J ILE* 4.2 10.3 - - + -
103J CYS 3.6 4.0 - - - +
104J CYS* 4.1 3.8 - - - -
105J ARG* 6.0 0.7 - - - -
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Residues in contact with GLU 22 (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 VAL* 1.3 70.9 - - - +
23J GLU* 1.3 72.4 + - - +
29J ALA* 3.9 27.2 - - + +
30J LEU 3.9 0.4 - - - -
31J TRP* 2.8 30.1 + - - -
101J ILE* 3.6 5.4 - - - +
102J ASP* 3.2 35.4 + - + +
103J CYS* 2.8 41.3 + - - +
105J ARG* 3.2 27.9 + - - +
117J ASN* 4.8 0.3 + - - -
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Residues in contact with GLU 23 (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 VAL* 3.8 13.5 - - + +
22J GLU* 1.3 84.6 - - - +
24J THR* 1.3 65.4 + - - +
25J ILE* 3.6 3.6 + - + +
29J ALA* 4.5 1.1 - - - -
30J LEU* 2.8 38.1 + - - +
32J ASN* 4.0 4.2 - - - +
100J ASP 4.1 11.3 - - - +
101J ILE* 3.6 17.3 - - + -
102J ASP* 4.3 1.3 - - - -
119J ARG* 2.7 45.2 + - - -
157J SO4 3.2 27.8 + - - -
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Residues in contact with THR 24 (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 GLU* 1.3 73.3 - - - +
25J ILE* 1.3 62.6 + - - +
27J GLY* 3.7 29.4 - - - +
28J LYS 3.3 16.8 - - - +
29J ALA* 4.2 10.2 - - - +
100J ASP 4.7 3.2 + - - +
102J ASP* 2.7 30.1 + - - -
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Residues in contact with ILE 25 (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 GLU* 3.6 2.7 + - + +
24J THR* 1.3 76.2 - - - +
26J ASN* 1.3 80.7 + - - +
28J LYS* 3.3 11.4 + - - +
30J LEU* 3.6 32.0 - - + +
119J ARG* 4.4 27.8 - - - +
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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