Contacts of the strand formed by residues 17 - 25 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13E HIS* 3.1 30.7 + - - -
14E ALA 3.1 9.7 + - - +
15E GLU 2.9 9.6 + - - +
16E GLY* 1.3 86.1 + - - +
18E PHE* 1.3 66.2 + - - +
91E ILE* 4.3 9.6 - - + -
106E TRP* 3.4 39.7 - - + +
107E VAL* 3.2 18.4 - - - +
108E SER* 4.2 9.5 - - - +
111E GLU* 5.4 2.9 - - - -
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Residues in contact with PHE 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E VAL* 3.8 18.8 - - + -
12E VAL 3.2 13.0 - - - +
13E HIS* 3.3 35.4 - + + -
16E GLY 4.8 2.9 - - - -
17E LYS* 1.3 78.6 - - - +
19E LEU* 1.3 64.7 + - - +
20E VAL* 3.3 2.3 + - - +
105E ARG 3.3 5.0 - - - +
106E TRP* 3.5 2.9 - - - -
107E VAL* 2.6 41.6 + - - +
109E ALA* 3.7 35.9 - - + -
112E ILE* 3.7 21.0 - - + +
127E ILE* 4.8 13.5 - - + -
130E TYR* 3.6 33.0 - + + -
131E GLN* 5.3 2.2 - - + -
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Residues in contact with LEU 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E CYS 4.9 1.6 - - - +
12E VAL* 2.8 28.8 + - + +
18E PHE* 1.3 70.7 - - - +
20E VAL* 1.3 65.0 - - - +
32E ASN 4.4 0.2 - - - +
33E GLN* 4.5 3.6 + - - +
34E PRO* 3.2 23.0 - - + +
52E LEU* 4.3 9.9 - - + -
56E THR* 3.7 25.6 - - + +
58E ILE* 3.5 29.8 - - + -
94E THR* 4.3 2.2 - - + -
104E CYS* 3.9 24.0 - - + -
105E ARG 3.8 3.1 - - - +
106E TRP* 3.4 41.8 - - + +
112E ILE* 5.9 0.2 - - - -
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Residues in contact with VAL 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E PHE 3.3 4.5 + - - +
19E LEU* 1.3 77.3 - - - +
21E VAL* 1.3 64.3 + - - +
31E TRP* 3.8 47.6 - - + -
32E ASN 3.1 22.9 - - - +
33E GLN* 5.1 2.2 - - - +
104E CYS* 3.5 8.0 - - - +
105E ARG* 3.1 50.5 + - + +
107E VAL* 4.9 3.6 - - + -
112E ILE* 4.4 20.2 - - + -
123E VAL* 5.0 5.8 - - + -
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Residues in contact with VAL 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E VAL* 1.3 81.3 - - - +
22E GLU* 1.3 59.0 + - - +
23E GLU* 4.4 12.5 - - - +
30E LEU 3.3 5.0 - - - +
31E TRP* 3.3 2.5 - - - -
32E ASN* 3.0 42.7 + - + +
33E GLN 3.9 12.3 - - - +
34E PRO* 3.9 14.8 - - + -
55E GLU* 3.9 22.2 - - + +
56E THR* 3.7 28.9 - - + -
101E ILE* 4.3 14.4 - - + -
103E CYS 3.8 3.6 - - - -
104E CYS* 4.4 2.0 - - - -
157E SO4 4.5 0.9 - - - +
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Residues in contact with GLU 22 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20E VAL* 5.0 0.2 - - - +
21E VAL* 1.3 71.6 - - - +
23E GLU* 1.3 62.5 + - - +
29E ALA* 3.7 28.2 - - + +
30E LEU 3.2 2.7 - - - -
31E TRP* 2.8 32.8 + - + +
101E ILE* 3.9 5.0 - - - +
102E ASP* 3.1 30.6 + - + +
103E CYS* 3.0 37.6 + - - +
104E CYS* 4.8 0.4 - - - +
105E ARG* 3.4 31.8 + - + +
117E ASN* 5.7 0.2 - - - -
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Residues in contact with GLU 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E VAL* 4.4 8.6 - - - +
22E GLU* 1.3 76.1 - - - +
24E THR* 1.3 60.7 + - - +
25E ILE* 2.8 27.0 + - + +
29E ALA* 4.2 0.4 - - - -
30E LEU* 2.7 37.7 + - + +
32E ASN* 4.6 2.7 - - + +
100E ASP* 3.8 24.6 - - + +
101E ILE* 3.6 19.1 - - + +
102E ASP* 3.9 3.1 - - - -
119E ARG* 3.0 28.6 + - - +
157E SO4 2.8 29.8 + - - -
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Residues in contact with THR 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E GLU* 1.3 70.0 - - - +
25E ILE* 1.3 63.4 + - - +
26E ASN* 3.5 4.7 + - - +
27E GLY 4.2 20.6 - - - +
28E LYS 3.3 12.8 + - - +
29E ALA* 4.3 7.5 + - - +
100E ASP 4.6 1.6 + - - -
102E ASP* 2.6 30.2 + - - -
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Residues in contact with ILE 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E GLU* 2.8 40.4 + - + +
24E THR* 1.3 76.8 - - - +
26E ASN* 1.3 83.4 + - - +
27E GLY 3.3 1.2 + - - -
28E LYS* 3.0 14.9 + - - +
30E LEU* 3.8 24.0 - - + +
119E ARG* 3.9 29.2 - - - +
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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