Contacts of the strand formed by residues 17 - 24 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13F HIS* 3.1 19.6 + - - -
14F ALA 3.0 22.2 + - - +
15F GLU 3.0 6.5 + - - +
16F GLY* 1.3 83.7 - - - +
18F PHE* 1.3 66.0 + - - +
91F ILE* 4.8 6.1 - - + -
106F TRP* 3.3 36.3 + - + +
107F VAL 3.2 14.6 - - - +
108F SER* 4.1 8.3 - - - +
111F GLU* 3.4 26.1 + - - -
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Residues in contact with PHE 18 (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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11F VAL* 3.6 32.8 - - + -
12F VAL 3.6 7.9 - - - -
13F HIS* 3.4 29.4 - + + -
16F GLY 4.4 4.3 - - - -
17F LYS* 1.3 78.1 - - - +
19F LEU* 1.3 66.8 + - - +
20F VAL* 3.1 7.3 + - - +
105F ARG 3.6 0.3 - - - +
106F TRP* 3.5 2.9 - - - -
107F VAL* 2.4 36.5 + - - +
109F ALA* 3.7 38.1 - - + -
112F ILE* 3.8 17.0 - - + -
127F ILE* 4.2 17.3 - - + -
130F TYR* 3.5 28.0 - + - -
131F GLN* 5.4 2.0 - - + -
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Residues in contact with LEU 19 (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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10F CYS 4.8 2.6 - - - +
11F VAL* 5.9 0.2 - - - -
12F VAL* 3.1 25.9 + - + +
18F PHE* 1.3 70.2 - - - +
20F VAL* 1.3 76.2 + - - +
33F GLN* 4.5 4.2 - - - +
34F PRO* 3.6 22.8 - - + +
52F LEU* 4.2 10.5 - - + -
56F THR* 4.0 11.4 - - + -
58F ILE* 3.8 29.6 - - + -
94F THR* 5.0 1.6 - - + -
104F CYS* 3.7 23.1 - - + -
105F ARG 3.8 5.4 - - - +
106F TRP* 3.2 42.7 - - + +
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Residues in contact with VAL 20 (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 PHE 3.8 8.5 - - - +
19F LEU* 1.3 75.6 - - - +
21F VAL* 1.3 62.0 + - - +
31F TRP* 3.4 39.0 - - + -
32F ASN 2.7 26.2 - - - +
33F GLN* 5.0 1.1 - - - +
34F PRO* 4.6 0.7 - - - -
104F CYS* 3.3 7.1 - - - +
105F ARG* 3.0 46.8 + - + +
107F VAL* 4.1 20.9 - - + -
112F ILE* 4.8 12.3 - - + -
123F VAL* 5.3 3.6 - - + -
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Residues in contact with VAL 21 (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* 1.3 76.7 - - - +
22F GLU* 1.3 60.7 + - - +
23F GLU* 4.9 2.6 - - + +
30F LEU 3.8 0.5 - - - +
31F TRP* 3.3 8.4 - - - -
32F ASN* 3.1 40.1 + - + +
33F GLN 4.0 14.8 - - - +
34F PRO* 4.2 13.0 - - + +
55F GLU* 3.7 22.4 - - + +
56F THR* 3.6 29.8 - - + -
101F ILE* 3.8 25.1 - - + -
103F CYS 3.6 5.6 - - - +
104F CYS* 3.8 5.2 - - - -
105F ARG* 6.5 0.2 - - - -
157F SO4 4.4 2.5 - - - +
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Residues in contact with GLU 22 (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 VAL* 1.3 71.8 - - - +
23F GLU* 1.3 67.4 + - - +
29F ALA* 4.3 22.1 - - + +
30F LEU 4.0 2.0 - - - -
31F TRP* 3.7 17.5 + - + +
101F ILE* 3.6 7.3 - - - +
102F ASP* 3.1 35.0 + - + +
103F CYS* 2.8 42.4 + - - +
104F CYS* 4.7 0.2 - - - +
105F ARG* 3.0 42.0 + - - +
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Residues in contact with GLU 23 (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 VAL* 4.9 4.0 - - + +
22F GLU* 1.3 79.1 - - - +
24F THR* 1.3 67.3 + - - +
28F LYS 3.5 0.3 - - - +
29F ALA* 4.4 0.7 - - - -
30F LEU* 2.5 50.0 + - - +
32F ASN* 5.4 1.1 - - + +
100F ASP* 3.4 36.0 - - + +
101F ILE* 3.9 11.5 - - + +
102F ASP* 4.0 6.0 + - - -
119F ARG* 2.8 39.4 + - - +
157F SO4 3.1 22.9 + - - -
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Residues in contact with THR 24 (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 GLU* 1.3 82.0 - - - +
25F ILE* 1.3 62.7 + - - +
27F GLY* 3.4 17.7 - - - +
28F LYS* 3.0 34.1 + - - +
29F ALA* 4.4 5.1 - - - +
30F LEU* 5.8 0.2 - - - -
100F ASP 4.8 0.8 + - - -
102F ASP* 3.0 22.6 + - - -
119F ARG* 6.6 0.4 - - - -
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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