Contacts of the strand formed by residues 55 - 58 (chain E) in PDB entry 3SKJ
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 ASN 55 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22E HIS 3.8 3.6 - - - +
23E PRO* 4.3 9.9 - - - +
26E LYS* 4.4 8.5 - - - +
27E GLY* 3.7 28.5 + - - -
28E TRP* 3.2 13.1 + - + -
45E VAL* 4.1 1.4 - - + +
47E ASN* 3.8 7.3 + - - -
53E GLN* 2.7 33.0 + - - +
54E ASP* 1.3 78.7 + - - +
56E TRP* 1.3 62.2 + - - +
159E GLN* 3.3 1.4 - - - -
160E ASP* 2.6 63.8 + - + +
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Residues in contact with TRP 56 (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 THR* 3.4 5.2 - - - -
22E HIS* 2.9 43.7 + + + +
28E TRP* 3.6 6.9 - - - -
54E ASP* 3.1 29.8 + - - -
55E ASN* 1.3 77.4 - - - +
57E LEU* 1.3 60.1 + - - +
58E ARG 4.3 0.2 - - - -
98E TYR* 3.6 55.2 - + + -
110E PHE* 3.8 28.9 - + + -
112E LYS* 3.6 43.0 - - + +
115E PHE* 4.6 4.9 - - + -
157E ALA* 3.9 19.3 - - + -
158E PHE 3.4 3.8 - - - -
159E GLN* 3.7 28.0 - - + -
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Residues in contact with LEU 57 (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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19E TRP* 3.7 36.6 - - + -
20E LEU 3.5 9.6 - - - +
21E THR* 4.0 5.2 - - + -
28E TRP* 3.7 26.2 - - + +
43E TYR* 3.4 57.0 - - + -
56E TRP* 1.3 74.3 - - - +
58E ARG* 1.3 59.3 - - - +
157E ALA* 2.9 8.9 - - - +
158E PHE* 2.8 55.5 + - + +
167E LEU* 4.3 6.1 - - + -
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Residues in contact with ARG 58 (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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19E TRP* 3.1 21.6 - - - +
20E LEU* 2.9 51.7 + - + +
56E TRP 4.3 0.4 - - - -
57E LEU* 1.3 75.0 - - - +
59E THR* 1.3 89.0 + - - +
60E ASN* 4.6 4.8 - - - +
61E TRP 5.1 0.2 - - - +
105E ASP* 5.3 1.0 + - - -
107E GLY* 2.8 30.9 + - - +
108E THR* 5.3 0.2 - - - +
109E ASN 4.1 12.5 + - - -
110E PHE* 3.8 27.8 - - + +
115E PHE* 3.9 22.2 - - + -
155E TYR* 3.5 34.3 + - + -
156E LEU 3.5 8.7 - - - +
157E ALA* 4.5 0.7 - - + -
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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