Contacts of the strand formed by residues 16 - 20 (chain E) in PDB entry 4XCS
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 16 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14E ASN* 5.6 0.9 - - - +
15E PHE* 1.3 74.5 - - - +
17E ALA* 1.3 64.4 + - - +
28E ASP* 3.4 43.9 + - + +
29E ILE* 3.1 6.7 - - - +
30E SER* 3.5 18.9 + - - +
33E ASP* 5.1 3.6 + - - -
112E ILE* 5.1 1.2 - - - +
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Residues in contact with ALA 17 (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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15E PHE* 4.0 5.3 - - + -
16E LYS* 1.3 77.4 - - - +
18E THR* 1.3 64.8 + - - +
19E ALA* 3.4 1.4 + - - +
28E ASP* 4.1 5.2 - - - -
29E ILE* 2.7 35.4 + - - +
105E VAL* 3.8 12.6 - - + -
106E SER 3.7 13.0 - - - +
112E ILE* 3.7 27.6 - - + -
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Residues in contact with THR 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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201D CPS 6.4 0.9 - - + -
17E ALA* 1.3 73.1 - - - +
19E ALA* 1.3 63.6 + - - +
26E PHE* 4.1 7.8 - - - +
27E LYS 3.5 6.3 - - - -
28E ASP* 3.0 22.2 - - - +
81E HIS* 3.5 39.4 + - + +
105E VAL* 4.7 0.2 - - - -
106E SER* 2.7 39.9 + - - +
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Residues in contact with ALA 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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18E THR* 1.3 78.3 + - - +
20E VAL* 1.3 64.7 + - - +
21E MET* 3.8 11.6 + - - +
25E GLN 3.6 1.0 - - - +
26E PHE* 3.2 6.2 - - - -
27E LYS 2.9 36.5 + - - +
29E ILE* 4.0 26.9 - - + -
81E HIS* 5.1 0.7 - - - -
103E PRO* 4.5 0.2 - - + -
104E LEU 3.1 20.4 - - - +
105E VAL* 4.1 3.6 - - - -
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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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19E ALA* 1.3 72.3 - - - +
21E MET* 1.3 69.2 + - - +
24E GLY* 4.2 18.6 - - - +
25E GLN 3.5 3.4 - - - -
26E PHE* 3.8 15.0 - - + -
81E HIS* 3.3 30.5 - - - +
84E HIS* 3.6 18.8 - - + -
85E LEU* 3.8 18.2 - - + +
88E VAL* 4.8 13.9 - - + -
102E ILE 4.2 1.6 - - - +
103E PRO* 3.4 3.1 - - - +
104E LEU* 2.9 35.0 + - + +
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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