Contacts of the strand formed by residues 26 - 32 (chain E) in PDB entry 1CSE
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 VAL 26 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23E GLY 3.0 18.7 + - - +
24E ALA 3.8 8.3 - - - +
25E ASN* 1.3 82.0 - - - +
27E LYS* 1.3 63.4 - - - +
28E VAL* 3.7 7.5 + - + -
88E VAL* 3.7 3.8 - - - +
89E SER* 2.8 24.7 + - - +
120E ASP* 3.6 21.3 - - + +
121E VAL* 4.3 3.8 - - + -
232E ALA* 3.6 45.5 - - + +
235E LEU* 4.1 12.3 - - + +
236E SER* 4.0 12.1 - - - +
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Residues in contact with LYS 27 (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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25E ASN 4.5 9.5 + - - +
26E VAL* 1.3 76.8 - - - +
28E VAL* 1.3 61.5 + - - +
29E ALA 4.1 0.2 - - - -
89E SER* 3.4 10.8 - - - +
91E TYR* 3.8 28.5 - - + +
117E ASN 4.4 4.3 - - - +
118E GLY* 3.5 23.4 + - - +
119E MET* 3.7 23.1 - - + -
120E ASP* 2.8 43.0 + - - +
121E VAL 3.2 7.6 + - - +
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Residues in contact with VAL 28 (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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26E VAL* 4.1 2.9 - - + -
27E LYS* 1.3 78.6 - - - +
29E ALA* 1.4 69.7 + - - +
30E VAL* 4.0 8.3 - - + -
72E VAL* 4.1 18.8 - - + -
88E VAL* 3.6 34.3 - - + -
89E SER 2.9 12.1 + - - +
90E LEU* 3.7 4.4 - - + +
91E TYR* 2.8 28.4 + - - +
119E MET* 4.3 1.6 - - - -
121E VAL* 3.5 27.8 - - + +
123E ASN* 5.2 1.3 - - + -
228E ALA* 4.7 8.1 - - + +
232E ALA* 3.8 15.9 - - + -
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Residues in contact with ALA 29 (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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28E VAL* 1.4 74.7 - - - +
30E VAL* 1.3 62.7 + - - +
31E LEU* 3.8 10.7 + - + +
91E TYR* 3.5 4.3 - - + +
93E VAL* 3.7 23.8 - - + -
114E ALA* 4.5 1.3 - - + -
119E MET* 3.6 30.4 - - + -
121E VAL 2.8 12.5 + - - +
122E ILE* 3.4 6.2 - - + -
123E ASN* 2.9 28.6 + - - +
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Residues in contact with VAL 30 (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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28E VAL* 4.8 3.8 - - + -
29E ALA* 1.3 72.9 - - - +
31E LEU* 1.3 61.4 + - - +
32E ASP* 3.5 21.7 + - + +
34E GLY 5.9 0.3 + - - -
35E ILE* 4.2 11.6 - - + +
65E GLY 4.2 11.0 - - - +
68E VAL* 3.9 22.4 - - + -
69E ALA* 4.2 13.9 - - + -
72E VAL* 4.3 14.4 - - + -
90E LEU* 3.6 26.5 - - + -
91E TYR 3.0 11.0 + - - +
92E ALA* 3.9 1.0 - - - -
93E VAL 2.9 25.1 + - - +
123E ASN* 4.0 8.3 - - + +
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Residues in contact with LEU 31 (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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29E ALA* 3.9 18.2 - - + +
30E VAL* 1.3 73.5 - - - +
32E ASP* 1.3 64.3 - - - +
93E VAL* 3.4 37.0 - - + -
95E VAL* 3.8 16.8 - - + -
107E ILE* 4.3 4.5 - - + +
110E GLY* 3.7 6.1 - - - +
111E ILE* 3.6 46.7 - - + +
114E ALA* 4.9 0.4 - - + -
122E ILE* 4.5 13.7 - - + -
123E ASN 3.0 21.9 + - - +
124E MET* 3.9 19.6 - - + -
126E LEU* 3.6 15.4 - - - +
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Residues in contact with ASP 32 (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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30E VAL* 3.5 19.6 + - + +
31E LEU* 1.3 77.7 - - - +
33E THR* 1.3 77.6 + - - +
34E GLY 3.2 10.5 + - - +
64E HIS* 2.7 41.4 + - - -
65E GLY* 3.3 17.1 - - - -
68E VAL* 3.9 9.5 - - - +
93E VAL 2.9 8.1 + - - -
94E LYS* 3.3 0.7 - - - -
95E VAL* 2.9 25.1 + - - +
96E LEU* 3.2 19.4 + - - +
123E ASN* 5.1 0.2 - - - +
125E SER* 3.9 12.1 + - - +
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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