Contacts of the strand formed by residues 104 - 108 (chain E) in PDB entry 2CNW
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 104 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E GLY 5.0 0.4 - - - -
103E ARG* 1.3 83.2 + - - +
105E VAL* 1.3 63.4 - - - +
177E VAL* 4.2 15.5 - - + -
180E MET* 4.2 19.1 - - + -
188E LEU* 3.5 8.5 - - + +
190E VAL* 3.9 25.8 - - + -
213E ILE* 3.7 13.0 - - + -
220E GLU* 3.1 30.9 + - + +
221E PRO* 3.5 20.1 - - + +
222E LYS* 3.4 20.4 + - - +
223E GLU* 3.4 7.6 + - - +
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Residues in contact with VAL 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E PRO* 4.4 15.9 - - + -
102E GLY 5.4 0.4 - - - +
104E VAL* 1.3 77.7 - - - +
106E LEU* 1.3 62.5 + - - +
107E VAL* 3.8 8.5 + - + +
187E LEU* 4.7 8.1 - - + -
188E LEU 2.8 10.4 + - - +
189E PHE* 3.4 32.0 - - + -
190E VAL* 2.9 27.4 + - - +
223E GLU* 3.5 24.7 - - + +
225E TRP* 3.6 40.4 - - + -
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Residues in contact with LEU 106 (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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104E VAL 4.1 0.8 - - - -
105E VAL* 1.3 71.5 - - - +
107E VAL* 1.3 60.5 + - - +
108E VAL* 3.9 15.6 + - + -
190E VAL* 3.9 21.8 - - + -
192E THR* 3.7 28.9 - - + -
206E LEU* 4.8 7.9 - - + +
209E VAL* 4.2 10.1 - - + -
210E LYS* 4.1 30.5 - - + +
213E ILE* 4.2 4.7 - - + -
221E PRO* 4.2 15.3 - - + -
223E GLU 2.8 15.3 + - - +
224E VAL* 3.3 19.9 - - + +
225E TRP 2.8 27.4 + - - -
247E VAL* 5.2 3.4 - - + -
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Residues in contact with VAL 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E VAL* 4.2 20.0 - - + +
106E LEU* 1.3 75.4 - - - +
108E VAL* 1.3 53.6 + - - +
115E LYS* 3.9 20.9 - - + +
118E THR* 5.4 2.9 - - + -
119E ILE* 3.7 30.7 - - + -
122E LEU* 4.9 6.1 - - + -
189E PHE* 4.7 6.3 - - + -
190E VAL 3.0 15.6 + - - +
191E ASP* 4.9 0.2 - - - -
192E THR* 2.8 34.7 + - - +
225E TRP* 3.5 9.6 - - + +
227E VAL* 3.5 31.0 - - + -
253E ILE* 6.1 0.7 - - + -
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Residues in contact with VAL 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E LEU* 4.0 16.2 - - + -
107E VAL* 1.3 78.6 - - - +
109E GLY* 1.3 54.0 - - - +
115E LYS* 3.4 8.0 - - - +
192E THR* 3.8 4.7 - - - +
206E LEU* 3.7 33.4 - - + -
224E VAL* 4.3 11.0 - - + -
225E TRP 3.0 12.3 + - - +
226E LEU* 3.4 3.5 - - + -
227E VAL* 2.8 31.5 + - - -
243E PHE* 3.7 24.9 - - + -
247E VAL* 4.6 2.7 - - + -
249E LEU* 3.9 26.2 - - + -
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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