Contacts of the strand formed by residues 148 - 153 (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 148 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120E ASP 2.9 14.7 + - - +
121E VAL* 3.3 9.8 - - + +
122E ILE 2.8 27.5 + - - +
143E TYR* 5.0 3.1 - - + -
146E GLY 3.8 1.3 + - - +
147E VAL* 1.3 72.7 - - - +
149E VAL* 1.3 57.1 + - - +
150E VAL* 4.1 5.4 - - + -
175E ILE* 3.8 27.6 - - + -
231E ALA* 4.2 17.0 - - + -
235E LEU* 4.6 7.4 - - + -
243E ALA* 3.9 28.5 - - + +
246E VAL* 4.0 24.9 - - + -
247E ARG* 5.0 2.7 - - + -
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Residues in contact with VAL 149 (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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122E ILE* 3.5 28.9 - - + -
124E MET* 3.5 31.0 - - + -
139E VAL* 4.3 13.9 - - + +
142E ALA* 4.1 13.5 - - + -
143E TYR* 4.4 3.6 - - + +
147E VAL* 3.6 18.3 + - + +
148E VAL* 1.3 72.2 - - - +
150E VAL* 1.3 63.5 + - - +
173E SER 3.9 15.2 + - - +
174E VAL* 3.6 18.3 - - + -
175E ILE* 2.8 32.1 + - - +
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Residues in contact with VAL 150 (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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121E VAL* 4.2 9.0 - - + -
122E ILE 2.9 15.7 + - - +
123E ASN* 3.6 5.0 - - - +
124E MET* 2.9 27.2 + - - +
148E VAL* 4.4 12.6 - - + -
149E VAL* 1.3 79.9 - - - +
151E ALA* 1.3 66.7 + - - +
174E VAL* 4.1 1.1 - - - -
175E ILE* 3.7 11.2 - - + +
177E VAL* 3.7 18.8 - - + -
224E SER* 3.3 30.2 + - - +
227E VAL* 4.0 10.8 - - + +
228E ALA* 3.9 20.9 - - - +
231E ALA* 5.5 0.2 - - + -
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Residues in contact with ALA 151 (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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124E MET* 3.1 19.5 - - + +
126E LEU 4.8 2.0 - - - +
150E VAL* 1.3 77.2 - - - +
152E ALA* 1.4 58.9 - - - +
168E PRO* 4.3 4.9 - - + -
169E ALA* 4.0 19.7 - - + +
174E VAL* 3.5 21.1 - - + +
175E ILE 2.8 13.0 + - - +
176E ALA* 3.4 1.9 - - - -
177E VAL* 2.8 31.5 + - - +
224E SER* 3.5 7.9 - - - -
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Residues in contact with ALA 152 (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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124E MET 3.2 4.8 + - - -
125E SER* 4.0 16.8 - - - -
126E LEU 4.2 5.2 - - - +
127E GLY* 5.5 0.3 - - - -
151E ALA* 1.4 72.6 - - - +
153E ALA* 1.3 62.8 + - - +
154E GLY 3.1 4.0 + - - -
166E GLY 5.8 0.3 - - - -
167E TYR 6.1 0.2 - - - -
169E ALA* 3.3 10.9 - - - +
177E VAL 3.7 6.5 - - - -
220E THR* 3.5 29.4 - - - +
221E SER* 3.8 2.7 - - - +
224E SER* 3.6 5.9 + - - -
45I LEU* 3.4 27.9 - - + +
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Residues in contact with ALA 153 (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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151E ALA 3.5 1.6 + - - -
152E ALA* 1.3 72.5 - - - +
154E GLY* 1.3 59.1 + - - +
165E ILE* 3.4 13.9 - - + +
166E GLY* 3.1 26.3 + - - -
169E ALA* 3.8 11.4 - - - +
176E ALA* 4.4 4.5 - - + -
177E VAL 2.8 31.2 + - - +
178E GLY* 4.0 3.8 - - - +
191E SER* 3.6 12.3 - - - +
196E LEU* 3.8 20.6 - - + -
220E THR* 4.0 0.6 + - + -
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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