Contacts of the strand formed by residues 143 - 149 (chain E) in PDB entry 5B6N
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 LEU 143 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5E LEU* 4.0 21.5 - - + +
6E LEU 3.1 31.6 - - - +
7E LEU* 3.1 24.3 - - + +
8E GLY* 3.7 17.7 + - - +
9E ASP* 3.0 14.3 + - + +
135E PHE* 3.8 21.8 - - + -
136E VAL 3.8 4.3 - - - +
137E PHE* 3.6 22.1 - - + -
142E LYS* 1.3 74.4 - - - +
144E LYS* 1.3 63.9 + - - +
145E LEU 3.8 22.9 - - - +
146E SER* 5.0 5.2 - - - -
148F LEU* 5.8 0.7 - - + -
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Residues in contact with LYS 144 (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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7E LEU* 3.4 14.5 - - - +
33E TRP* 3.5 30.7 - - + -
136E VAL* 3.2 11.7 + - + +
138E GLY* 3.2 22.8 - - - +
139E PRO* 4.1 1.8 - - - +
140E ASP* 3.1 33.2 + - - -
142E LYS* 3.5 20.0 - - - +
143E LEU* 1.3 78.6 - - - +
145E LEU* 1.3 62.5 + - - +
167E LEU* 3.5 24.5 - - + -
150F PRO* 3.6 22.9 - - - +
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Residues in contact with LEU 145 (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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7E LEU* 4.1 3.8 - - - +
134E VAL* 3.9 2.2 - - + +
136E VAL* 3.3 44.1 + - + +
143E LEU* 3.7 8.8 - - - +
144E LYS* 1.3 80.7 - - - +
146E SER* 1.3 65.0 + - - +
147E ILE* 4.5 9.6 - - + -
160E ILE* 5.2 5.4 - - + -
163E VAL* 3.8 33.9 - - + -
167E LEU* 4.3 6.3 - - + -
148F LEU 3.2 14.1 - - - +
149F TYR* 3.6 43.1 - - + +
150F PRO* 3.7 14.4 - - + -
153F THR* 4.6 2.0 - - + -
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Residues in contact with SER 146 (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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5E LEU 5.6 2.0 + - - -
133E VAL* 5.6 0.4 - - - -
134E VAL 3.4 11.2 - - - -
135E PHE* 4.0 21.1 - - - -
143E LEU* 4.8 8.5 - - - -
145E LEU* 1.3 76.5 - - - +
147E ILE* 1.3 64.5 + - - +
146F SER* 5.1 3.5 + - - -
147F ILE* 3.5 0.5 - - - -
148F LEU* 2.4 65.2 + - - +
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Residues in contact with ILE 147 (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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132E ARG 3.6 14.8 - - - +
133E VAL* 3.1 24.5 - - - +
134E VAL* 3.4 38.9 + - + -
145E LEU* 4.5 9.2 - - + -
146E SER* 1.3 81.5 - - - +
148E LEU* 1.3 59.8 + - - +
149E TYR* 3.5 33.4 - - + -
155E ARG* 3.9 11.9 - - + -
160E ILE* 4.7 12.1 - - + -
146F SER* 3.3 7.0 - - - +
147F ILE* 4.0 15.3 - - + -
149F TYR* 4.3 16.4 - - + +
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Residues in contact with LEU 148 (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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116E MET* 5.6 4.3 - - - -
117E LEU 5.9 1.3 - - - +
131E ALA* 4.7 2.5 - - + -
132E ARG 4.5 0.2 - - - -
133E VAL* 3.6 28.5 - - + -
147E ILE* 1.3 69.1 - - - +
149E TYR* 1.3 64.5 + - - +
5F LEU 5.0 1.8 - - - +
6F LEU* 4.6 10.5 - - + -
7F LEU* 3.6 49.9 - - + +
143F LEU* 5.0 0.7 - - + -
145F LEU* 3.3 9.9 - - - +
146F SER* 2.3 68.7 + - - +
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Residues in contact with TYR 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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131E ALA* 3.5 8.1 - - - +
132E ARG* 3.2 46.1 + - + +
147E ILE* 3.5 32.0 - - + +
148E LEU* 1.3 79.1 - - - +
150E PRO* 1.3 65.5 - - + +
153E THR* 4.1 8.3 - - + +
154E GLY 3.6 27.8 - - - -
155E ARG* 3.8 17.0 - - + -
156E ASN 4.9 1.1 + - - -
7F LEU* 4.2 4.9 - - - +
145F LEU* 3.6 23.5 - - + +
147F ILE* 4.3 8.0 - - + +
159F GLU* 2.7 30.5 + - - +
163F VAL* 3.2 24.7 - - + +
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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