Contacts of the strand formed by residues 147 - 152 (chain F) in PDB entry 1LVO
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 147 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13F VAL* 4.3 11.4 - - + -
17F ILE* 4.0 25.4 - - + -
29F GLY 5.4 0.2 - - - +
30F LEU* 4.2 21.5 - - + -
112F ASN 3.8 0.3 - - - +
113F ILE* 3.6 4.4 - - - -
114F LEU* 2.8 36.0 + - + +
116F CYS* 5.2 0.4 - - - -
145F GLY 3.5 15.9 - - - +
146F SER* 1.3 75.6 - - - +
148F GLY* 1.3 67.4 + - - +
149F TYR* 4.1 2.5 - - + +
158F PHE* 3.8 33.2 - - + -
160F TYR 3.3 5.2 - - - +
161F MET* 4.3 7.2 - - + -
176F PHE* 4.7 4.0 - - + -
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Residues in contact with GLY 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F PHE* 4.0 5.6 - - - -
112F ASN 2.9 12.3 - - - -
113F ILE* 4.1 4.7 - - - -
147F VAL* 1.3 79.5 - - - +
149F TYR* 1.3 59.5 + - - +
158F PHE* 3.8 1.4 - - - -
159F VAL* 2.9 29.0 + - - -
160F TYR* 2.6 33.5 + - - +
176F PHE* 4.6 0.2 - - - -
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Residues in contact with TYR 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F GLN* 2.9 25.0 + - + -
9F PRO 3.4 18.6 + - - -
10F SER* 3.4 9.5 - - - -
13F VAL* 3.9 21.1 - - + -
111F PHE* 3.7 1.5 - - - +
112F ASN* 2.9 68.6 + - + +
113F ILE 4.5 0.4 - - - -
114F LEU* 4.1 22.2 - - + -
124F VAL* 3.4 16.1 - - - +
147F VAL 4.1 6.7 - - - -
148F GLY* 1.3 75.2 - - - +
150F VAL* 1.3 69.1 + - - +
151F LEU* 4.6 4.5 - - + -
156F LEU* 4.0 22.7 - - + -
157F TYR 3.0 15.7 - - - +
158F PHE* 4.3 11.0 - - + -
159F VAL* 4.2 2.6 - - - +
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Residues in contact with VAL 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F GLN* 3.7 7.0 - - - +
103F LYS* 4.5 5.4 - - - +
105F ILE* 4.5 6.1 - - + -
110F SER 3.7 8.3 - - - +
111F PHE* 3.2 39.5 - - + -
112F ASN* 3.8 2.5 - - - +
149F TYR* 1.3 73.8 - - - +
151F LEU* 1.3 64.8 + - - +
152F GLU* 4.0 17.0 - - + +
155F ILE 3.5 1.4 - - - +
156F LEU* 3.8 2.1 - - - +
157F TYR* 2.9 57.3 + - + -
159F VAL* 4.0 11.7 - - + -
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Residues in contact with LEU 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F GLN* 2.8 58.8 + - + +
9F PRO* 4.0 23.1 - - + +
12F LEU* 4.4 17.5 - - + -
149F TYR* 4.6 5.2 - - + -
150F VAL* 1.3 73.9 - - - +
152F GLU* 1.3 62.8 + - - +
153F ASN 4.1 0.7 - - - -
154F GLY* 5.3 4.7 - - - +
155F ILE 3.4 5.8 - - - +
156F LEU* 3.6 39.5 - - + +
294F ARG* 5.2 4.3 + - - -
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Residues in contact with GLU 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F LYS* 2.9 30.2 + - - -
105F ILE* 5.8 0.3 - - - +
150F VAL* 4.0 12.7 + - + +
151F LEU* 1.3 76.4 - - - +
153F ASN* 1.3 73.9 + - + +
155F ILE* 3.1 24.8 + - - +
157F TYR* 3.2 30.2 + - + +
294F ARG* 6.0 4.7 - - - +
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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