Contacts of the strand formed by residues 113 - 117 (chain D) in PDB entry 4LOU
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 THR 113 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145C THR* 5.3 5.8 - - - +
111D ALA 3.5 3.7 + - - -
112D PRO* 1.3 68.8 - - - +
114D VAL* 1.3 64.4 + - - +
115D SER* 3.8 7.9 + - - +
134D PHE 3.3 10.4 - - - +
136D ASN* 3.0 31.5 + - + +
137D ASN* 5.5 3.6 + - - +
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Residues in contact with VAL 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D PRO* 3.5 12.6 + - + +
113D THR* 1.3 74.4 - - - +
115D SER* 1.3 63.9 + - - +
133D CYS* 3.9 22.0 - - - -
134D PHE 3.4 3.4 - - - -
135D LEU* 3.9 11.0 - - + -
193D CYS 4.9 1.8 - - - +
195D ALA* 3.7 28.7 - - + -
204D ILE* 3.8 31.0 - - + +
206D LYS* 3.1 48.4 - - + +
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Residues in contact with SER 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C THR* 3.4 27.2 + - - +
113D THR* 4.3 7.3 + - - +
114D VAL* 1.3 77.9 + - - +
116D ILE* 1.3 62.0 + - - +
117D PHE* 3.6 25.2 - - - -
132D VAL 4.0 0.7 - - - +
133D CYS* 3.3 6.2 - - - -
134D PHE* 2.9 38.4 + - - -
206D LYS* 4.5 2.7 - - - -
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Residues in contact with ILE 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C PRO* 4.9 1.0 - - - +
135C GLY* 4.6 7.8 + - - -
115D SER* 1.3 73.8 - - - +
117D PHE* 1.3 73.5 + - - +
118D PRO* 4.5 2.1 - - - +
131D VAL* 4.5 0.7 - - + -
132D VAL 3.7 7.4 - - - +
133D CYS* 4.1 9.0 - - - -
147D TRP* 4.2 18.6 - - + -
191D TYR 3.7 17.0 - - - +
193D CYS* 3.8 16.4 - - + +
206D LYS* 3.7 33.8 - - + +
207D SER 3.8 28.7 - - - +
208D PHE* 4.0 18.6 - - + -
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Residues in contact with PHE 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C LEU* 3.6 45.5 - - + -
133C ALA 3.3 28.0 - - - +
134C PRO* 3.9 6.3 - - + -
145C THR* 3.0 38.4 - - + -
146C LEU* 4.4 3.1 - - - -
115D SER* 3.6 20.0 - - - -
116D ILE* 1.3 80.6 - - - +
118D PRO* 1.3 69.9 - - + +
131D VAL* 3.1 23.8 - - - +
132D VAL* 3.0 25.9 + - + +
134D PHE* 3.5 27.8 - + - -
208D PHE* 4.3 3.1 - - - -
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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