Contacts of the strand formed by residues 131 - 136 (chain D) in PDB entry 3LUE
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 ALA 131 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D PRO* 3.3 13.1 - - + +
103D VAL 3.1 20.3 + - - -
124D PHE* 4.0 4.7 - - - -
129D THR* 3.1 9.9 - - - +
130D PRO* 1.4 81.7 - - + +
132D MET* 1.3 68.9 + - - +
353D GLN* 4.9 4.3 - - - +
356D TRP* 3.8 24.7 - - + -
357D ILE 3.2 14.6 - - - +
358D SER* 4.2 5.2 - - - -
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Residues in contact with MET 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D VAL* 3.3 18.6 - - + +
105D LEU* 3.5 36.1 - - + -
119D MET 3.9 5.4 - - - +
120D THR* 4.1 21.3 - - - -
123D MET* 3.8 20.6 - - + -
124D PHE* 3.6 25.6 - - + -
129D THR* 4.8 2.2 - - + -
131D ALA* 1.3 79.0 - - - +
133D TYR* 1.3 61.8 + - - +
134D VAL* 4.0 23.8 - - + -
356D TRP* 3.4 4.5 - - - -
357D ILE* 2.9 46.1 + - - +
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Residues in contact with TYR 133 (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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103D VAL 3.1 5.2 + - - +
104D LEU* 3.4 9.5 - - + -
105D LEU* 2.8 32.2 + - - +
132D MET* 1.3 77.2 - - - +
134D VAL* 1.3 84.2 + - - +
135D ALA* 3.9 12.8 - - + -
346D LEU* 5.1 2.0 - - + -
352D PHE* 3.5 23.1 - + + -
355D MET* 3.1 45.3 - - + +
356D TRP* 3.4 21.1 - - + -
373D LYS 3.7 17.8 + - - -
374D CYS* 3.7 32.0 - - - -
375D PHE* 4.5 12.6 + - - -
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Residues in contact with VAL 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D LEU* 3.4 11.9 - - + +
107D GLU* 3.4 41.4 - - + +
116D ARG* 4.4 9.0 - - + +
119D MET* 3.9 25.4 - - + -
132D MET* 4.0 20.0 - - + -
133D TYR* 1.3 86.6 + - - +
135D ALA* 1.3 57.7 + - - +
136D ILE 4.3 0.2 + - - -
370D VAL* 3.8 24.0 - - + -
374D CYS* 3.7 22.7 - - - +
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Residues in contact with ALA 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D LEU* 4.4 15.2 - - + +
105D LEU 3.4 4.9 + - - -
106D THR* 3.2 6.1 - - - -
107D GLU* 2.7 33.1 + - - -
133D TYR* 3.9 19.4 - - + -
134D VAL* 1.3 74.5 - - - +
136D ILE* 1.3 57.3 + - - +
139D VAL* 6.1 2.2 - - + -
140D LEU* 3.4 26.5 - - + -
346D LEU* 5.3 3.6 - - + -
375D PHE* 6.6 0.4 - - - -
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Residues in contact with ILE 136 (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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107D GLU* 3.3 28.0 + - - +
108D ALA 4.4 7.0 - - - +
109D PRO* 3.8 28.0 - - + -
135D ALA* 1.3 71.4 - - - +
137D GLN* 1.3 64.7 + - - +
138D ALA* 3.9 10.5 - - + +
139D VAL* 3.5 23.3 + - + +
140D LEU* 2.9 19.4 - - - +
161D HIS* 4.2 24.9 - - + +
163D VAL* 5.4 0.4 - - + -
175D ILE* 5.6 2.9 - - + -
374D CYS 6.1 0.9 - - - +
375D PHE* 4.2 32.8 - - + -
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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