Contacts of the strand formed by residues 131 - 136 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102H PRO* 3.3 13.6 - - + +
103H VAL 3.1 20.5 + - - -
124H PHE* 4.0 4.7 - - - -
129H THR* 3.1 9.7 - - - +
130H PRO* 1.4 83.0 - - + +
132H MET* 1.3 67.9 + - - +
353H GLN* 4.9 4.3 - - - +
356H TRP* 3.8 24.2 - - + -
357H ILE 3.2 14.8 - - - +
358H SER* 4.2 5.4 - - - -
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Residues in contact with MET 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H VAL* 3.3 18.8 - - + +
105H LEU* 3.5 35.2 - - + -
119H MET 3.9 5.4 - - - +
120H THR* 4.1 21.1 - - - -
123H MET* 3.8 21.1 - - + -
124H PHE* 3.6 26.2 - - + -
129H THR* 4.8 1.8 - - + -
131H ALA* 1.3 79.8 - - - +
133H TYR* 1.3 62.2 + - - +
134H VAL* 4.0 24.0 - - + -
356H TRP* 3.4 5.2 - - - -
357H ILE* 2.9 45.5 + - - +
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Residues in contact with TYR 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H VAL 3.1 5.4 + - - +
104H LEU* 3.4 9.6 - - + -
105H LEU* 2.8 32.6 + - - +
132H MET* 1.3 76.2 - - - +
134H VAL* 1.3 83.3 + - - +
135H ALA* 3.9 13.5 - - + -
346H LEU* 5.1 2.0 - - + -
352H PHE* 3.5 22.4 - + + -
355H MET* 3.1 45.0 - - + +
356H TRP* 3.4 21.8 - - + -
357H ILE* 5.1 0.7 - - + -
373H LYS 3.7 18.2 + - - -
374H CYS* 3.7 32.0 - - - -
375H PHE* 4.5 12.6 + - - -
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Residues in contact with VAL 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H LEU* 3.4 12.8 - - + +
107H GLU* 3.4 40.7 - - + +
116H ARG* 4.4 9.0 - - + +
119H MET* 3.9 24.9 - - + -
132H MET* 4.0 20.9 - - + -
133H TYR* 1.3 85.9 + - - +
135H ALA* 1.3 57.7 + - - +
370H VAL* 3.8 23.8 - - + -
374H CYS* 3.7 23.1 - - - +
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Residues in contact with ALA 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H LEU* 4.4 15.2 - - + +
105H LEU 3.4 5.1 + - - -
106H THR* 3.2 6.2 - - - -
107H GLU* 2.7 33.7 + - - -
133H TYR* 3.9 19.2 - - + -
134H VAL* 1.3 74.9 - - - +
136H ILE* 1.3 57.6 + - - +
139H VAL* 6.1 2.2 - - + -
140H LEU* 3.4 26.2 - - + -
346H LEU* 5.3 3.6 - - + -
375H PHE* 6.6 0.7 - - - -
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Residues in contact with ILE 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H GLU* 3.3 28.7 + - + +
108H ALA 4.4 6.5 - - - +
109H PRO* 3.8 27.6 - - + -
110H LEU 5.3 0.2 - - - +
134H VAL 4.3 0.2 + - - -
135H ALA* 1.3 70.6 - - - +
137H GLN* 1.3 65.0 + - - +
138H ALA* 3.9 10.5 - - + +
139H VAL* 3.5 23.1 + - + +
140H LEU* 2.9 19.2 - - - +
161H HIS* 4.2 24.2 - - + +
163H VAL* 5.4 1.1 - - + -
175H ILE* 5.6 3.1 - - + -
374H CYS 6.1 0.7 - - - +
375H PHE* 4.2 32.4 - - + -
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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