Contacts of the strand formed by residues 131 - 136 (chain V) in PDB entry 1O1D
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 V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102V PRO* 3.2 12.8 - - + +
103V THR 2.9 21.9 + - - -
124V PHE* 3.8 3.4 - - - -
129V VAL* 3.4 6.1 - - - +
130V PRO* 1.3 83.1 - - + +
132V MET* 1.3 64.4 + - - +
356V TRP* 4.0 22.2 - - + -
357V ILE 3.0 20.6 - - - +
358V THR* 3.9 10.1 - - + -
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Residues in contact with MET 132 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103V THR* 3.2 18.4 - - - +
105V LEU* 3.7 15.9 - - + -
119V MET 4.0 0.4 - - - +
120V THR* 3.8 28.9 - - - +
123V MET* 3.6 35.9 - - + -
124V PHE* 3.4 33.2 - - + -
129V VAL* 4.2 7.0 - - + -
131V ALA* 1.3 75.4 - - - +
133V TYR* 1.3 65.3 + - - +
134V VAL* 4.1 9.9 - - + -
356V TRP* 3.4 6.6 - - - -
357V ILE* 2.8 30.6 + - - +
370V VAL* 4.3 11.9 - - - -
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Residues in contact with TYR 133 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103V THR 3.3 2.1 + - - +
104V LEU* 3.5 15.3 - - + +
105V LEU* 2.8 27.9 + - - +
132V MET* 1.3 81.9 - - - +
134V VAL* 1.3 74.2 + - - +
135V ALA* 4.0 12.6 - - + -
346V LEU* 4.5 4.9 - - + +
352V PHE* 3.3 32.2 - + + -
355V MET* 3.5 41.2 - - + +
356V TRP* 3.9 16.4 - - + -
357V ILE* 5.1 2.5 - - + -
370V VAL* 4.7 4.3 - - + -
372V ARG* 2.9 43.2 + - - -
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Residues in contact with VAL 134 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105V LEU* 3.4 5.4 - - + -
106V THR 4.4 3.1 - - - -
107V GLU* 3.6 47.6 - - + +
116V ARG* 3.2 43.2 + - + +
119V MET* 4.3 18.8 - - + -
120V THR* 4.5 5.8 - - - +
132V MET* 4.1 20.6 - - + -
133V TYR* 1.3 87.7 - - - +
135V ALA* 1.3 55.2 + - - +
370V VAL* 4.6 9.4 - - + +
372V ARG* 4.5 3.7 + - - +
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Residues in contact with ALA 135 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104V LEU* 4.2 7.4 - - + -
105V LEU 2.9 10.8 + - - +
106V THR* 3.3 4.5 - - - -
107V GLU* 3.0 23.0 + - - -
133V TYR* 4.0 17.3 - - + -
134V VAL* 1.3 73.8 - - - +
136V ILE* 1.3 62.9 + - - +
139V VAL* 6.1 1.6 - - + -
140V LEU* 3.6 37.9 - - + -
346V LEU* 4.7 1.3 - - + -
372V ARG* 5.9 0.4 - - - +
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Residues in contact with ILE 136 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107V GLU* 3.7 26.5 - - + +
108V ALA 4.6 2.2 - - - +
109V PRO* 4.2 32.3 - - + +
116V ARG* 4.0 15.0 - - - +
134V VAL 4.3 0.2 + - - -
135V ALA* 1.3 71.9 - - - +
137V GLN* 1.3 69.9 + - - +
138V ALA* 4.2 8.1 - - + +
139V VAL* 3.2 38.7 + - + +
140V LEU* 3.2 11.2 + - - +
163V VAL* 5.1 0.9 - - + -
170V ALA* 4.8 14.8 - - + -
175V ILE* 6.5 0.2 - - + -
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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