Contacts of the strand formed by residues 81 - 88 (chain C) in PDB entry 4J1R
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 LEU 81 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C GLN* 3.3 26.9 - - - +
73C ALA 3.4 8.5 - - - +
74C LYS* 3.6 27.1 - - + -
79C GLY 4.6 2.2 - - - +
80C GLU* 1.3 74.6 - - - +
82C VAL* 1.3 64.8 + - - +
113C ARG* 4.2 7.1 + - - -
134C TYR* 3.6 42.3 + - + +
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Residues in contact with VAL 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C TYR* 5.5 0.7 - - + -
72C GLN* 3.5 4.9 - - - +
73C ALA* 2.9 44.0 + - + +
75C LEU* 4.0 32.8 - - + -
80C GLU 4.6 0.2 - - - +
81C LEU* 1.3 79.5 - - - +
83C ALA* 1.3 59.3 + - - +
84C ILE* 4.4 13.9 - - + -
113C ARG* 3.8 20.6 - - + +
131C VAL* 3.7 27.8 - - + -
132C LEU 3.2 14.8 - - - +
134C TYR* 3.5 11.4 - - - +
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Residues in contact with ALA 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ILE* 4.5 1.1 - - + -
70C VAL* 4.2 14.8 - - + -
71C TYR 3.2 8.3 - - - +
72C GLN* 4.6 0.2 - - - +
82C VAL* 1.3 76.6 - - - +
84C ILE* 1.3 62.6 + - - +
85C LYS 4.0 0.7 - - - +
130C LEU 3.3 2.4 - - - +
131C VAL* 3.4 3.5 - - - -
132C LEU* 2.8 37.7 + - + +
133C ASP 4.5 0.7 - - - +
134C TYR* 3.8 8.7 - - + +
502C I5R 4.1 34.5 - - + +
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Residues in contact with ILE 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C TYR* 3.8 39.0 - - + +
59C THR* 5.4 0.4 - - + +
70C VAL* 3.3 4.4 - - - -
71C TYR* 2.8 55.7 + - + +
73C ALA* 4.0 15.9 - - + -
82C VAL* 4.4 13.0 - - + +
83C ALA* 1.3 77.7 - - - +
85C LYS* 1.3 60.4 + - - +
86C LYS 3.4 2.1 + - - -
116C PHE* 4.4 7.9 - - + -
129C ASN* 3.8 33.7 - - + +
130C LEU 3.3 7.4 - - - +
131C VAL* 4.5 10.3 - - + -
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Residues in contact with LYS 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C PHE* 3.6 46.0 - - + +
69C VAL 3.5 4.0 - - - -
70C VAL* 4.1 9.8 - - + +
83C ALA* 4.0 1.4 - - - +
84C ILE* 1.3 68.5 - - - +
86C LYS* 1.3 58.8 + - - +
87C VAL* 3.6 17.7 + - + +
97C GLU* 3.0 39.1 + - - +
128C LEU 3.3 6.2 - - - +
129C ASN* 4.3 0.9 - - - -
130C LEU* 2.9 47.2 + - + +
132C LEU* 4.8 10.3 - - + +
200C ASP* 3.5 20.6 + - - -
202C GLY* 3.8 8.1 - - - -
502C I5R 4.1 15.7 + - + -
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Residues in contact with LYS 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C PHE* 3.6 0.7 - - - +
68C GLY* 3.4 8.3 - - - -
69C VAL* 2.7 40.1 + - + +
71C TYR* 4.0 32.2 + - + +
84C ILE 3.4 1.4 + - - -
85C LYS* 1.3 70.0 - - - +
87C VAL* 1.3 61.2 + - - +
88C LEU 4.2 0.2 + - - -
118C SER* 3.6 24.6 + - - -
119C SER 5.2 2.0 + - - -
127C TYR* 3.6 39.2 - - + -
128C LEU 3.6 3.1 - - - -
129C ASN* 3.6 20.4 - - - +
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Residues in contact with VAL 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C PHE* 3.5 22.7 - - + +
85C LYS* 3.8 38.4 - - + +
86C LYS* 1.3 75.8 - - - +
88C LEU* 1.3 74.6 + - - +
89C GLN* 3.4 1.1 + - - +
95C ASN* 4.4 20.2 - - - +
97C GLU* 5.0 4.3 - - - +
127C TYR* 3.8 2.9 - - - -
128C LEU* 2.6 51.7 + - + +
130C LEU* 5.4 5.2 - - + -
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Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C PHE 3.7 8.7 + - - +
86C LYS 4.2 0.2 + - - -
87C VAL* 1.3 83.6 - - - +
89C GLN* 1.3 66.8 + - - +
120C GLY 4.5 5.4 - - - +
126C VAL 3.4 30.1 - - - +
127C TYR* 3.4 39.1 - - + +
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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