Contacts of the strand formed by residues 82 - 86 (chain M) in PDB entry 3J0S
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 TYR 82 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37M LEU* 3.5 2.4 - - - +
38M PHE* 2.5 60.2 + - + +
39M CYS* 4.3 4.0 - - - -
40M LEU* 3.4 25.4 - - + -
47M ILE* 5.3 7.0 - - + -
81M ARG* 1.3 73.1 - - - +
83M ALA* 1.3 59.4 + - - +
101M PHE* 3.5 30.5 - + + -
102M ILE 4.2 0.4 - - - -
103M PHE* 3.8 7.0 - + - -
117M TYR* 3.0 52.5 + + - -
120M SER* 3.0 34.7 - - - -
121M LYS* 4.7 0.7 - - - -
124M ILE* 3.4 33.9 - - + -
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Residues in contact with ALA 83 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36M VAL 3.3 7.0 - - - +
37M LEU* 3.4 24.7 - - + -
38M PHE* 4.1 2.5 - - - -
71M PHE* 3.7 23.8 - - + -
75M LEU* 5.4 1.8 - - + -
81M ARG 5.3 0.7 - - - +
82M TYR* 1.3 77.9 - - - +
84M LEU* 1.3 59.6 + - - +
101M PHE* 3.4 11.3 - - - -
102M ILE* 2.6 44.7 + - + +
104M TRP* 6.2 0.2 - - + -
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Residues in contact with LEU 84 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11M VAL* 5.7 0.9 - - + -
15M PHE* 3.5 35.9 - - + -
18M MET* 4.0 20.3 - - + +
34M LYS 4.6 0.2 - - - -
35M ALA* 3.0 5.4 - - - +
36M VAL* 2.8 47.9 + - + +
38M PHE* 3.3 29.4 - - + -
83M ALA* 1.3 72.5 - - - +
85M TYR* 1.3 60.6 + - - +
99M LEU* 6.2 0.2 - - + -
100M VAL 3.7 5.2 - - - +
101M PHE* 3.1 42.8 - - + -
128M LEU* 4.9 3.1 - - + -
131M ILE* 4.2 12.8 - - + -
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Residues in contact with TYR 85 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M MET* 5.6 0.2 - - - -
34M LYS* 3.4 33.0 + - + +
35M ALA* 3.3 24.0 - - + -
55M ILE* 4.9 2.2 - - + -
67M PRO* 4.8 4.5 - - + -
68M TYR* 3.2 53.2 + + + +
71M PHE* 4.6 12.1 - + + -
83M ALA 4.2 0.4 - - - -
84M LEU* 1.3 75.4 - - - +
86M ASP* 1.3 90.8 + - - +
87M ALA* 4.3 5.6 + - - -
100M VAL* 3.0 41.7 + - + +
102M ILE* 3.8 22.9 - - + +
149M LEU* 4.1 17.7 - - + +
161M LEU* 6.1 0.5 - - - +
162M GLU* 4.2 10.2 + - - -
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Residues in contact with ASP 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18M MET* 3.3 30.8 - - - +
32M ARG* 4.9 7.8 + - - -
33M LYS 3.4 16.8 - - - +
34M LYS* 2.7 25.5 + - + +
57M VAL* 5.1 1.0 - - + +
85M TYR* 1.3 94.2 - - - +
87M ALA* 1.3 66.6 + - - +
88M THR* 3.4 10.6 + - - +
97M GLU* 3.4 29.2 - - + +
98M ASP 4.0 2.9 - - - -
99M LEU* 4.6 11.8 - - - +
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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