Contacts of the helix formed by residues 81 - 94 (chain M) in PDB entry 1J0B
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 SER 81 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77M GLY* 4.1 2.4 - - - -
78M ALA 2.9 32.5 - - - -
79M VAL 3.0 3.2 - - - +
80M HIS* 1.3 81.4 - - - +
82M ASN* 1.3 62.0 + - - +
83M HIS* 3.4 2.6 + - - +
84M ALA* 2.5 42.0 + - - +
85M PHE* 3.5 10.9 + - - +
111M ASN* 3.8 11.1 - - - +
115M ASP* 5.4 0.9 - - - +
256M TYR* 5.8 0.2 - - - -
282M TYR* 5.6 1.3 - - - -
1131M 5PA 3.4 16.4 + - - -
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Residues in contact with ASN 82 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M ILE* 3.8 16.4 - - + +
51M GLY 6.0 0.9 - - - +
54M LYS* 5.4 1.6 - - + -
80M HIS 3.1 4.5 + - - +
81M SER* 1.3 71.2 - - - +
83M HIS* 1.3 64.9 + - - +
85M PHE* 3.3 4.5 + - - +
86M VAL* 3.1 27.2 + - + +
111M ASN* 3.1 28.2 - - - +
279M ASP* 5.0 1.2 + - - +
282M TYR* 3.3 22.3 - - - -
310M GLY* 3.2 35.4 + - - +
312M SER* 4.2 1.8 - - - -
313M GLY* 4.3 3.0 - - - +
1131M 5PA 3.0 29.2 + - + +
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Residues in contact with HIS 83 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54M LYS* 3.3 31.5 - - + +
57M LYS* 6.2 0.2 - - + -
58M LEU* 4.3 10.3 - - + -
61M LEU* 5.3 0.4 - - + -
75M THR* 3.3 23.5 + - - -
76M VAL 3.8 9.9 - - - -
82M ASN* 1.3 77.7 - - - +
84M ALA* 1.3 57.4 + - - +
86M VAL* 3.5 1.1 + - - +
87M THR* 2.6 50.3 + - - -
154M ILE* 4.1 4.8 - - + +
157M GLY* 3.2 24.7 - - - -
158M GLY* 3.1 30.6 + - - -
1131M 5PA 2.7 32.8 + - + +
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Residues in contact with ALA 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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75M THR* 4.2 15.0 - - + +
76M VAL 4.6 7.6 - - - +
78M ALA 4.7 0.2 - - - +
81M SER* 2.5 31.9 + - - +
83M HIS* 1.3 75.2 - - - +
85M PHE* 1.3 62.5 + - - +
87M THR* 4.3 0.9 - - - -
88M GLY 3.2 14.0 + - - -
100M LEU* 2.9 38.3 - - + +
102M LEU* 4.5 9.6 - - + -
115M ASP* 5.6 1.3 - - - +
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Residues in contact with PHE 85 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49M GLY* 4.5 5.2 - - - -
50M ILE* 4.2 12.3 - - + -
81M SER 3.5 9.6 + - - +
82M ASN 3.3 6.8 + - - +
84M ALA* 1.3 78.1 - - - +
86M VAL* 1.3 56.2 + - + +
88M GLY* 3.4 1.0 + - - -
89M LEU* 2.7 63.9 + - + +
100M LEU* 3.9 1.1 - - - +
111M ASN* 3.7 21.1 - - - +
114M LEU* 3.5 32.5 - - + -
115M ASP* 3.4 26.0 + - - +
118M MET* 3.6 31.9 - - + -
120M ILE* 3.9 7.0 - - + -
277N ILE* 4.0 18.8 - - + -
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Residues in contact with VAL 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48M LEU* 4.0 14.4 - - + +
49M GLY* 4.6 1.8 - - - -
50M ILE* 4.2 16.2 - - + +
51M GLY 3.9 20.4 - - - +
54M LYS* 3.8 23.8 - - + -
55M ILE* 3.2 30.5 - - + -
58M LEU* 4.0 6.7 - - + +
82M ASN 3.1 17.8 + - - +
83M HIS 4.1 2.0 - - - +
85M PHE* 1.3 79.7 - - + +
87M THR* 1.3 59.2 + - - +
89M LEU* 4.5 3.4 - - - +
90M ALA* 3.0 25.2 + - - +
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Residues in contact with THR 87 (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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58M LEU* 3.4 25.3 - - + +
62M LEU* 4.9 1.3 - - + +
73M VAL* 4.3 10.1 - - + -
75M THR* 4.4 11.2 - - - +
83M HIS* 2.6 44.1 + - + +
84M ALA 4.3 2.5 - - - -
86M VAL* 1.3 75.5 - - - +
88M GLY* 1.3 60.8 + - - +
90M ALA* 3.8 0.7 - - - +
91M ALA* 2.9 31.9 + - - +
154M ILE* 3.3 34.8 - - + -
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Residues in contact with GLY 88 (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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73M VAL* 6.4 0.2 - - - -
84M ALA 3.2 13.6 + - - -
85M PHE 3.8 2.0 - - - -
87M THR* 1.3 81.2 - - - +
89M LEU* 1.3 61.8 + - - +
91M ALA 3.6 0.2 + - - -
92M LYS* 3.4 19.4 + - - +
98M ALA* 3.7 27.5 - - - +
100M LEU* 3.9 11.6 - - - +
120M ILE* 3.7 10.5 - - - +
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Residues in contact with LEU 89 (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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48M LEU* 4.2 6.3 - - + -
49M GLY* 3.8 24.9 - - - +
85M PHE* 2.7 45.7 + - + +
86M VAL* 5.7 0.2 - - - -
88M GLY* 1.3 68.8 - - - +
90M ALA* 1.3 66.7 + - - +
91M ALA 2.9 3.1 + - - -
92M LYS* 2.9 16.1 + - - +
93M LYS* 3.2 11.5 + - - +
118M MET* 3.8 28.0 - - + -
120M ILE* 3.6 5.5 - - + +
271N GLY* 3.2 37.8 - - - +
272N THR* 4.1 6.3 - - + +
275N GLY* 4.0 13.5 - - - +
277N ILE* 4.9 3.6 - - + -
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Residues in contact with ALA 90 (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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17M LEU* 4.7 3.5 - - + +
48M LEU* 3.5 31.4 - - + +
58M LEU* 4.2 7.9 - - + -
62M LEU* 3.6 27.0 - - + +
86M VAL* 3.0 21.9 + - + +
87M THR 3.9 1.3 - - - +
89M LEU* 1.3 78.0 - - - +
91M ALA* 1.3 62.1 + - - +
93M LYS* 3.8 8.1 + - - +
94M LEU* 3.6 15.9 + - - +
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Residues in contact with ALA 91 (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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62M LEU* 4.2 20.6 - - + -
73M VAL* 4.5 10.8 - - + -
87M THR 2.9 18.9 + - - +
88M GLY 3.8 4.7 - - - +
89M LEU 3.0 0.2 - - - -
90M ALA* 1.3 76.5 - - - +
92M LYS* 1.3 63.1 + - - +
94M LEU* 3.1 10.9 + - - +
96M LEU* 2.9 36.0 + - + +
98M ALA* 4.3 14.1 - - + -
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Residues in contact with LYS 92 (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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88M GLY 3.4 10.8 + - - +
89M LEU* 2.9 9.9 + - - +
91M ALA* 1.3 75.3 - - - +
93M LYS* 1.3 59.1 + - - +
95M GLY* 2.6 24.4 + - - -
96M LEU 3.5 17.0 + - - +
97M ASP* 4.6 13.1 + - - +
98M ALA* 5.0 8.2 + - + +
118M MET 4.4 0.7 - - - +
119M GLY 3.0 30.5 + - - -
120M ILE* 4.2 14.8 - - + +
121M GLU 5.4 1.1 - - - +
272N THR* 3.3 41.8 - - + +
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Residues in contact with LYS 93 (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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16M GLU 5.4 2.0 + - - -
17M LEU* 4.7 26.6 + - + +
48M LEU* 5.1 11.3 - - + +
89M LEU 3.2 8.4 + - - +
90M ALA* 3.9 11.7 - - - +
91M ALA 3.2 0.2 - - - -
92M LYS* 1.3 77.6 - - - +
94M LEU* 1.3 68.7 + - + +
95M GLY* 3.0 4.7 + - - -
25N GLN* 5.9 0.8 + - - -
28N PRO* 6.1 3.7 - - - +
29N ASN* 4.7 11.8 + - - +
272N THR 3.4 11.7 + - - +
273N ARG* 3.1 27.9 - - - +
274N GLU* 4.1 25.5 + - - +
275N GLY* 4.4 8.5 - - - +
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Residues in contact with LEU 94 (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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15M VAL* 3.6 31.2 - - + -
17M LEU* 5.1 2.7 - - + -
62M LEU* 4.0 21.1 - - + -
66M LEU* 3.5 37.3 - - + +
90M ALA 3.6 8.8 + - - +
91M ALA* 3.1 10.6 + - - +
93M LYS* 1.3 90.5 - - + +
95M GLY* 1.3 61.2 + - - +
96M LEU* 3.5 13.8 - - + +
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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
------------------------------------------------------------
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