Contacts of the strand formed by residues 78 - 86 (chain B) in PDB entry 1JTO
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 THR 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B SER* 4.7 1.3 - - - -
22B CYS 3.1 20.2 - - - +
23B ALA* 3.4 19.8 - - + +
53B MET* 4.8 0.8 - - - +
72B GLN* 3.3 4.2 - - - +
73B ASP* 2.7 44.3 + - - +
76B LYS* 3.2 20.4 + - - +
77B ASN* 1.3 76.2 - - - +
79B VAL* 1.3 67.5 + - - +
80B TYR* 3.7 31.1 - - + +
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B SER* 3.4 3.5 - - - -
22B CYS* 2.9 48.6 + - + +
34B MET* 3.8 38.4 - - + -
35B GLY 5.5 0.2 - - - +
36B TRP* 3.9 18.2 - - + +
51B ILE* 4.1 11.2 - - + -
53B MET* 3.9 16.8 - - - -
70B ILE* 4.8 7.0 - - + -
71B SER 3.1 11.2 - - - +
72B GLN* 4.1 3.4 - - + -
78B THR* 1.3 78.6 - - - +
80B TYR* 1.3 64.6 + - - +
96B CYS* 4.8 1.3 - - - -
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Residues in contact with TYR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ARG* 3.6 47.3 - - - +
20B LEU 3.5 4.3 - - - +
21B SER* 3.6 28.9 - - - -
36B TRP* 4.7 2.7 - - - -
69B THR 3.5 1.2 - - - +
70B ILE* 3.3 5.9 - - - +
71B SER* 2.5 53.5 + - - +
72B GLN 4.8 0.7 - - - -
73B ASP* 3.8 36.1 + - + +
76B LYS* 5.2 6.2 + - - +
78B THR* 3.7 19.4 - - + +
79B VAL* 1.3 74.3 - - - +
81B LEU* 1.3 61.1 + - - +
82B LEU* 3.9 1.8 - - + +
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU 3.8 0.3 - - - +
19B ARG* 3.6 2.8 - - - -
20B LEU* 2.8 45.0 + - + +
36B TRP* 3.6 42.8 - - + +
48B VAL* 4.5 8.1 - - + -
49B ALA* 4.0 26.2 - - + -
68B PHE* 4.3 11.9 - - + -
69B THR 3.4 16.8 - - - +
70B ILE* 4.2 2.2 - - + -
79B VAL 4.4 0.2 + - - -
80B TYR* 1.3 73.1 - - - +
82B LEU* 1.3 60.4 + - - +
83B MET* 3.6 34.1 + - + +
94B TYR* 4.4 6.5 - - + -
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B SER* 5.2 3.8 - - - -
18B LEU 3.8 10.1 - - - +
19B ARG* 4.7 18.4 - - + +
67B ARG 4.1 0.3 - - - +
68B PHE* 3.2 7.3 - - - +
69B THR* 2.7 51.0 + - + +
80B TYR* 3.9 3.1 - - + +
81B LEU* 1.3 70.1 - - - +
83B MET* 1.3 65.3 + - - +
84B ASN* 3.4 34.7 + - - +
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Residues in contact with MET 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B GLY 3.8 0.5 - - - +
17B SER* 2.9 28.6 - - - -
18B LEU* 2.8 24.7 + - - +
20B LEU* 4.1 20.9 - - - -
68B PHE* 3.3 31.4 - - + -
81B LEU* 4.0 25.1 - - + +
82B LEU* 1.3 77.8 - - - +
84B ASN* 1.3 61.7 + - - +
86B LEU* 3.4 29.6 - - + +
94B TYR* 3.2 43.5 - - + +
129B VAL* 4.7 8.3 - - + -
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Residues in contact with ASN 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B SER* 3.0 21.2 + - - +
66B GLY 5.9 0.2 - - - +
67B ARG* 3.1 38.7 + - - +
68B PHE* 4.2 1.9 - - - -
69B THR* 5.4 3.2 + - - -
82B LEU* 3.4 34.9 + - - +
83B MET* 1.3 75.4 - - - +
85B SER* 1.3 77.6 + - - +
86B LEU 3.4 0.7 - - - -
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLY* 4.1 17.8 + - - -
16B GLY 3.1 8.3 + - - -
17B SER* 4.1 0.8 + - - -
67B ARG* 2.6 42.8 + - - +
84B ASN* 1.3 77.6 - - - +
86B LEU* 1.3 54.7 + - - +
87B GLU* 3.3 11.3 + - - +
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 3.6 26.0 - - + -
14B ALA* 3.1 16.1 - - - -
15B GLY 3.9 3.5 - - - +
16B GLY 3.3 10.5 + - - +
17B SER* 4.1 2.7 - - - -
18B LEU* 4.0 34.8 - - + +
68B PHE* 3.5 21.8 - - + -
83B MET* 3.4 35.4 - - + +
84B ASN 3.4 0.6 - - - -
85B SER* 1.3 72.0 - - - +
87B GLU* 1.3 61.9 + - - +
90B ASP* 3.6 7.4 - - + +
129B VAL* 4.8 3.1 - - + -
131B VAL* 3.0 33.7 - - + +
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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