Contacts of the helix formed by residues 74 - 86 (chain B) in PDB entry 1JT0
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 74 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LYS* 1.3 91.8 - - + +
75B ASN* 1.3 56.7 + - - +
76B ARG* 3.4 8.0 + - - +
77B GLU* 2.7 57.8 + - + +
78B LYS* 2.9 11.9 + - - +
137B ASN* 5.7 1.3 - - - +
139B GLU* 3.3 17.9 - - - +
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Residues in contact with ASN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B THR* 1.3 67.8 - - - +
76B ARG* 1.3 64.7 + - - +
78B LYS* 3.1 23.2 + - - +
79B PHE* 3.0 20.6 + - - +
130B ILE* 3.6 25.4 - - + +
133B GLU* 3.1 28.7 + - - +
134B GLY* 3.5 24.9 - - - +
137B ASN* 4.1 10.3 - - - +
139B GLU* 2.6 31.1 + - - +
140B TRP* 3.9 6.2 - - + -
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Residues in contact with ARG 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B THR* 3.0 6.2 - - - +
75B ASN* 1.3 80.0 - - - +
77B GLU* 1.3 63.2 + - - +
79B PHE* 3.3 9.2 + - - +
80B TYR* 3.0 52.7 + - + -
139B GLU* 3.1 19.9 + - + +
140B TRP* 3.8 18.1 - - + -
180B GLN* 5.0 5.9 + - - +
183B LEU* 3.8 32.2 - - + +
184B ASN* 5.2 2.0 - - - +
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS 3.3 8.8 - - - +
72B ALA* 3.0 24.4 - - + +
73B LYS* 2.4 36.9 + - - +
74B THR* 2.7 36.9 + - + +
76B ARG* 1.3 69.5 - - - +
78B LYS* 1.3 64.0 + - - +
80B TYR* 3.0 19.3 + - - +
81B LEU* 3.0 17.1 + - + +
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Residues in contact with LYS 78 (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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65B TRP* 3.5 20.2 - - + -
69B GLN* 3.1 51.2 + - + +
72B ALA* 3.8 21.5 - - + +
73B LYS 5.9 0.9 - - - -
74B THR 2.9 13.7 + - - +
75B ASN* 3.1 23.8 + - - +
77B GLU* 1.3 73.9 - - - +
79B PHE* 1.3 54.6 + - - +
81B LEU* 3.2 2.6 + - - -
82B TYR* 2.7 37.2 + - - +
130B ILE* 4.3 12.8 - - + -
133B GLU* 5.2 6.9 + - - -
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Residues in contact with PHE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASN 3.0 10.8 + - - +
76B ARG* 3.5 10.5 - - - +
77B GLU 3.1 0.2 + - - -
78B LYS* 1.3 76.8 - - - +
80B TYR* 1.3 63.9 + - - +
82B TYR* 3.8 0.5 - - - +
83B ASN* 2.8 51.9 + - - -
127B TYR* 3.6 29.4 - + - -
130B ILE* 4.2 16.1 - - + +
131B PHE* 3.6 28.3 - + - -
140B TRP* 5.1 1.3 - - + -
152B ALA* 4.2 6.3 - - + -
156B VAL* 5.2 0.2 - - + -
178B PHE* 4.6 5.8 - + - -
179B SER* 3.9 23.8 - - - -
182B PHE* 4.0 24.0 - + + -
183B LEU* 3.4 35.7 - - + -
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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
----------------------------------------------------------
76B ARG* 3.0 54.8 + - + -
77B GLU* 3.0 10.3 + - - +
79B PHE* 1.3 79.5 - - - +
81B LEU* 1.3 66.2 + - + +
83B ASN* 3.4 2.6 + - - +
84B GLU* 3.0 22.8 + - - +
176B ASN* 3.5 47.5 + - + +
179B SER* 3.6 14.1 - - - -
180B GLN* 3.2 26.8 - - + +
183B LEU* 3.6 19.7 - - + -
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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
----------------------------------------------------------
65B TRP* 4.1 9.2 - - + -
68B GLU* 3.6 38.4 - - - +
69B GLN* 4.9 1.1 - - - -
71B LYS* 4.4 8.1 - - + +
72B ALA* 3.7 31.4 - - + +
77B GLU* 3.0 17.6 + - + +
78B LYS* 3.6 7.0 - - - +
80B TYR* 1.3 76.9 - - + +
82B TYR* 1.3 59.1 + - - +
84B GLU* 2.8 19.7 + - - +
85B LEU* 2.7 36.4 + - - +
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Residues in contact with TYR 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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61B TRP* 3.7 25.1 + + - -
65B TRP* 3.3 48.8 - + + -
78B LYS 2.7 21.0 + - - +
79B PHE 3.8 3.1 - - - +
81B LEU* 1.3 72.4 - - - +
83B ASN* 1.3 57.1 + - - +
85B LEU* 3.5 3.9 + - - +
86B SER* 2.8 29.2 + - - -
93B TYR* 4.0 10.8 - - - -
123B TYR* 3.3 28.2 + - - -
126B ALA* 3.3 33.6 - - + +
127B TYR* 3.3 41.5 - + + -
130B ILE* 4.2 11.0 - - + -
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Residues in contact with ASN 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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79B PHE* 2.8 46.6 + - - +
80B TYR 3.7 4.0 - - - +
81B LEU 3.1 1.2 - - - -
82B TYR* 1.3 72.7 - - - +
84B GLU* 1.3 67.2 + - - +
86B SER* 3.1 16.6 + - - -
87B LEU* 3.6 2.8 + - - +
127B TYR* 2.6 32.5 + - - -
156B VAL* 3.0 18.0 - - - +
175B MET* 3.2 36.0 - - + +
178B PHE* 5.1 0.2 - - - -
179B SER* 3.2 19.2 + - - +
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Residues in contact with GLU 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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80B TYR 3.0 12.6 + - - +
81B LEU* 2.8 29.3 + - - +
83B ASN* 1.3 68.2 - - - +
85B LEU* 1.3 56.0 + - - +
86B SER 2.9 1.3 - - - -
87B LEU* 2.7 38.8 + - - +
88B THR* 3.2 16.6 - - + +
172B ILE* 3.0 41.3 - - + +
175B MET* 4.5 4.7 - - - +
176B ASN* 4.2 12.0 - - - +
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B TRP* 3.4 23.6 - - + -
64B GLN* 3.4 27.6 - - + +
65B TRP* 3.6 46.4 - - + +
68B GLU* 4.4 22.9 - - + +
81B LEU 2.7 21.2 + - - +
82B TYR 3.7 3.4 - - - +
84B GLU* 1.3 73.5 - - - +
86B SER* 1.3 61.7 + - - +
87B LEU 3.1 1.4 + - - -
88B THR* 3.8 13.9 - - - +
89B THR* 3.1 27.3 + - - +
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Residues in contact with SER 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B TRP* 3.6 10.5 - - - -
82B TYR* 2.8 16.6 + - - -
83B ASN* 3.1 17.4 + - - -
84B GLU 2.9 0.4 + - - -
85B LEU* 1.3 78.1 - - - +
87B LEU* 1.3 56.1 + - - +
89B THR* 3.7 2.6 - - - +
93B TYR* 3.2 52.7 - - - +
156B VAL* 3.8 7.0 - - - +
160B VAL* 3.2 23.9 - - - +
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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