Contacts of the helix formed by residues 74 - 89 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C LYS* 1.3 82.7 - - + +
75C ASN* 1.3 58.3 + - - +
76C ARG* 4.6 2.6 - - - +
77C GLU* 2.9 33.4 + - - +
78C LYS* 2.8 32.1 + - - +
139C GLU* 3.0 21.8 - - - +
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Residues in contact with ASN 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C THR* 1.3 68.5 - - - +
76C ARG* 1.3 59.7 + - - +
78C LYS* 2.8 39.6 + - - +
79C PHE* 3.0 6.6 + - - +
130C ILE* 3.5 21.6 - - - +
133C GLU* 3.0 35.3 + - - +
134C GLY* 3.0 34.4 - - - +
137C ASN* 4.0 7.3 - - - +
139C GLU* 2.7 19.8 + - + +
140C TRP* 3.6 11.0 - - + -
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Residues in contact with ARG 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C THR* 4.6 2.9 - - - +
75C ASN* 1.3 77.4 - - - +
77C GLU* 1.3 61.8 + - - +
79C PHE* 3.4 9.7 - - - +
80C TYR* 3.3 45.3 + - - -
139C GLU* 2.9 22.5 + - - +
140C TRP* 3.4 27.9 - - + -
180C GLN* 5.1 3.2 + - - +
183C LEU* 3.3 47.9 - - + +
184C ASN 5.5 0.8 - - - +
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Residues in contact with GLU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LYS 4.3 4.2 - - - +
72C ALA* 3.6 14.9 - - + -
73C LYS* 2.8 34.2 + - - +
74C THR* 2.9 29.9 + - - +
75C ASN 3.0 0.2 - - - -
76C ARG* 1.3 78.3 - - - +
78C LYS* 1.3 64.2 + - - +
80C TYR* 3.8 7.0 + - - +
81C LEU* 3.3 19.9 + - + +
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Residues in contact with LYS 78 (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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65C TRP* 3.9 5.9 - - + -
69C GLN* 3.4 53.6 + - + +
72C ALA* 4.1 14.1 - - + -
73C LYS 5.4 2.7 - - - -
74C THR 2.8 20.9 + - - +
75C ASN* 2.8 23.3 + - - +
77C GLU* 1.3 73.4 - - - +
79C PHE* 1.3 57.8 + - - +
81C LEU* 2.7 9.9 + - - +
82C TYR* 2.7 34.3 + - - +
129C VAL* 5.6 0.8 - - - +
130C ILE* 3.6 32.5 - - + +
133C GLU* 4.6 9.9 + - - -
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Residues in contact with PHE 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ASN 3.0 6.2 + - - +
76C ARG 3.4 11.7 - - - +
78C LYS* 1.3 80.0 - - - +
80C TYR* 1.3 67.5 + - - +
82C TYR* 3.0 5.4 + - - +
83C ASN* 2.9 51.4 + - - -
127C TYR* 4.1 19.1 - + - -
130C ILE* 3.9 12.9 - - + +
131C PHE* 3.2 37.0 - + - -
140C TRP* 5.4 0.9 - + + -
152C ALA* 4.1 7.9 - - + -
156C VAL* 5.3 0.2 - - + -
178C PHE* 4.6 4.3 - + - -
179C SER* 4.2 18.2 - - - -
182C PHE* 3.5 32.1 - + + -
183C LEU* 4.0 24.7 - - + -
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Residues in contact with TYR 80 (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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76C ARG* 3.3 40.2 + - - -
77C GLU* 4.0 9.0 - - - +
78C LYS 3.4 0.4 - - - -
79C PHE* 1.3 78.1 - - - +
81C LEU* 1.3 57.0 + - - +
83C ASN* 3.5 2.1 + - - +
84C GLU* 2.9 33.1 + - - +
175C MET* 5.5 0.2 - - - +
176C ASN* 3.5 40.2 - - + +
179C SER* 3.9 18.6 + - - -
180C GLN* 3.1 34.7 - - + +
183C LEU* 3.1 27.4 - - + -
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Residues in contact with LEU 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C TRP* 3.7 12.8 - - + -
68C GLU* 3.1 41.7 - - + +
71C LYS* 4.7 5.6 - - + +
72C ALA* 4.3 15.7 - - + -
77C GLU* 3.3 11.3 + - + +
78C LYS* 2.7 14.4 + - - +
80C TYR* 1.3 72.2 - - - +
82C TYR* 1.3 66.0 + - - +
84C GLU* 3.3 14.7 + - + +
85C LEU* 2.8 40.2 + - + +
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Residues in contact with TYR 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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61C TRP* 3.1 36.9 + + - -
65C TRP* 3.6 42.0 - + + -
78C LYS 2.7 14.8 + - - +
79C PHE* 3.6 8.7 - - - +
81C LEU* 1.3 70.5 - - - +
83C ASN* 1.3 57.8 + - - +
85C LEU* 2.8 22.1 + - - +
86C SER* 2.9 17.0 + - - -
93C TYR* 4.9 4.9 - - - -
123C TYR* 3.3 28.1 + + - -
126C ALA* 3.1 33.7 - - + +
127C TYR* 3.3 51.1 - + - -
130C ILE* 5.6 5.6 - - + -
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Residues in contact with ASN 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C PHE* 2.9 52.1 + - - +
80C TYR 3.8 2.9 - - - +
82C TYR* 1.3 80.9 - - - +
84C GLU* 1.3 59.9 + - - +
86C SER* 2.9 23.2 + - - -
87C LEU* 3.9 2.9 - - - +
127C TYR* 2.9 30.2 + - - -
156C VAL* 3.1 19.1 - - - +
175C MET* 3.5 30.2 - - + +
178C PHE* 4.6 2.2 - - - -
179C SER* 4.0 9.8 + - - +
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Residues in contact with GLU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C TYR* 2.9 18.2 + - - +
81C LEU* 3.8 15.3 - - + +
83C ASN* 1.3 73.9 - - - +
85C LEU* 1.3 60.1 + - + +
87C LEU* 3.2 16.1 - - - +
88C THR* 2.6 27.4 + - - +
172C ILE* 3.8 37.2 - - + +
175C MET* 4.2 8.5 - - + +
176C ASN* 4.0 18.8 + - - +
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Residues in contact with LEU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C TRP* 3.1 33.9 - - + -
64C GLN* 3.2 28.7 - - + +
65C TRP* 4.8 5.8 - - + +
68C GLU* 3.9 38.1 - - + +
81C LEU* 2.8 22.3 + - + +
82C TYR* 2.8 12.3 + - - +
84C GLU* 1.3 74.1 - - + +
86C SER* 1.3 51.6 + - - +
87C LEU 2.7 16.4 + - - -
88C THR* 2.9 9.9 + - - +
89C THR* 2.7 30.7 + - - +
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Residues in contact with SER 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C TRP* 3.8 7.4 - - - -
82C TYR* 2.9 12.9 + - - -
83C ASN* 2.9 22.4 + - - -
85C LEU* 1.3 72.5 - - - +
87C LEU* 1.3 56.3 + - - +
89C THR* 3.8 4.5 - - - -
93C TYR* 3.0 47.7 - - - -
127C TYR* 5.0 1.7 + - - -
156C VAL* 3.8 14.7 - - - +
160C VAL* 3.2 23.7 - - - +
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Residues in contact with LEU 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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83C ASN 3.9 3.6 - - - +
84C GLU* 3.2 11.7 - - - +
85C LEU 2.7 1.6 + - - -
86C SER* 1.3 75.0 - - - +
88C THR* 1.3 66.5 + - - +
89C THR* 3.6 4.4 - - - +
93C TYR* 5.9 0.9 - - - -
159C ILE* 5.4 1.8 - - + +
160C VAL* 3.8 32.9 - - + +
168C ILE* 3.7 16.4 - - + +
171C ARG* 3.8 49.3 - - + +
172C ILE* 3.8 11.0 - - + +
175C MET* 3.6 37.0 - - + -
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Residues in contact with THR 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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84C GLU* 2.6 21.5 + - - +
85C LEU* 3.2 18.1 + - - +
87C LEU* 1.3 79.2 - - - +
89C THR* 1.3 64.5 + - - +
90C GLU* 3.6 2.9 + - - +
168C ILE* 4.2 11.9 - - + -
172C ILE* 3.9 24.0 - - + -
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Residues in contact with THR 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C TRP* 3.5 17.2 - - + -
64C GLN* 2.8 35.8 + - - -
85C LEU* 2.7 26.0 + - - +
86C SER* 3.8 11.2 - - - -
87C LEU 4.5 4.0 - - - +
88C THR* 1.3 76.9 - - - +
90C GLU* 1.3 61.3 + - - +
91C TYR* 2.8 30.4 + - - +
93C TYR* 4.0 10.3 - - + +
94C PRO* 3.7 10.7 - - - +
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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