Contacts of the helix formed by residues 81 - 94 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76C VAL 4.2 0.3 + - - -
77C GLY* 3.7 5.4 - - - -
78C ALA 2.7 32.0 + - - -
79C VAL 3.3 1.1 - - - +
80C HIS* 1.3 83.8 - - - +
82C ASN* 1.3 63.1 + - - +
83C HIS* 3.5 1.4 - - - +
84C ALA* 3.0 36.8 + - - +
85C PHE 3.7 1.9 + - - -
111C ASN* 3.1 11.1 + - - +
115C ASP* 5.4 0.5 - - - +
1031C 5PA 2.8 31.0 + - - -
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Residues in contact with ASN 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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50C ILE* 3.4 20.9 - - + +
54C LYS* 5.1 3.1 - - + -
80C HIS* 4.4 1.6 + - - +
81C SER* 1.3 70.1 - - - +
83C HIS* 1.3 67.4 + - - +
85C PHE* 3.2 5.0 + - - +
86C VAL* 2.9 28.2 + - + +
111C ASN* 2.9 27.2 - - - +
281C VAL* 5.3 1.4 - - - +
282C TYR* 3.5 20.1 - - - -
310C GLY* 3.5 25.4 + - - +
312C SER* 3.9 7.5 - - - -
313C GLY 4.8 1.0 - - - +
1031C 5PA 2.8 32.3 + - + +
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Residues in contact with HIS 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LYS* 3.6 34.1 - - + +
57C LYS* 6.0 1.1 - - + -
58C LEU* 4.9 1.8 - - + -
61C LEU* 4.7 7.0 - - + -
75C THR* 3.0 27.5 + - + -
76C VAL 3.8 15.0 - - - -
81C SER* 3.5 1.6 - - - +
82C ASN* 1.3 78.6 - - - +
84C ALA* 1.3 60.9 + - - +
86C VAL* 4.4 0.7 - - - -
87C THR* 2.7 48.2 + - - -
154C ILE* 4.1 6.8 - - + +
155C PRO 3.7 2.4 + - - -
157C GLY 3.6 14.8 - - - -
158C GLY* 3.5 27.1 + - - -
1031C 5PA 3.0 29.9 + + + +
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Residues in contact with ALA 84 (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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75C THR* 3.8 18.6 - - + -
76C VAL 4.7 4.0 - - - +
78C ALA 4.8 0.7 - - - +
79C VAL 5.9 0.4 - - - +
81C SER* 3.0 29.3 + - - +
82C ASN 3.2 0.2 - - - -
83C HIS* 1.3 77.2 - - - +
85C PHE* 1.3 64.7 + - - +
87C THR* 3.7 2.3 - - - -
88C GLY 3.0 16.5 + - - -
100C LEU* 3.5 33.0 - - + +
102C LEU* 4.5 11.4 - - + -
115C ASP* 5.0 2.9 - - - +
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Residues in contact with PHE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLY* 4.0 2.5 - - - -
50C ILE* 3.9 38.6 - - + -
81C SER 3.7 2.0 + - - +
82C ASN 3.2 7.0 + - - +
84C ALA* 1.3 77.2 - - - +
86C VAL* 1.3 71.0 + - - +
88C GLY* 2.7 23.0 + - - -
89C LEU* 2.8 46.9 + - + +
100C LEU* 4.5 0.2 - - - -
111C ASN* 4.0 20.0 - - + +
114C LEU* 3.9 34.1 - - + -
115C ASP* 3.6 23.9 + - - +
118C MET* 3.7 28.0 - - + -
120C ILE* 4.0 5.1 - - + +
277D ILE* 4.3 8.1 - - + -
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Residues in contact with VAL 86 (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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48C LEU* 4.0 19.3 - - + +
50C ILE* 4.2 12.3 - - + -
51C GLY 4.1 11.0 - - - +
54C LYS* 3.4 22.0 - - + -
55C ILE* 3.4 26.7 - - + -
58C LEU* 3.2 25.1 - - + -
82C ASN* 2.9 15.7 + - + +
83C HIS 3.9 2.5 - - - +
85C PHE* 1.3 86.0 - - + +
87C THR* 1.3 58.6 + - - +
89C LEU* 4.9 0.2 - - - -
90C ALA* 3.0 31.2 + - - +
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Residues in contact with THR 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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58C LEU* 4.0 20.9 - - + +
62C LEU* 4.6 2.6 - - + +
73C VAL* 3.9 12.1 - - + -
75C THR* 4.3 13.2 - - - -
83C HIS* 2.7 51.7 + - - -
84C ALA 3.7 3.6 - - - -
86C VAL* 1.3 72.7 - - - +
88C GLY* 1.3 59.0 + - - +
90C ALA* 3.6 1.8 - - - +
91C ALA* 3.1 25.6 + - - +
98C ALA* 4.7 0.6 - - - +
100C LEU* 5.7 1.1 - - + -
154C ILE* 3.6 31.4 - - + -
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Residues in contact with GLY 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 ALA 3.0 10.4 + - - -
85C PHE 2.7 13.6 + - - -
87C THR* 1.3 71.5 - - - +
89C LEU* 1.3 61.3 + - - -
90C ALA 3.2 0.2 - - - -
91C ALA* 3.7 1.7 + - - +
92C LYS* 3.3 29.3 + - - +
98C ALA* 3.7 21.2 - - - +
100C LEU* 4.3 4.7 - - - +
120C ILE* 3.7 13.9 - - - -
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Residues in contact with LEU 89 (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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48C LEU* 4.4 5.8 - - + -
49C GLY* 4.1 16.2 - - - -
85C PHE* 2.8 40.8 + - + +
86C VAL 4.2 2.7 - - - +
88C GLY* 1.3 74.8 - - - +
90C ALA* 1.3 67.1 + - - +
92C LYS* 3.5 5.3 + - - +
93C LYS* 3.1 23.1 + - - +
118C MET* 3.2 44.2 - - + -
120C ILE* 3.9 3.5 - - + +
271D GLY* 3.7 26.1 - - - +
272D THR* 4.2 8.2 - - + +
275D GLY* 4.2 12.5 - - - -
277D ILE* 4.9 3.6 - - + -
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Residues in contact with ALA 90 (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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17C LEU* 4.9 2.5 - - + -
48C LEU* 4.2 23.5 - - + +
58C LEU* 4.1 12.1 - - + -
62C LEU* 3.4 22.2 - - + -
86C VAL 3.0 20.5 + - - +
87C THR 3.6 4.7 - - - +
88C GLY 3.2 0.2 - - - -
89C LEU* 1.3 74.9 - - - +
91C ALA* 1.3 70.4 + - - +
93C LYS* 3.2 10.5 + - - +
94C LEU* 3.2 16.9 + - - +
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Residues in contact with ALA 91 (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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62C LEU* 3.8 10.0 - - + +
73C VAL* 4.6 9.4 - - + -
87C THR 3.1 14.4 + - - +
88C GLY 3.8 5.8 - - - +
90C ALA* 1.3 76.5 - - - +
92C LYS* 1.3 55.3 + - - +
94C LEU* 2.7 37.6 + - - +
95C GLY 3.5 0.5 + - - -
96C LEU* 3.9 20.9 + - + -
97C ASP 4.0 12.6 - - - +
98C ALA* 3.9 17.3 - - + -
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Residues in contact with LYS 92 (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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88C GLY 3.3 13.6 + - - +
89C LEU* 3.7 7.4 - - - +
90C ALA 3.4 0.2 - - - -
91C ALA* 1.3 80.2 - - + +
93C LYS* 1.3 61.7 + - - +
94C LEU 3.5 0.2 + - - -
95C GLY* 3.6 10.6 + - - +
96C LEU 3.8 14.3 + - - +
97C ASP* 4.4 14.3 + - - -
98C ALA* 5.2 4.7 + - + +
118C MET 4.3 0.7 - - - -
119C GLY 3.5 15.5 + - - -
120C ILE* 3.6 42.7 - - + +
121C GLU 5.3 0.4 - - - +
272D THR* 3.0 42.8 - - + +
273D ARG* 4.6 2.9 - - - +
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Residues in contact with LYS 93 (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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16C GLU 4.7 5.7 + - - -
17C LEU* 4.0 19.6 + - + +
48C LEU* 4.7 14.6 - - + +
89C LEU 3.1 10.7 + - - +
90C ALA* 3.6 7.6 - - - +
91C ALA 2.8 3.0 + - - -
92C LYS* 1.3 76.7 - - - +
94C LEU* 1.3 83.7 + - + +
95C GLY 3.3 3.9 + - - -
28D PRO* 6.3 1.3 - - - -
29D ASN* 3.9 15.1 + - - +
272D THR 3.0 12.7 + - - +
273D ARG 3.2 20.6 - - - +
274D GLU* 3.7 25.0 + - - +
275D GLY* 4.2 6.5 - - - +
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Residues in contact with LEU 94 (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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15C VAL* 3.3 34.5 - - + -
17C LEU* 4.1 8.1 - - + -
62C LEU* 4.1 26.5 - - + -
66C LEU* 3.3 40.2 - - + +
90C ALA 3.6 8.3 - - - +
91C ALA* 2.7 15.6 + - - +
93C LYS* 1.3 99.6 - - + +
95C GLY* 1.3 55.7 + - - -
96C LEU* 3.2 8.8 + - + +
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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