Contacts of the helix formed by residues 93 - 115 (chain L) in PDB entry 4B86
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 ASN 93 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239J GLN* 5.5 1.2 + - - -
1L MET 3.3 19.0 + - - -
2L ASN* 4.5 0.8 - - - +
3L PRO* 3.9 9.4 - - - +
54L PRO 3.8 7.9 + - - +
56L ALA* 3.5 18.4 - - + +
65L TYR* 5.4 0.6 - - - -
91L GLU* 2.8 32.8 + - - +
92L GLU* 1.3 70.0 - - - +
94L LYS* 1.3 65.4 + - - +
95L GLN* 3.3 19.9 + - - +
96L LEU* 3.3 33.2 + - + +
97L SER* 3.5 21.3 + - - -
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Residues in contact with LYS 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235J GLN* 3.4 37.8 - - + +
238J GLN* 4.2 16.9 + - - +
92L GLU 3.4 10.5 + - - +
93L ASN* 1.3 69.5 + - - +
95L GLN* 1.3 67.1 + - - +
96L LEU 3.1 1.6 - - - -
97L SER* 2.9 19.3 + - - -
98L ILE* 3.0 19.6 + - + +
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Residues in contact with GLN 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237I GLN* 3.2 24.5 - - - +
232J LEU* 3.6 21.4 - - + +
235J GLN* 4.6 9.3 + - + +
236J GLN* 3.0 27.3 + - - +
239J GLN* 3.1 23.5 + - - +
2L ASN* 3.3 19.2 - - - +
3L PRO* 3.6 12.8 - - + +
7L THR* 3.4 17.7 - - + +
93L ASN* 3.3 9.6 + - - +
94L LYS* 1.3 77.2 - - - +
96L LEU* 1.3 57.1 + - - +
98L ILE* 3.5 9.7 + - - +
99L LEU* 2.9 33.8 + - - +
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Residues in contact with LEU 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L PRO* 3.7 18.6 - - + +
6L ALA* 4.8 0.4 - - + -
42L LEU* 4.0 22.9 - - + -
51L LEU* 4.1 9.6 - - + -
54L PRO* 3.9 12.8 - - + -
56L ALA* 4.0 2.2 - - + +
65L TYR* 3.5 60.1 - - + -
93L ASN* 3.3 35.5 + - + +
94L LYS 3.1 0.4 - - - -
95L GLN* 1.3 76.2 - - - +
97L SER* 1.3 58.9 + - - +
99L LEU* 3.2 6.1 + - + +
100L VAL* 2.9 33.7 + - - +
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Residues in contact with SER 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53L ASP* 5.2 1.6 + - - -
54L PRO* 3.6 26.0 + - - +
93L ASN 3.5 11.2 + - - -
94L LYS* 2.9 10.4 + - - -
96L LEU* 1.3 72.9 - - - +
98L ILE* 1.3 69.3 + - - +
100L VAL* 2.9 16.0 + - - +
101L ASN* 3.0 20.8 + - - +
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Residues in contact with ILE 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228J LEU* 3.6 30.7 - - + +
231J ASP* 3.6 36.6 - - + +
232J LEU* 3.6 22.7 - - + +
235J GLN* 3.8 21.8 - - + -
94L LYS* 3.0 14.8 + - + +
95L GLN* 3.7 8.1 - - - +
97L SER* 1.3 76.2 - - - +
99L LEU* 1.3 56.3 + - - +
101L ASN* 3.6 6.3 + - - +
102L CYS* 2.9 32.6 + - - +
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Residues in contact with LEU 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232J LEU* 4.3 16.8 - - + -
3L PRO* 3.7 20.4 - - + -
6L ALA* 3.8 17.5 - - + +
7L THR* 3.5 34.1 - - + -
10L TYR* 4.1 31.9 - - + -
38L PHE* 4.5 2.4 - - + -
42L LEU* 3.6 16.4 - - + +
95L GLN* 2.9 27.3 + - + +
96L LEU* 3.4 6.3 - - - +
97L SER 3.1 0.2 - - - -
98L ILE* 1.3 75.4 - - - +
100L VAL* 1.3 58.1 + - - +
102L CYS* 3.3 5.7 + - + +
103L TYR* 2.9 28.9 + - - +
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Residues in contact with VAL 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L LEU* 4.1 18.2 - - + -
50L LEU* 3.7 24.9 - - + -
51L LEU* 3.6 47.3 - - + +
54L PRO* 4.2 7.4 - - + -
96L LEU 2.9 20.2 + - - +
97L SER* 2.9 7.4 + - - +
99L LEU* 1.3 75.0 - - - +
101L ASN* 1.3 63.3 + - - +
103L TYR* 3.2 5.4 + - - +
104L LYS* 3.0 37.3 + - + +
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Residues in contact with ASN 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228J LEU* 3.5 27.7 - - + +
97L SER* 3.0 18.3 + - - +
98L ILE* 4.0 3.1 - - - +
100L VAL* 1.3 78.3 - - - +
102L CYS* 1.3 57.9 + - - +
104L LYS* 3.2 22.3 + - - +
105L LYS* 2.9 36.5 + - + +
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Residues in contact with CYS 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225J ILE* 4.6 4.7 - - - +
228J LEU* 3.5 26.1 - - - +
229J GLN* 4.5 8.7 - - - -
232J LEU* 5.1 4.0 - - - -
10L TYR* 3.4 44.0 - - + -
98L ILE* 2.9 32.2 + - - +
99L LEU* 3.4 11.2 - - - +
100L VAL 3.3 0.2 - - - -
101L ASN* 1.3 75.0 - - - +
103L TYR* 1.3 56.4 + - - +
105L LYS* 3.5 2.6 + - - +
106L LEU* 2.9 30.0 + - - +
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Residues in contact with TYR 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10L TYR* 4.6 0.4 - - - -
35L LEU* 4.7 12.0 - - + +
38L PHE* 3.4 35.0 - + + -
39L ARG* 3.0 45.9 + - + +
42L LEU* 3.7 15.9 - - + -
50L LEU* 3.7 31.0 - - + -
99L LEU 2.9 13.7 + - - +
100L VAL 3.3 7.4 - - - +
102L CYS* 1.3 72.8 - - - +
104L LYS* 1.3 63.7 + - + +
106L LEU* 3.1 6.0 + - + +
107L CYS* 2.9 57.4 + - - -
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Residues in contact with LYS 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50L LEU* 3.7 26.9 - - + -
100L VAL* 3.0 23.2 + - + +
101L ASN* 3.2 25.1 + - - +
103L TYR* 1.3 78.4 - - + +
105L LYS* 1.3 62.6 + - + +
107L CYS* 3.3 8.6 + - - +
108L GLU* 3.0 24.8 + - - +
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Residues in contact with LYS 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221J CYS* 3.8 10.6 - - - -
224J GLN* 3.1 45.3 + - + +
225J ILE* 4.4 21.2 - - + +
228J LEU* 3.8 18.2 - - + -
101L ASN* 2.9 20.8 + - - +
102L CYS 4.0 3.6 - - - +
104L LYS* 1.3 76.2 - - - +
106L LEU* 1.3 61.1 + - - +
108L GLU* 3.1 29.3 + - - +
109L TYR* 3.0 24.4 + - - +
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Residues in contact with LEU 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225J ILE* 4.1 17.8 - - + +
10L TYR* 4.8 2.2 - - + -
13L ALA* 4.2 15.5 - - + +
14L SER* 3.5 40.6 - - - +
17L VAL* 3.9 25.1 - - + -
18L LEU* 5.8 3.6 - - + -
35L LEU* 4.3 13.5 - - + -
38L PHE* 4.4 12.8 - - + -
102L CYS 2.9 19.1 + - - +
103L TYR* 3.1 5.6 + - + +
105L LYS* 1.3 74.7 - - - +
107L CYS* 1.3 58.0 + - - +
109L TYR* 3.2 9.1 + - + +
110L ILE* 2.9 37.9 + - + +
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Residues in contact with CYS 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L LEU* 5.0 12.1 - - - -
103L TYR* 2.9 58.1 + - - -
104L LYS* 3.4 11.0 - - - +
106L LEU* 1.3 76.1 - - - +
108L GLU* 1.3 56.9 + - - +
110L ILE* 3.2 10.8 + - - +
111L THR* 2.9 33.5 + - - +
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Residues in contact with GLU 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221J CYS* 3.9 17.5 - - - +
224J GLN* 5.0 4.9 + - - -
104L LYS 3.0 13.7 + - - +
105L LYS* 3.1 41.2 + - - +
107L CYS* 1.3 76.8 - - - +
109L TYR* 1.3 56.7 + - - +
111L THR* 3.1 9.0 + - - +
112L GLN* 3.0 41.0 + - + +
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Residues in contact with TYR 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223I LYS* 3.9 26.4 + - + +
218J GLN* 3.5 37.5 + - + -
221J CYS* 4.0 6.8 - - + -
222J LEU* 3.9 32.5 - - + +
225J ILE* 5.9 4.5 - - + -
17L VAL* 3.9 32.5 - - + -
18L LEU* 5.0 9.2 - - + -
105L LYS 3.0 12.4 + - - +
106L LEU* 3.2 13.0 + - + +
108L GLU* 1.3 72.9 - - - +
110L ILE* 1.3 61.3 + - - +
112L GLN* 3.3 18.2 + - - +
113L THR* 2.9 46.8 + - + +
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Residues in contact with ILE 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L VAL* 3.9 35.2 - - + -
31L ILE* 5.3 4.5 - - + -
35L LEU* 3.7 34.3 - - + -
106L LEU* 2.9 27.7 + - + +
107L CYS* 3.2 11.6 + - - +
109L TYR* 1.3 74.8 - - - +
111L THR* 1.3 61.0 + - + +
113L THR* 3.1 9.7 + - - +
114L THR* 2.9 40.4 + - - +
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Residues in contact with THR 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107L CYS 2.9 19.5 + - - +
108L GLU* 3.1 15.1 + - - +
110L ILE* 1.3 78.8 - - + +
112L GLN* 1.3 55.5 + - - +
114L THR* 4.4 6.1 - - - -
115L LEU* 3.1 42.0 + - + +
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Residues in contact with GLN 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217J SER* 3.1 39.1 + - - +
218J GLN* 3.4 27.5 + - + +
221J CYS* 3.3 31.3 - - - +
108L GLU* 3.0 30.1 + - + +
109L TYR* 3.5 9.1 - - - +
110L ILE 3.2 0.2 - - - -
111L THR* 1.3 77.5 - - - +
113L THR* 1.3 60.2 + - - +
115L LEU* 3.3 19.7 - - - +
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Residues in contact with THR 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218J GLN* 3.5 20.6 - - - +
17L VAL* 5.9 1.0 - - - +
20L TYR* 5.1 13.5 - - - -
22L PRO* 6.0 2.6 - - - +
109L TYR* 2.9 46.6 + - + +
110L ILE* 3.1 15.8 + - - +
112L GLN* 1.3 73.7 - - - +
114L THR* 1.3 64.0 + - - +
115L LEU* 4.5 3.0 - - - +
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Residues in contact with THR 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28L PHE* 5.5 9.2 - - + -
110L ILE* 2.9 26.3 + - - +
111L THR* 4.0 8.0 - - - -
113L THR* 1.3 77.7 + - - +
115L LEU* 1.3 73.3 + - + +
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Residues in contact with LEU 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111L THR* 3.1 26.0 + - + +
112L GLN* 3.3 16.9 - - - +
113L THR 3.3 2.8 - - - +
114L THR* 1.3 92.6 - - + +
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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