Contacts of the helix formed by residues 79 - 105 (chain D) in PDB entry 5OMA
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 PRO 79 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D GLY* 1.4 78.5 - - - +
80D GLU* 1.4 75.6 + - - +
81D VAL 3.3 2.9 - - - -
82D ARG* 3.3 34.8 + - + +
83D GLU* 3.2 35.4 + - - +
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Residues in contact with GLU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B HIS* 5.6 2.4 - - + +
5B SER* 2.9 45.9 + - - +
8B GLN* 2.8 39.0 + - - +
9B LYS* 3.4 29.6 - - + +
12B LEU* 4.3 3.0 - - + +
78D GLY* 3.2 16.4 - - - -
79D PRO* 1.4 87.3 - - - +
81D VAL* 1.4 61.7 + - - +
83D GLU* 3.5 6.5 + - - +
84D TYR* 3.2 21.8 + - - +
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Residues in contact with VAL 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLN* 4.1 17.3 - - - +
12B LEU* 4.0 19.3 - - + -
62D LEU* 3.9 15.3 - - + +
65D ILE* 4.1 17.5 - - + -
66D GLU* 3.9 38.4 - - + +
69D SER* 5.6 6.1 - - - +
78D GLY 4.1 11.4 - - - +
79D PRO 3.3 0.2 - - - -
80D GLU* 1.4 72.5 - - - +
82D ARG* 1.4 58.9 + - - +
84D TYR* 3.4 2.6 + - - +
85D ARG* 2.9 32.0 + - + +
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Residues in contact with ARG 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D GLU* 3.4 29.0 + - + +
79D PRO* 3.3 35.8 + - + +
81D VAL* 1.4 75.4 - - - +
83D GLU* 1.3 68.2 + - - +
85D ARG* 3.2 10.8 + - - +
86D GLU* 2.9 64.0 + - - +
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Residues in contact with GLU 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B HIS* 3.2 47.2 - - + +
9B LYS* 2.8 38.8 + - - +
79D PRO* 3.2 26.2 + - + +
80D GLU* 3.7 9.9 + - - +
81D VAL 3.4 0.2 - - - -
82D ARG* 1.3 86.6 + - - +
84D TYR* 1.3 57.4 + - - +
86D GLU* 3.5 14.2 + - - +
87D LYS* 3.1 24.1 + - - +
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Residues in contact with TYR 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LYS* 4.3 14.3 - - + +
12B LEU* 4.1 16.6 - - + -
13B ALA* 3.5 28.9 - - + +
16B ALA* 4.7 2.9 - - + -
18B ARG* 3.2 22.1 - - - +
21B ASP* 3.0 32.8 + - - +
25B PHE* 3.9 24.5 - + - -
62D LEU* 3.7 31.0 - - + -
80D GLU 3.2 14.4 + - - +
81D VAL 4.0 2.7 - - - +
83D GLU* 1.3 76.0 - - - +
85D ARG* 1.3 65.8 + - - +
87D LYS* 3.2 17.8 + - + -
88D VAL* 3.1 30.1 + - + +
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Residues in contact with ARG 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D TRP* 3.4 32.4 - - + +
62D LEU* 3.9 31.2 - - + +
63D SER* 4.0 12.7 + - - +
66D GLU* 2.7 40.7 + - - +
81D VAL 2.9 18.2 + - - +
82D ARG* 3.7 16.9 - - - +
84D TYR* 1.3 75.8 - - - +
86D GLU* 1.4 78.3 + - - +
88D VAL* 3.5 3.1 + - - +
89D GLU* 2.8 61.8 + - - +
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Residues in contact with GLU 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D ARG* 2.9 54.1 + - - +
83D GLU* 3.5 13.0 - - - +
85D ARG* 1.4 92.6 + - - +
87D LYS* 1.4 56.1 + - - +
89D GLU* 3.3 9.3 + - - +
90D THR* 2.8 39.5 + - - +
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Residues in contact with LYS 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ARG* 4.1 0.9 - - - +
21B ASP* 3.4 34.2 + - - +
24B ALA* 6.1 2.0 - - - +
25B PHE* 5.1 7.9 - - + -
83D GLU 3.1 13.8 + - - +
84D TYR* 3.2 28.8 + - + +
86D GLU* 1.4 76.2 - - - +
88D VAL* 1.3 62.5 - - - +
90D THR* 3.6 5.8 - - - -
91D GLU* 3.1 41.4 + - - +
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Residues in contact with VAL 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ARG* 4.1 32.5 - - + +
55D GLN* 3.7 28.5 - - + +
58D ALA* 4.4 6.1 - - + -
59D TRP* 3.9 20.2 - - + +
62D LEU* 3.7 19.1 - - + -
84D TYR* 3.1 22.3 + - + +
85D ARG 3.8 6.5 - - - +
87D LYS* 1.3 73.4 - - - +
89D GLU* 1.3 62.8 + - - +
91D GLU* 3.3 9.0 + - - +
92D LEU* 3.1 22.6 + - + +
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Residues in contact with GLU 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D TRP* 3.0 33.9 + - - +
85D ARG* 2.8 46.8 + - - +
86D GLU* 3.4 7.7 - - - +
88D VAL* 1.3 75.4 - - - +
90D THR* 1.4 56.9 + - - +
92D LEU* 3.3 9.3 + - - +
93D GLN* 3.0 53.4 + - - +
134D VAL* 3.9 18.8 - - + +
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Residues in contact with THR 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D GLU* 2.8 22.8 + - - +
87D LYS* 3.6 7.0 - - - -
89D GLU* 1.4 71.8 - - - +
91D GLU* 1.3 65.6 + - - +
93D GLN* 3.4 15.4 + - - +
94D GLY* 3.2 19.2 + - - -
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Residues in contact with GLU 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ARG* 2.8 39.9 + - - +
21B ASP* 5.3 0.2 - - - +
55D GLN* 3.5 17.1 + - - +
87D LYS* 3.1 28.4 + - - +
88D VAL* 3.4 11.2 - - - +
90D THR* 1.3 75.2 - - - +
92D LEU* 1.3 62.1 + - - +
94D GLY* 3.4 10.6 + - - -
95D VAL* 3.4 18.2 + - + +
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Residues in contact with LEU 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D VAL* 3.8 21.1 - - + -
55D GLN* 3.5 31.1 - - + +
56D ARG* 3.9 35.4 - - + +
59D TRP* 4.4 7.9 - - + -
88D VAL 3.1 12.3 + - - +
89D GLU 3.3 9.6 - - - +
91D GLU* 1.3 72.0 - - - +
93D GLN* 1.3 68.2 + - + +
95D VAL* 3.3 5.2 + - - +
96D CYS* 3.2 29.2 + - - -
130D TYR* 5.1 10.1 - - + +
131D LEU* 5.7 1.8 - - + -
134D VAL* 4.2 23.8 - - + -
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Residues in contact with GLN 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D GLU* 3.0 35.2 + - - +
90D THR* 3.6 16.1 + - - +
91D GLU 3.4 0.2 - - - -
92D LEU* 1.3 76.6 - - + +
94D GLY* 1.3 56.7 + - - +
96D CYS* 3.3 2.3 + - - +
97D ASP* 2.9 42.1 + - - +
131D LEU* 3.9 24.7 - - + +
134D VAL* 3.6 26.5 - - + +
135D ALA* 6.1 0.4 - - - +
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Residues in contact with GLY 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D THR 3.2 9.8 + - - -
91D GLU 3.4 5.1 + - - -
92D LEU 3.3 0.2 - - - -
93D GLN* 1.3 78.5 - - - +
95D VAL* 1.4 50.7 + - - +
97D ASP* 3.8 7.4 - - - +
98D THR* 2.8 37.7 + - - -
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Residues in contact with VAL 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D TYR* 4.0 25.4 - - + +
51D VAL* 4.2 20.6 - - + -
52D VAL* 4.3 17.0 - - + -
55D GLN* 3.6 22.2 - - - +
91D GLU* 3.4 14.0 + - + +
92D LEU 3.3 9.0 + - - +
94D GLY* 1.4 72.3 - - - +
96D CYS* 1.3 59.2 + - - +
98D THR* 3.2 7.9 + - - +
99D VAL* 2.9 34.6 + - + +
127D TYR* 5.2 0.4 - - + -
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Residues in contact with CYS 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D VAL* 4.0 10.5 - - - -
92D LEU* 3.2 33.6 + - - +
93D GLN 3.3 2.0 + - - +
95D VAL* 1.3 74.1 - - - +
97D ASP* 1.3 57.8 + - - +
99D VAL* 3.3 1.9 + - - +
100D LEU* 2.9 36.1 + - - +
127D TYR* 3.9 30.5 - - + +
130D TYR* 3.9 14.8 - - - -
131D LEU* 3.6 30.7 - - + -
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Residues in contact with ASP 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D GLN* 2.9 28.9 + - - +
94D GLY* 3.8 7.7 + - - +
96D CYS* 1.3 74.3 - - - +
98D THR* 1.4 53.4 + - - +
100D LEU* 3.8 6.2 - - - +
101D GLY* 2.8 31.9 + - - -
131D LEU* 4.0 18.9 - - - +
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Residues in contact with THR 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LYS* 3.7 30.7 - - + -
48D TYR* 3.9 20.2 - - + +
94D GLY 2.8 19.3 + - - -
95D VAL* 3.2 12.5 + - - +
97D ASP* 1.4 72.4 - - - +
99D VAL* 1.3 58.1 - - - +
101D GLY* 3.4 2.3 + - - -
102D LEU* 2.9 31.3 + - + +
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Residues in contact with VAL 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D TYR* 3.3 37.5 - - + -
95D VAL* 2.9 20.9 + - + +
96D CYS 3.7 5.8 - - - +
98D THR* 1.3 75.3 - - - +
100D LEU* 1.3 57.4 + - - +
102D LEU* 3.0 11.4 + - - +
103D LEU* 2.8 34.7 + - + +
123D MET* 3.9 17.3 - - + -
127D TYR* 3.7 46.2 - - + -
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Residues in contact with LEU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D CYS 2.9 20.8 + - - +
97D ASP* 4.0 6.5 - - - +
99D VAL* 1.3 73.8 - - - +
101D GLY* 1.3 56.8 + - - +
103D LEU* 3.9 6.0 - - + +
104D ASP* 3.0 31.2 + - - +
124D LYS* 3.5 51.1 + - + +
127D TYR* 3.8 19.5 - - + -
128D TYR* 3.8 26.9 - - + +
131D LEU* 3.7 28.0 - - + -
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Residues in contact with GLY 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ASP 2.8 19.0 + - - -
98D THR* 3.7 2.7 - - - -
100D LEU* 1.3 77.4 - - - +
102D LEU* 1.4 54.8 + - - +
104D ASP* 4.7 2.0 - - - -
105D SER* 2.9 36.3 + - - +
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Residues in contact with LEU 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LYS* 3.7 39.5 - - + +
30D VAL* 3.8 24.5 - - + +
31D GLU* 4.2 24.7 - - + +
44D LEU* 5.2 6.1 - - + -
48D TYR* 4.2 15.0 - - + +
98D THR* 2.9 17.9 + - + +
99D VAL* 3.4 9.4 - - - +
101D GLY* 1.4 74.8 - - - +
103D LEU* 1.4 64.5 + - + +
104D ASP 3.3 0.4 - - - -
105D SER 3.7 19.7 - - - +
106D HIS 3.8 1.2 + - - +
107D LEU* 3.3 25.3 - - + +
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Residues in contact with LEU 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D LEU* 5.5 1.3 - - + -
99D VAL* 2.8 38.6 + - + +
100D LEU* 3.9 8.5 - - + +
102D LEU* 1.4 71.8 - - + +
104D ASP* 1.4 58.2 + - - +
107D LEU* 3.2 14.5 - - + +
108D ILE* 2.8 38.5 + - + +
120D TYR* 3.9 39.9 - - + +
123D MET* 3.9 20.9 - - + +
124D LYS* 3.6 43.5 - - + +
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Residues in contact with ASP 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D LEU 3.0 19.3 + - - +
101D GLY* 4.1 4.3 - - - +
103D LEU* 1.4 78.3 - - - +
105D SER* 1.3 64.7 + - - +
106D HIS* 3.3 3.0 - - - -
108D ILE* 4.0 5.4 - - - +
109D LYS* 3.2 59.9 + - - +
124D LYS* 2.9 24.0 + - - +
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Residues in contact with SER 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D GLY* 2.9 22.9 + - - +
102D LEU* 3.7 14.0 - - - +
104D ASP* 1.3 83.4 + - - +
106D HIS* 1.3 69.7 + - - +
109D LYS* 5.3 1.6 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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