Contacts of the helix formed by residues 82 - 106 (chain D) in PDB entry 4NEF
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 82 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D VAL* 1.3 81.0 - - - +
83D VAL* 1.3 62.8 + - - +
84D LEU* 3.1 14.1 + - - +
85D ARG* 3.4 17.5 + - - +
86D ALA* 3.3 18.4 + - - +
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Residues in contact with VAL 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D LEU* 4.5 24.1 - - + +
81D VAL 3.7 1.4 + - - -
82D SER* 1.3 70.5 - - - +
84D LEU* 1.4 59.4 + - + +
86D ALA* 3.7 7.9 - - + +
87D ALA* 3.1 30.7 + - + +
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Residues in contact with LEU 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D PHE* 3.8 28.7 - - + -
82D SER* 3.1 12.5 - - - +
83D VAL* 1.4 79.0 - - + +
85D ARG* 1.4 64.9 - - - +
87D ALA* 3.4 4.7 + - + +
88D PHE* 3.2 52.5 + - + -
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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
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8D ALA* 5.8 0.6 - - - +
9D PHE* 3.8 37.6 - - + +
12D ALA* 3.7 14.6 - - - +
63D SER* 4.9 0.8 + - - +
81D VAL* 3.8 31.3 - - + +
82D SER* 3.4 9.0 + - - +
84D LEU* 1.4 76.2 - - + +
86D ALA* 1.4 56.6 + - - +
88D PHE* 3.3 1.6 + - - +
89D TYR* 2.8 92.2 + - + +
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Residues in contact with ALA 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D THR* 3.4 21.7 - - + +
73D VAL* 6.5 0.2 - - + -
76D LEU* 3.6 34.3 - - + -
81D VAL* 4.6 4.8 - - + +
82D SER 3.3 10.2 + - - +
83D VAL* 3.7 7.6 - - + +
85D ARG* 1.4 77.4 - - - +
87D ALA* 1.4 55.4 + - - +
89D TYR* 5.6 0.2 - - - -
90D VAL* 3.0 35.6 + - + +
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Residues in contact with ALA 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D VAL* 3.1 20.0 + - + +
84D LEU* 3.7 6.7 - - + +
85D ARG 3.3 0.2 - - - -
86D ALA* 1.4 74.7 - - - +
88D PHE* 1.4 58.0 + - + +
90D VAL* 3.4 5.6 + - - +
91D ALA* 2.9 37.1 + - - +
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Residues in contact with PHE 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D PHE* 3.5 35.7 - + + -
13D VAL* 3.7 24.5 - - + +
84D LEU* 3.2 47.5 + - + +
85D ARG 3.6 2.5 - - - +
87D ALA* 1.4 81.1 - - + +
89D TYR* 1.4 58.1 + - - +
91D ALA* 4.0 5.8 - - - +
92D ALA* 3.1 27.7 + - - +
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Residues in contact with TYR 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D PHE* 4.8 0.2 - + - -
12D ALA* 3.2 24.3 - - + +
13D VAL* 4.1 12.1 - - + -
16D GLU* 3.7 24.4 - - + +
63D SER 2.8 20.2 + - - -
66D HIS* 3.3 40.6 - + - -
72D THR* 3.6 19.7 - - + -
85D ARG* 2.8 67.1 + - + +
86D ALA* 5.6 0.2 - - - -
88D PHE* 1.4 75.8 - - - +
90D VAL* 1.4 54.3 + - - +
92D ALA* 3.1 6.9 + - - +
93D GLN* 2.8 44.5 + - - +
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Residues in contact with VAL 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D PRO* 3.9 29.4 - - + +
72D THR* 3.8 17.9 - - + -
73D VAL* 4.8 9.0 - - + -
86D ALA* 3.0 22.1 + - + +
87D ALA* 3.9 5.2 - - - +
89D TYR* 1.4 73.0 - - - +
91D ALA* 1.4 57.4 + - - +
93D GLN* 3.3 9.0 + - - +
94D LEU* 3.0 51.2 + - + +
205D TRP* 6.1 2.2 - - + -
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Residues in contact with ALA 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D ALA 2.9 19.4 + - - +
88D PHE* 4.0 6.5 - - - +
90D VAL* 1.4 75.3 - - - +
92D ALA* 1.4 56.6 - - - +
94D LEU* 3.6 9.3 + - - +
95D LEU* 3.1 42.4 + - + +
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Residues in contact with ALA 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D VAL* 3.5 32.1 - - + +
16D GLU* 4.2 4.0 - - + -
17D PHE* 3.4 26.5 - - + +
88D PHE 3.1 20.2 + - - +
89D TYR 3.1 5.5 + - - +
91D ALA* 1.4 72.6 - - - +
93D GLN* 1.3 60.1 + - - +
95D LEU* 3.6 5.8 + - - -
96D GLY 2.9 23.7 + - - -
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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
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16D GLU* 2.9 29.5 + - + +
20D THR* 3.4 30.0 - - + +
66D HIS* 3.7 5.5 - - - +
68D ASN 3.8 12.3 - - - +
69D PRO* 3.0 37.8 - - + +
72D THR* 2.8 22.6 + - - -
89D TYR* 2.8 27.6 + - - +
90D VAL* 3.6 8.4 - - - +
92D ALA* 1.3 73.3 - - - +
94D LEU* 1.4 59.2 + - - +
97D ALA* 2.9 32.4 + - - +
186D ALA* 4.1 3.1 - - + -
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Residues in contact with LEU 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D PRO* 4.3 7.2 - - + -
90D VAL* 3.0 37.9 + - + +
91D ALA* 4.0 7.2 - - - +
93D GLN* 1.4 73.5 - - - +
95D LEU* 1.4 62.1 + - + +
97D ALA* 3.7 1.7 + - - +
98D VAL* 3.2 30.9 + - - +
186D ALA* 4.1 22.4 - - + -
189D LEU* 3.8 23.3 - - + +
205D TRP* 3.8 29.8 - - + -
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Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D PHE* 3.9 14.9 - - + -
91D ALA* 3.1 29.6 + - + +
92D ALA* 3.9 5.4 - - - +
94D LEU* 1.4 75.1 - - + +
96D GLY* 1.3 58.5 + - - +
98D VAL* 3.4 13.0 - - + +
99D ALA* 3.1 29.6 + - - +
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Residues in contact with GLY 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D PHE* 3.4 36.7 - - - -
20D THR* 4.6 0.2 - - - -
21D LEU* 3.1 20.8 - - - +
92D ALA 2.9 13.4 + - - -
93D GLN 3.8 0.9 - - - -
95D LEU* 1.3 74.5 - - - +
97D ALA* 1.3 57.2 + - - +
99D ALA* 3.3 1.4 + - - +
100D GLY 2.9 24.3 + - - -
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Residues in contact with ALA 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D THR* 3.9 6.1 - - + -
24D VAL* 3.3 27.5 - - + +
93D GLN 2.9 19.1 + - - +
94D LEU* 3.9 4.5 - - - +
96D GLY* 1.3 73.6 - - - +
98D VAL* 1.4 57.3 + - - +
100D GLY 3.0 2.4 + - - -
101D ALA 3.0 24.4 + - - -
186D ALA* 3.3 34.3 - - + +
190D ALA* 3.3 8.2 - - + +
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Residues in contact with VAL 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D LEU 3.2 14.7 + - - +
95D LEU* 3.4 24.2 - - + +
97D ALA* 1.4 76.7 - - + +
99D ALA* 1.4 55.8 + - - +
101D ALA* 3.4 2.5 + - - +
102D ALA* 2.9 31.5 + - - +
189D LEU* 4.6 8.3 - - + -
190D ALA* 3.8 27.6 - - - +
193D VAL* 4.2 29.4 - - + -
194D VAL* 4.0 4.0 - - + +
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Residues in contact with ALA 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D PHE* 4.5 7.6 - - + -
21D LEU* 3.8 19.7 - - + -
95D LEU 3.1 20.0 + - - +
96D GLY* 3.5 5.8 - - - +
97D ALA 3.2 0.2 - - - -
98D VAL* 1.4 77.5 - - + +
100D GLY* 1.3 57.0 + - - +
102D ALA* 3.9 5.8 - - - +
103D LEU* 3.0 33.2 + - + +
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Residues in contact with GLY 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LEU* 3.5 30.5 - - - +
24D VAL* 4.1 5.8 - - - -
25D PHE* 3.7 13.9 - - - -
96D GLY 2.9 11.4 + - - -
97D ALA 3.0 4.4 + - - -
99D ALA* 1.3 75.7 - - - +
101D ALA* 1.4 56.6 + - - +
103D LEU* 3.7 2.6 + - - -
104D LEU* 3.1 27.9 + - - +
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Residues in contact with ALA 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D VAL* 3.7 7.7 - - + +
28D LEU* 4.2 9.0 - - + -
97D ALA 3.0 14.6 + - - +
98D VAL 3.7 3.1 - - - +
100D GLY* 1.4 73.1 - - - +
102D ALA* 1.4 59.7 + - - +
103D LEU 3.4 0.2 - - - -
104D LEU* 3.7 5.0 + - - +
105D HIS* 3.1 26.5 + - - +
116D LEU* 3.7 11.5 - - + +
190D ALA* 3.6 33.9 - - + +
191D PRO* 4.1 4.5 - - + -
194D VAL* 3.8 6.7 - - + +
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Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D VAL 2.9 17.6 + - - +
99D ALA* 3.9 6.3 - - - +
100D GLY 3.4 0.2 - - - -
101D ALA* 1.4 72.8 - - - +
103D LEU* 1.3 63.9 + - - +
105D HIS* 3.5 10.1 + - - +
106D GLU* 3.3 23.9 + - - +
194D VAL* 3.8 15.0 - - + +
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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
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132A THR* 4.4 4.9 - - + -
136A PHE* 3.6 42.2 - - + -
21D LEU* 4.1 18.6 - - + -
25D PHE* 3.7 18.6 - - + -
99D ALA* 3.0 20.7 + - + +
100D GLY 3.7 6.3 - - - +
102D ALA* 1.3 74.5 - - - +
104D LEU* 1.3 64.0 + - - +
106D GLU* 3.4 7.7 + - - +
107D ILE* 3.3 32.1 + - + +
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Residues in contact with LEU 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A LEU* 4.4 2.9 - - + -
178A TYR* 3.4 25.4 - - - +
24D VAL 4.8 1.3 - - - +
25D PHE* 3.8 26.2 - - + +
28D LEU* 3.7 20.9 - - + -
29D GLY* 3.5 36.6 - - - +
32D LEU* 4.7 4.0 - - + -
100D GLY 3.1 16.5 + - - +
101D ALA* 3.9 3.6 - - - +
103D LEU* 1.3 74.0 - - - +
105D HIS* 1.3 60.3 + - - +
107D ILE* 3.0 15.6 + - + +
108D THR* 2.5 30.6 + - - +
116D LEU* 4.1 20.4 - - + -
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Residues in contact with HIS 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ALA 3.1 19.0 + - - +
102D ALA* 3.5 7.8 + - - +
103D LEU 3.4 0.2 - - - -
104D LEU* 1.3 76.3 - - - +
106D GLU* 1.3 87.5 + - + +
107D ILE 3.2 4.7 + - - -
108D THR* 3.3 5.9 + - - +
113D ARG* 2.8 65.1 + - + +
116D LEU* 4.3 13.4 - - + +
194D VAL* 4.1 20.9 - - + +
195D THR* 5.6 7.2 - - + -
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Residues in contact with GLU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLN* 3.2 21.9 + - - +
102D ALA 3.3 11.8 + - - +
103D LEU* 3.4 6.3 + - - +
104D LEU 3.3 0.6 - - - -
105D HIS* 1.3 105.8 - - + +
107D ILE* 1.3 58.8 + - - +
113D ARG* 3.8 11.1 + - - +
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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) + - + + + + + -
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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