Contacts of the helix formed by residues 28 - 49 (chain G) in PDB entry 2VT5
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 GLY 28 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E MET* 3.5 21.8 - - - +
22E ARG* 4.0 4.9 - - - -
27G THR* 1.3 77.3 - - - +
29G GLU* 1.3 55.7 + - - +
31G THR 3.4 0.7 + - - -
32G GLN* 3.0 33.3 + - - +
1337G ROK 3.1 35.2 + - - -
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Residues in contact with GLU 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ARG* 3.7 22.2 + - - +
27G THR* 3.4 17.7 + - - +
28G GLY* 1.3 75.5 - - - +
30G LEU* 1.3 65.8 + - - +
32G GLN* 3.5 1.7 + - - +
33G LEU 3.1 17.2 + - - -
88G SER 5.8 0.2 - - - +
89G PHE 4.2 7.0 - - - +
90G ALA* 3.2 31.5 - - + +
111G GLY* 3.2 8.9 - - - -
112G LYS* 2.7 51.1 + - - +
113G TYR* 4.1 8.7 - - + +
1337G ROK 3.3 1.0 + - - +
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Residues in contact with LEU 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G GLU* 1.3 77.9 - - - +
31G THR* 1.3 56.7 + - - +
33G LEU* 3.2 10.2 + - + +
34G LEU* 2.9 54.2 + - + +
113G TYR* 3.6 29.0 - - + +
138G ILE* 4.0 30.7 - - + -
160G VAL* 3.8 24.9 - - + +
161G ALA* 4.8 5.6 - - + -
177G MET* 5.1 2.5 - - - -
1337G ROK 3.1 42.3 + - + +
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Residues in contact with THR 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E MET* 3.7 26.0 - - + -
14G THR 5.3 0.9 - - - +
17G VAL* 3.4 26.3 + - + +
18G MET* 4.0 16.8 - - + +
28G GLY 3.6 5.4 - - - -
30G LEU* 1.3 75.2 - - - +
32G GLN* 1.3 57.1 + - - +
34G LEU* 3.4 1.2 + - - +
35G ASN* 2.9 43.5 + - - +
1337G ROK 2.7 38.7 + - - -
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Residues in contact with GLN 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E THR 4.4 0.9 - - - +
15E ARG* 3.5 47.4 + - - +
18E MET* 3.7 22.1 - - - +
19E GLU* 3.8 22.0 + - - +
22E ARG* 3.3 25.5 - - - +
28G GLY 3.0 15.3 + - - +
29G GLU* 3.8 5.2 - - - +
30G LEU 3.3 0.2 - - - -
31G THR* 1.3 71.3 - - - +
33G LEU* 1.3 66.4 - - - +
35G ASN* 3.3 10.1 + - - +
36G SER* 2.9 28.6 + - - +
88G SER* 4.0 21.0 + - - +
90G ALA* 5.0 0.2 - - + -
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Residues in contact with LEU 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G GLU 3.1 12.6 + - - +
30G LEU* 3.2 11.4 + - + +
32G GLN* 1.3 77.6 - - - +
34G LEU* 1.3 59.6 + - + +
36G SER* 3.3 2.8 + - - -
37G LEU* 2.9 35.0 + - + +
85G LEU* 3.7 18.4 - - + +
88G SER* 4.2 10.8 - - - -
90G ALA* 3.8 4.1 - - + +
91G THR* 3.7 22.9 - - + -
113G TYR* 3.5 40.6 - - + -
115G VAL* 4.0 10.5 - - + -
138G ILE* 3.9 30.3 - - + -
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Residues in contact with LEU 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G LEU* 4.9 5.1 - - + +
17G VAL* 3.7 36.3 - - + -
30G LEU* 2.9 40.4 + - + +
31G THR 3.8 4.3 - - - +
33G LEU* 1.3 72.6 - - + +
35G ASN* 1.3 59.9 + - - +
37G LEU* 3.7 10.0 - - + +
38G CYS* 3.0 28.1 + - - +
136G PHE* 4.3 7.2 - - + -
138G ILE* 3.7 28.5 - - + -
161G ALA* 5.0 2.0 - - + -
175G LEU* 4.3 21.3 - - + -
177G MET* 4.4 15.7 - - - -
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Residues in contact with ASN 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E THR* 3.3 33.3 - - + +
15E ARG* 6.1 1.8 - - + +
18E MET* 5.2 2.6 - - - -
13G LEU* 5.5 2.6 - - - +
14G THR* 3.6 30.1 + - - +
17G VAL* 4.9 5.2 - - - +
31G THR* 2.9 32.8 + - - +
32G GLN* 3.8 13.2 + - - +
34G LEU* 1.3 78.2 - - - +
36G SER* 1.3 62.5 + - - +
38G CYS* 3.8 9.5 - - - +
39G THR* 3.1 27.5 + - - -
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Residues in contact with SER 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E ARG* 2.6 30.1 + - - -
32G GLN* 2.9 11.7 + - - +
33G LEU 3.5 8.1 - - - -
35G ASN* 1.3 72.6 - - - +
37G LEU* 1.3 64.7 + - - +
39G THR* 3.2 3.5 + - - -
40G ALA 3.1 17.7 + - - -
84G MET* 3.2 42.4 + - - +
85G LEU* 4.5 2.0 - - - -
88G SER* 3.2 14.7 - - - -
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Residues in contact with LEU 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G LEU* 2.9 19.5 + - + +
34G LEU* 3.7 15.5 - - + +
35G ASN 3.3 0.2 - - - -
36G SER* 1.3 78.4 - - - +
38G CYS* 1.3 56.4 + - - +
40G ALA* 3.4 5.8 + - + +
41G VAL* 2.9 39.3 + - + +
81G VAL* 3.9 32.5 - - + -
84G MET* 5.3 0.4 - - - -
85G LEU* 4.2 17.0 - - + +
115G VAL* 5.3 2.2 - - + -
117G PHE* 5.8 0.4 - - + -
134G THR* 5.6 3.4 - - + -
136G PHE* 3.5 57.4 - - + -
138G ILE* 4.6 4.5 - - + -
173G LEU* 5.7 2.0 - - + -
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Residues in contact with CYS 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192E GLU* 5.3 0.4 - - - -
13G LEU* 3.7 23.6 - - + -
14G THR* 5.1 9.6 - - - -
34G LEU 3.0 18.9 + - - +
35G ASN* 3.8 10.1 - - - +
36G SER 3.2 0.2 - - - -
37G LEU* 1.3 73.6 - - - +
39G THR* 1.3 68.2 + - - +
41G VAL* 3.3 8.4 + - - +
42G LYS* 3.0 37.0 + - - +
173G LEU* 4.7 4.9 - - + +
193G PHE* 3.6 25.1 - - + -
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Residues in contact with THR 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E THR* 4.5 8.7 + - + +
190E ILE* 4.5 0.9 - - + +
192E GLU* 3.0 39.2 + - + -
194E ILE* 5.7 0.9 - - + -
59F ILE* 3.9 17.9 - - + -
35G ASN 3.1 14.1 + - - -
36G SER* 3.2 8.0 + - - -
38G CYS* 1.3 75.0 - - - +
40G ALA* 1.3 65.0 + - - +
42G LYS* 3.2 12.8 + - - +
43G ALA* 3.1 20.6 + - - +
84G MET* 3.8 23.5 - - + +
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Residues in contact with ALA 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F ILE* 5.3 0.2 - - - -
36G SER 3.1 9.7 + - - +
37G LEU* 3.5 12.6 - - - +
39G THR* 1.3 79.1 - - - +
41G VAL* 1.3 56.2 + - - +
43G ALA* 3.2 7.4 + - - +
44G ILE* 2.8 34.9 + - - +
80G LEU* 3.8 16.5 - - - +
81G VAL* 4.0 21.8 - - + +
84G MET* 3.8 19.4 - - + +
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Residues in contact with VAL 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G LEU* 2.9 28.9 + - + +
38G CYS* 3.6 7.4 - - - +
39G THR 3.2 0.4 - - - -
40G ALA* 1.3 77.2 - - + +
42G LYS* 1.3 55.2 + - - +
44G ILE* 3.4 5.5 + - + +
45G SER* 2.9 27.9 + - - -
81G VAL* 5.8 0.4 - - + -
134G THR* 4.6 14.8 - - + +
136G PHE* 5.8 2.9 - - + -
165G ALA* 3.6 28.9 - - + -
167G TYR* 3.8 18.5 + - + +
171G THR* 4.8 2.0 - - + -
173G LEU* 4.4 10.1 - - + -
193G PHE* 3.4 26.9 - - + -
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Residues in contact with LYS 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E LYS* 4.4 2.0 - - - +
189E ALA 4.7 0.2 - - - +
190E ILE* 3.1 31.1 - - + +
191E GLY 3.3 8.5 + - - -
192E GLU* 2.6 33.4 + - - -
38G CYS* 3.0 29.3 + - - +
39G THR* 3.2 8.7 + - - +
41G VAL* 1.3 75.6 - - - +
43G ALA* 1.3 57.7 + - - +
45G SER* 3.4 7.6 + - - -
46G SER* 3.2 27.0 + - - -
186G LEU* 4.1 16.5 - - + +
191G GLY* 2.9 34.0 + - - +
192G GLU* 5.1 1.0 + - - +
193G PHE* 3.6 17.9 - - + -
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Residues in contact with ALA 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E ILE* 3.5 17.7 - - + +
55F HIS* 4.8 8.9 + - + +
59F ILE* 3.9 14.1 - - + -
39G THR 3.1 12.2 + - - +
40G ALA 3.2 4.7 + - - +
42G LYS* 1.3 73.2 - - - +
44G ILE* 1.3 65.7 + - - +
46G SER* 3.5 3.1 + - - -
47G ALA* 3.3 21.3 + - - +
80G LEU* 3.6 33.7 - - + +
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Residues in contact with ILE 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G ALA 2.8 23.8 + - - +
41G VAL* 3.4 2.2 + - + +
43G ALA* 1.3 76.8 - - - +
45G SER* 1.3 57.0 + - - +
47G ALA* 3.2 5.0 + - - +
48G VAL* 2.9 37.1 + - + +
77G SER* 3.6 32.3 - - - +
80G LEU* 3.7 18.6 - - + -
81G VAL* 3.6 30.1 - - + -
119G PRO 4.1 0.9 - - - +
120G LEU* 4.0 4.9 - - + -
134G THR* 3.9 14.6 - - + +
167G TYR* 3.5 31.0 - - + +
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Residues in contact with SER 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G VAL 2.9 17.6 + - - -
42G LYS 3.6 6.3 - - - -
43G ALA 3.3 0.2 - - - -
44G ILE* 1.3 76.0 - - - +
46G SER* 1.3 58.1 + - - +
48G VAL* 3.4 1.7 + - - -
49G ARG* 3.0 43.1 + - - +
167G TYR* 3.8 15.7 - - - -
171G THR* 2.7 34.9 + - - -
186G LEU* 4.1 11.2 - - - +
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Residues in contact with SER 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E ALA* 3.6 29.8 + - - +
190E ILE* 4.1 6.5 - - - -
42G LYS 3.2 16.0 + - - -
43G ALA 3.7 5.6 - - - -
44G ILE 3.2 0.2 - - - -
45G SER* 1.3 76.8 - - - +
47G ALA* 1.3 59.8 + - - +
49G ARG* 3.8 5.3 + - - +
50G LYS 3.5 2.8 + - - -
51G ALA* 3.0 44.3 + - - +
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Residues in contact with ALA 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F HIS* 6.2 0.7 - - - +
43G ALA 3.3 13.7 + - - +
44G ILE* 3.2 6.4 + - - +
46G SER* 1.3 78.7 - - - +
48G VAL* 1.3 63.7 + - - +
50G LYS* 3.1 18.4 + - - +
51G ALA 4.8 5.4 - - - +
73G LEU* 3.8 31.0 - - + +
76G LEU* 4.0 20.0 - - + -
77G SER* 6.1 0.2 - - - +
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Residues in contact with VAL 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G ILE* 2.9 26.7 + - + +
45G SER* 3.8 6.1 - - - +
47G ALA* 1.3 70.7 - - - +
49G ARG* 1.3 57.1 + - - +
50G LYS* 3.0 17.6 + - - +
73G LEU* 4.0 13.3 - - + +
120G LEU* 3.9 35.9 - - + -
126G ILE* 4.6 3.3 - - + +
132G VAL* 3.8 11.7 - - + -
167G TYR* 4.0 13.2 - - + -
169H SER* 3.3 39.9 + - - +
170H ALA* 3.4 10.7 - - - +
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Residues in contact with ARG 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G SER* 3.0 33.5 + - - +
46G SER* 4.2 4.7 - - - +
47G ALA 3.4 0.2 - - - -
48G VAL* 1.3 76.1 - - - +
50G LYS* 1.3 67.8 + - - +
51G ALA 3.5 1.1 - - - -
167G TYR* 3.8 8.2 - - - +
168G GLY 2.7 31.1 + - - +
169G SER 4.1 0.2 + - - -
170G ALA* 3.0 24.4 + - - +
171G THR* 2.9 28.6 + - - +
49H ARG* 3.3 33.3 - - + +
168H GLY 3.2 6.9 + - - -
169H SER* 3.0 26.8 + - - +
170H ALA* 4.0 7.5 - - - +
171H THR 4.9 1.4 + - - -
186H LEU 3.9 3.8 - - - +
188H PRO* 3.4 24.3 - - + +
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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