Contacts of the helix formed by residues 31 - 55 (chain C) in PDB entry 3VVK
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 ASP 31 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C PHE* 3.4 31.6 - - - +
28C VAL 3.3 13.1 - - - +
29C LEU 3.0 1.4 - - - -
30C ASN* 1.3 82.8 - - - +
32C PRO* 1.3 72.4 - - - +
33C LEU* 4.2 3.5 + - - +
34C LEU* 3.3 29.9 + - + +
35C ALA* 2.9 22.0 + - - +
241C VAL* 5.5 4.9 - - - +
242C GLY* 5.0 5.0 - - - -
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Residues in contact with PRO 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ASN 4.0 6.1 - - - +
31C ASP* 1.3 91.8 - - - +
33C LEU* 1.3 70.5 + - + +
35C ALA* 4.1 1.7 - - + +
36C SER* 3.1 24.6 + - - -
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Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ASP* 3.7 3.2 + - - +
32C PRO* 1.3 85.2 - - + +
34C LEU* 1.3 61.9 + - - +
36C SER* 3.1 6.1 + - - +
37C SER* 3.1 24.3 + - - -
242C GLY* 4.2 17.0 - - - +
243C TYR* 3.4 46.2 - - + +
246C TRP* 3.1 25.9 - - + +
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PHE* 3.9 31.0 - - + -
28C VAL* 4.2 19.7 - - + +
31C ASP* 3.3 28.0 + - + +
32C PRO 3.2 1.2 + - - -
33C LEU* 1.3 75.9 - - - +
35C ALA* 1.3 66.3 + - - +
37C SER* 2.9 17.1 + - - -
38C LEU* 3.3 18.3 + - + +
118C VAL* 5.4 1.8 - - + -
120C MET* 4.8 13.9 - - + -
241C VAL* 4.4 18.2 - - + -
242C GLY* 4.0 13.4 - - - -
245C SER* 3.7 30.5 - - - +
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Residues in contact with ALA 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C VAL* 3.3 32.4 + - + +
29C LEU* 4.5 8.1 - - + -
30C ASN 5.4 0.2 - - - +
31C ASP 2.9 16.1 + - - +
32C PRO* 4.1 1.8 - - + +
34C LEU* 1.3 73.0 - - - +
36C SER* 1.3 57.8 - - - +
38C LEU* 3.3 0.4 + - - -
39C TYR* 2.8 49.3 + - + +
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Residues in contact with SER 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C PRO 3.1 14.4 + - - -
33C LEU* 3.1 7.6 + - - +
35C ALA* 1.3 77.6 - - - +
37C SER* 1.3 55.9 + - - +
39C TYR* 4.6 2.2 - - - +
40C ILE* 2.8 44.8 + - - +
246C TRP* 2.8 32.1 + - - -
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Residues in contact with SER 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU 3.1 12.2 + - - -
34C LEU 2.9 14.9 + - - -
36C SER* 1.3 81.8 + - - +
38C LEU* 1.3 56.1 + - - +
40C ILE* 4.3 0.9 - - - -
41C ASN* 2.8 16.6 - - - +
82C TYR* 4.0 0.3 - - - -
245C SER* 3.0 21.8 + - - -
246C TRP* 3.4 38.8 - - - -
249C SER* 2.6 30.9 + - - -
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C VAL* 3.8 22.7 - - + -
34C LEU* 3.3 18.3 + - + +
35C ALA 3.8 2.9 - - - +
36C SER 3.1 0.4 - - - -
37C SER* 1.3 79.2 + - - +
39C TYR* 1.3 67.4 + - + +
40C ILE 3.2 1.3 - - - -
41C ASN* 3.3 13.3 + - - +
42C ILE* 3.3 18.4 + - - +
82C TYR* 3.7 20.9 - - + +
85C LEU* 4.2 17.0 - - + -
86C ALA* 4.4 20.4 - - + +
120C MET* 3.6 25.1 - - + -
123C ARG* 3.7 26.0 - - - +
245C SER* 3.9 7.9 - - - +
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Residues in contact with TYR 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B MET* 4.3 11.9 - - + +
25C PHE* 4.0 13.2 - - - -
28C VAL* 4.5 6.1 - - + -
29C LEU* 3.9 29.9 - - + +
35C ALA* 2.8 42.6 + - + +
36C SER* 4.5 2.0 - - - +
38C LEU* 1.3 75.0 - - + +
40C ILE* 1.3 60.8 + - + +
42C ILE* 3.5 20.0 + - + +
43C ALA* 3.3 21.7 + - - +
86C ALA* 3.8 35.3 + - + +
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Residues in contact with ILE 40 (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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36C SER* 2.8 34.8 + - - +
37C SER 4.6 1.3 - - - -
39C TYR* 1.3 77.7 - - - +
41C ASN* 1.3 59.0 + - - +
43C ALA* 3.4 6.9 + - + +
44C LEU* 3.0 48.4 + - + +
246C TRP* 4.2 25.6 - - + -
253C ILE* 4.5 5.6 - - + -
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Residues in contact with ASN 41 (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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37C SER 2.8 19.9 - - - +
38C LEU 3.3 4.0 + - - +
40C ILE* 1.3 80.5 - - - +
42C ILE* 1.3 59.8 + - - +
44C LEU* 3.8 3.1 - - - +
45C ALA* 2.8 33.4 + - - +
82C TYR* 3.4 44.5 + - + -
249C SER* 3.2 21.8 + - - +
252C ASP* 3.8 11.7 - - - +
253C ILE* 4.0 7.2 - - - +
257C TYR* 3.1 31.7 + - - +
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Residues in contact with ILE 42 (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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175B MET* 5.8 2.2 - - + -
178B PHE* 4.8 11.4 - - + -
38C LEU 3.3 11.3 + - - +
39C TYR* 3.7 31.9 - - + +
40C ILE 3.3 0.2 - - - -
41C ASN* 1.3 76.6 - - - +
43C ALA* 1.3 59.6 + - - +
45C ALA* 3.4 3.1 + - - +
46C GLY* 3.1 22.9 + - - -
79C ILE* 3.8 28.7 - - + +
82C TYR* 3.7 21.7 - - + +
83C THR* 3.8 31.2 - - + +
86C ALA* 4.2 8.3 - - + -
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Residues in contact with ALA 43 (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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39C TYR 3.3 10.3 + - - +
40C ILE* 3.6 11.9 - - + +
41C ASN 3.2 0.4 - - - -
42C ILE* 1.3 79.2 - - - +
44C LEU* 1.3 60.1 + - + +
46C GLY* 3.4 1.4 + - - -
47C LEU* 3.0 40.1 + - + +
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Residues in contact with LEU 44 (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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40C ILE* 3.0 41.8 + - + +
41C ASN* 4.0 0.7 - - - +
43C ALA* 1.3 75.5 - - + +
45C ALA* 1.3 56.5 + - - +
47C LEU* 4.0 15.5 - - + +
48C SER* 2.6 38.5 + - - +
253C ILE* 3.7 31.0 - - + -
257C TYR* 3.8 19.7 - - + -
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Residues in contact with ALA 45 (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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41C ASN 2.8 18.7 + - - +
42C ILE 3.6 4.3 - - - +
44C LEU* 1.3 76.2 - - - +
46C GLY* 1.3 60.4 + - - +
48C SER* 3.2 3.2 + - - -
49C ILE* 2.9 35.9 + - - +
75C PRO* 3.5 21.9 - - - +
78C SER 4.5 0.2 - - - -
79C ILE* 3.7 16.6 - - + +
257C TYR* 3.8 21.0 - - + +
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Residues in contact with GLY 46 (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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42C ILE 3.1 15.1 + - - -
43C ALA* 3.9 2.9 - - - -
44C LEU 3.4 0.2 - - - -
45C ALA* 1.3 76.4 - - - +
47C LEU* 1.3 59.9 - - - +
49C ILE* 3.3 9.1 + - - +
50C LEU* 3.2 29.8 + - - +
79C ILE* 4.2 14.1 - - - +
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ALA* 3.0 27.9 + - + +
44C LEU* 4.0 16.2 - - + +
46C GLY* 1.3 75.7 - - - +
48C SER* 1.3 62.7 + - - +
50C LEU* 3.8 17.0 - - + +
51C LEU* 3.1 25.3 + - - +
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Residues in contact with SER 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 2.6 24.2 + - - +
45C ALA* 3.2 6.2 + - - -
47C LEU* 1.3 75.8 - - - +
49C ILE* 1.3 59.5 + - - +
51C LEU* 3.3 5.2 + - - -
52C PHE* 2.8 59.6 + - - -
75C PRO* 4.0 10.5 - - - -
257C TYR* 3.5 24.7 - - - +
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Residues in contact with ILE 49 (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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45C ALA 2.9 23.4 + - - +
46C GLY* 3.3 9.2 + - - +
48C SER* 1.3 75.6 - - - +
50C LEU* 1.3 60.0 + - + +
52C PHE* 3.3 6.8 + - - +
53C VAL* 2.9 47.0 + - + +
72C ILE* 4.3 10.9 - - + +
75C PRO* 3.9 19.5 - - + +
76C VAL* 3.8 34.5 - - + +
79C ILE* 4.3 13.5 - - + -
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Residues in contact with LEU 50 (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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46C GLY 3.2 16.2 + - - +
47C LEU* 3.8 20.6 - - + +
49C ILE* 1.3 80.3 - - + +
51C LEU* 1.3 62.3 + - - +
53C VAL* 3.3 7.3 + - + +
54C PHE* 3.0 25.3 + - - +
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Residues in contact with LEU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU 3.1 16.0 + - - +
48C SER* 3.7 4.9 - - - +
50C LEU* 1.3 78.8 - - - +
52C PHE* 1.3 72.3 + - + +
54C PHE* 3.6 13.2 + - + +
55C MET* 2.9 50.1 + - + +
261C PHE* 4.4 17.3 - - + -
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Residues in contact with PHE 52 (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 SER* 2.8 45.0 + - - +
49C ILE* 3.7 3.6 - - - +
51C LEU* 1.3 93.2 - - + +
53C VAL* 1.3 63.5 + - - +
54C PHE 3.2 0.2 - - - -
55C MET* 3.4 8.4 + - - +
56C THR* 2.8 33.0 + - - +
72C ILE* 4.0 16.6 - - + -
75C PRO* 4.0 19.1 - - + -
256C LYS 4.7 1.3 - - - -
257C TYR 3.6 22.4 - - - -
260C ALA* 3.5 18.4 - - + -
261C PHE* 3.6 28.7 - - + -
264C LEU* 3.4 24.7 - - + -
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Residues in contact with VAL 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ILE* 2.9 40.8 + - + +
50C LEU* 3.7 7.9 - - + +
52C PHE* 1.3 76.1 - - - +
54C PHE* 1.3 63.3 + - - +
56C THR* 3.3 7.0 + - - -
57C ARG* 3.1 50.8 + - + +
72C ILE* 4.5 15.9 - - + -
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Residues in contact with PHE 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU 3.0 16.7 + - - +
51C LEU* 3.7 13.9 - - + +
53C VAL* 1.3 80.2 - - - +
55C MET* 1.3 70.1 + - + +
56C THR 3.4 0.5 + - - -
57C ARG* 3.5 41.7 + - - +
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Residues in contact with MET 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 2.9 43.5 + - + +
52C PHE* 3.7 15.7 - - - +
53C VAL 3.3 0.2 - - - -
54C PHE* 1.3 82.8 - - + +
56C THR* 1.3 63.9 + - + +
57C ARG 3.7 0.3 + - - -
58C GLY 4.6 2.9 + - - -
261C PHE* 3.8 31.0 - - + -
264C LEU* 3.7 12.6 - - + +
265C ASN* 3.5 41.7 - - + +
268C THR* 3.3 27.6 + - + +
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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) + - + + + + + -
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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