Contacts of the helix formed by residues 37 - 64 (chain B) in PDB entry 2YEV
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 PHE 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLN 4.9 1.4 + - - -
34B GLU 3.2 27.4 - - - -
35B VAL* 2.9 2.5 + - - -
36B ALA* 1.3 77.1 - - - +
38B LEU* 1.3 81.4 + - + +
39B PHE 3.4 0.2 - - - -
40B PRO* 3.3 12.8 - - - +
41B TRP* 3.3 30.0 - + - +
101B LEU* 3.9 25.1 - - + -
104B LYS* 5.1 13.2 - - + -
105B ALA* 3.8 31.6 - - + -
108B GLN* 5.5 4.0 - - - -
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Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A MET* 3.9 23.2 - - + +
371A PRO* 4.1 17.7 - - + -
372A LEU* 4.0 27.1 - - + -
35B VAL* 2.9 15.9 + - + +
37B PHE* 1.3 95.2 - - + +
39B PHE* 1.3 65.0 - - - +
41B TRP* 3.3 8.5 + - - +
42B VAL* 3.1 24.2 + - - +
101B LEU* 3.7 39.5 - - + +
102B THR* 4.2 1.8 - - - +
105B ALA* 3.9 17.9 - - + -
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Residues in contact with PHE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A MET* 4.6 3.6 - - + -
372A LEU* 3.6 37.0 - - + -
375A GLN* 6.3 0.9 - - + -
376A PHE* 4.0 10.5 - + - -
442A TYR* 3.3 26.2 - + - -
24B ILE* 4.1 25.1 - - + -
25B THR* 4.2 17.9 - - + -
35B VAL* 4.9 9.0 - - + -
36B ALA* 3.3 19.0 + - + +
38B LEU* 1.3 78.6 - - - +
40B PRO* 1.3 70.2 - - + +
42B VAL* 3.1 5.9 + - + +
43B TYR* 2.9 58.7 + + + -
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Residues in contact with PRO 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ALA 3.2 16.6 - - - +
37B PHE* 3.3 15.3 - - - +
39B PHE* 1.3 92.0 - - + +
41B TRP* 1.3 59.0 + - + +
43B TYR* 3.3 11.6 + - + +
44B PHE* 2.9 31.6 + - - +
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Residues in contact with TRP 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.3 29.3 - + - +
38B LEU* 3.3 8.2 + - + +
39B PHE 3.2 0.4 - - - -
40B PRO* 1.3 81.2 - - + +
42B VAL* 1.3 62.2 - - - +
44B PHE* 3.8 14.9 - + + +
45B PHE* 3.1 62.6 + + - -
97B VAL* 4.3 9.9 - - + -
98B LEU* 4.7 6.5 - - + -
101B LEU* 3.4 42.5 - - + +
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ILE* 5.2 0.4 - - + -
366A MET* 3.7 41.1 - - + -
369A MET* 3.5 34.8 - - + -
372A LEU* 4.5 8.3 - - + -
38B LEU 3.1 16.0 + - - +
39B PHE* 3.1 9.4 + - + +
41B TRP* 1.3 76.7 - - - +
43B TYR* 1.3 69.5 + - + +
45B PHE* 4.1 2.4 - - - +
46B SER* 2.6 40.4 + - - +
98B LEU* 4.5 9.0 - - + -
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Residues in contact with TYR 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A MET* 5.1 1.8 - - + -
442A TYR* 3.0 36.0 + + - -
25B THR* 5.4 1.4 - - - +
39B PHE* 2.9 51.5 + + + +
40B PRO* 3.7 9.0 - - + +
42B VAL* 1.3 88.1 - - + +
44B PHE* 1.3 55.7 + - - +
46B SER* 3.9 4.2 - - - -
47B PHE* 3.0 31.5 + - - +
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Residues in contact with PHE 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PRO 2.9 18.1 + - - +
41B TRP* 3.8 16.6 - + + +
42B VAL 3.3 0.2 - - - -
43B TYR* 1.3 75.7 - - - +
45B PHE* 1.3 87.2 + + - +
47B PHE* 3.2 9.3 + + - +
48B LEU* 3.1 56.8 + - + +
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Residues in contact with PHE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TRP* 3.1 47.6 + + - +
42B VAL* 4.2 2.5 - - - +
44B PHE* 1.3 97.4 - + - +
46B SER* 1.3 59.0 + - - +
48B LEU* 3.3 9.5 + - + +
49B ILE* 2.8 40.1 + - + +
94B ILE* 4.0 43.7 - - + -
97B VAL* 3.9 30.7 - - + -
98B LEU* 4.0 22.0 - - + -
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Residues in contact with SER 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ILE* 3.2 38.3 - - - +
42B VAL* 2.6 29.5 + - - +
43B TYR* 3.9 4.7 - - - -
45B PHE* 1.3 77.5 - - - +
47B PHE* 1.3 58.6 + - - +
49B ILE* 3.8 6.0 - - - +
50B PHE* 2.8 32.8 + - - +
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Residues in contact with PHE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TYR 3.0 20.1 + - - +
44B PHE* 3.5 9.6 - + + +
46B SER* 1.3 77.8 - - - +
48B LEU* 1.3 71.4 + - + +
50B PHE* 3.4 6.0 + + + +
51B LEU* 2.9 62.4 + - + +
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Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PHE* 3.1 56.0 + - + +
45B PHE* 3.8 10.5 - - + +
47B PHE* 1.3 90.5 - - + +
49B ILE* 1.3 68.0 + - + +
51B LEU* 3.3 9.2 + - + +
52B VAL* 3.0 34.2 + - + +
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Residues in contact with ILE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A PHE* 6.1 1.3 - - + -
358A LEU* 4.5 13.5 - - + -
362A ILE* 4.2 28.3 - - + -
45B PHE* 2.8 31.6 + - + +
46B SER* 4.0 4.3 - - - +
48B LEU* 1.3 73.6 - - + +
50B PHE* 1.3 58.9 + - - +
52B VAL* 4.9 3.4 - - - -
53B VAL* 3.0 43.4 + - + +
94B ILE* 4.2 31.9 - - + -
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Residues in contact with PHE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A PHE* 4.7 14.4 - + + -
358A LEU* 4.3 20.0 - - + -
359A LEU* 5.7 6.3 - - + -
46B SER 2.8 21.0 + - - +
47B PHE* 3.7 6.3 - + - +
48B LEU 3.1 0.2 - - - -
49B ILE* 1.3 75.6 - - - +
51B LEU* 1.3 73.4 + - + +
54B ALA* 3.0 51.9 + - + +
55B GLY 3.6 0.2 + - - -
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PHE* 2.9 59.2 + - + +
48B LEU* 3.3 12.3 + - + +
50B PHE* 1.3 80.4 - - + +
52B VAL* 1.3 64.0 + - + +
55B GLY* 3.1 21.3 + - - +
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Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.0 21.9 + - + +
49B ILE* 4.1 2.9 - - - +
51B LEU* 1.3 77.0 - - + +
53B VAL* 1.3 69.2 + - + +
56B SER* 2.9 40.5 + - - +
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A LEU* 6.1 2.2 - - + -
330A PHE* 3.4 35.0 - - + -
333A ILE* 3.9 23.1 - - + +
354A ILE* 5.4 2.7 - - + -
358A LEU* 3.6 29.2 - - + -
49B ILE* 3.0 28.3 + - + +
52B VAL* 1.3 81.0 - - + +
54B ALA* 1.3 65.1 + - - +
56B SER* 3.5 6.3 + - - -
57B LEU* 3.1 22.0 + - - +
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A PHE* 3.5 22.2 - - + -
358A LEU* 3.8 19.4 - - + +
50B PHE* 3.0 43.7 + - + +
53B VAL* 1.3 76.1 - - - +
55B GLY* 1.3 58.8 + - - +
57B LEU* 3.3 2.0 + - - +
58B ALA* 2.9 29.9 + - - +
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Residues in contact with GLY 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE 3.6 0.4 + - - -
51B LEU* 3.1 23.3 + - - +
54B ALA* 1.3 79.6 - - - +
56B SER* 1.3 55.4 + - - +
58B ALA* 3.2 8.0 + - - +
59B TYR* 2.8 29.7 + - - +
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Residues in contact with SER 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ILE* 4.9 9.9 - - - -
337A TRP* 4.3 15.9 - - - -
52B VAL* 2.9 27.9 + - - +
53B VAL* 3.7 7.2 - - - -
55B GLY* 1.3 75.0 - - - +
57B LEU* 1.3 57.9 + - - +
59B TYR* 3.3 8.2 + - - +
60B VAL* 2.9 34.0 + - - +
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Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ILE* 4.2 21.0 - - + +
336A LEU* 3.9 18.8 - - + -
351A LEU* 3.9 23.6 - - + +
354A ILE* 3.3 39.0 - - + -
355A PHE* 3.6 35.4 - - + +
358A LEU* 6.4 0.2 - - + -
53B VAL 3.1 17.7 + - - +
54B ALA* 3.8 4.3 - - - +
55B GLY 3.2 0.4 - - - -
56B SER* 1.3 76.9 - - - +
58B ALA* 1.3 63.0 + - - +
60B VAL* 3.4 5.9 + - + +
61B THR* 3.1 31.1 + - + +
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Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A PHE* 3.8 13.4 - - + -
54B ALA 2.9 18.3 + - - +
55B GLY* 3.5 7.2 - - - +
57B LEU* 1.3 74.5 - - - +
59B TYR* 1.3 64.4 + - - +
61B THR* 3.0 21.5 + - - -
62B TRP* 3.2 11.4 + - - +
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Residues in contact with TYR 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A TRP* 3.6 37.9 - + - -
55B GLY 2.8 13.3 + - - +
56B SER* 3.5 10.5 - - - +
58B ALA* 1.3 76.7 - - - +
60B VAL* 1.3 55.5 + - - +
62B TRP* 3.1 32.5 + + - +
63B LYS* 2.8 71.2 + - + +
64B PHE* 4.2 4.6 - + - -
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Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ILE* 4.5 8.5 - - + +
336A LEU* 3.6 42.0 - - + +
337A TRP* 3.1 48.9 - - + +
341A LEU* 4.0 9.1 - - + +
56B SER 2.9 16.9 + - - +
57B LEU* 3.7 10.1 - - + +
59B TYR* 1.3 75.6 - - - +
61B THR* 1.3 59.4 + - + +
64B PHE* 2.9 38.9 + - + +
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Residues in contact with THR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A LEU* 4.0 12.3 - - + -
343A MET* 4.1 14.8 - - - +
351A LEU* 3.7 37.9 - - + -
355A PHE* 5.1 5.4 - - + -
57B LEU* 3.1 20.0 + - + +
58B ALA* 3.0 17.4 + - - -
59B TYR 3.2 0.2 - - - -
60B VAL* 1.3 76.7 - - + +
62B TRP* 1.3 59.8 + - - +
65B ARG* 3.5 22.7 + - - +
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Residues in contact with TRP 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ALA 3.2 8.2 + - - +
59B TYR* 3.1 36.1 + + - +
61B THR* 1.3 84.5 + - - +
63B LYS* 1.3 92.3 + - + +
65B ARG* 4.1 8.9 + - - +
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Residues in contact with LYS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TYR* 2.8 55.9 + - + +
62B TRP* 1.3 95.7 - - + +
64B PHE* 1.3 89.2 + - + +
65B ARG 3.5 2.7 + - - +
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Residues in contact with PHE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A LEU 4.3 4.3 - - - +
337A TRP* 3.5 37.5 - + - -
338A GLY* 3.1 43.3 - - - -
339A GLY 3.2 20.6 - - - +
340A LYS* 3.4 1.0 - - - -
341A LEU* 2.8 30.3 + - + -
59B TYR* 4.2 6.7 - + - -
60B VAL* 2.9 29.5 + - + +
63B LYS* 1.3 105.1 - - + +
65B ARG* 1.3 63.3 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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