Contacts of the helix formed by residues 42 - 66 (chain B) in PDB entry 3RLQ
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 GLU 42 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ASN* 3.1 10.8 - - + +
41B LYS* 1.3 77.0 - - - +
43B ILE* 1.3 65.0 + - + +
44B PHE* 3.0 10.4 + - - -
45B LEU* 3.2 10.9 + - - +
46B ARG 4.2 0.3 + - - -
197B TYR* 3.5 22.5 + - + +
202B ARG* 2.6 44.9 + - - +
206B ILE* 3.8 24.2 - - + +
209B LYS* 3.0 25.6 + - - +
210B HIS* 2.8 33.0 + - + +
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Residues in contact with ILE 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ASN* 3.4 38.8 - - + +
41B LYS 4.4 2.2 - - - +
42B GLU* 1.3 82.6 - - + +
44B PHE* 1.3 68.5 + - - +
45B LEU 3.1 0.4 - - - -
46B ARG* 3.1 44.8 + - - +
47B GLU* 3.0 31.8 + - + +
128B ILE* 4.5 10.3 - - + +
129B SER* 5.0 2.7 - - - -
131B ILE* 4.3 9.2 - - + -
140B SER* 3.9 24.2 - - - +
143B LEU* 4.2 8.7 - - + -
210B HIS* 4.6 10.1 - - + -
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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
----------------------------------------------------------
41B LYS 3.2 23.3 + - - +
42B GLU 3.0 5.5 + - - -
43B ILE* 1.3 79.9 - - - +
45B LEU* 1.3 85.4 + - + +
47B GLU* 3.2 4.0 + - - +
48B LEU* 3.0 33.2 + - + +
89B LEU* 4.0 21.1 - - + -
140B SER* 3.4 40.3 + - - +
141B ALA* 4.2 2.5 - - - -
144B VAL* 3.6 25.4 - - + -
188B LEU* 3.4 31.6 - - + -
190B LEU* 5.5 0.2 - - + -
197B TYR* 3.7 37.5 - + + -
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Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLU 3.2 9.6 + - - +
43B ILE 3.1 0.6 - - - -
44B PHE* 1.3 102.1 - - + +
46B ARG* 1.3 66.7 + - - +
48B LEU* 3.4 3.1 + - + +
49B ILE* 3.0 50.4 + - + +
80B LEU* 4.4 6.7 - - + -
89B LEU* 4.8 7.2 - - + -
91B ILE* 4.1 23.3 - - + -
197B TYR* 6.2 0.2 - - + -
203B ILE* 4.4 17.9 - - + -
206B ILE* 4.0 27.8 - - + -
207B VAL* 4.2 19.7 - - + -
211B SER* 5.8 0.2 - - - +
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Residues in contact with ARG 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLU 4.2 1.0 + - - -
43B ILE* 3.1 38.4 + - - +
45B LEU* 1.3 79.9 - - - +
47B GLU* 1.3 84.5 + - - +
49B ILE* 3.9 1.4 - - - +
50B SER* 2.9 33.1 + - - -
129B SER* 2.9 29.1 + - - +
206B ILE* 5.0 2.0 - - - +
210B HIS* 3.7 58.4 + - + +
211B SER* 4.2 11.7 + - - +
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Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ILE* 3.0 17.8 + - + +
44B PHE 3.2 6.7 + - - +
46B ARG* 1.3 113.8 + - - +
48B LEU* 1.3 58.2 + - + +
50B SER* 3.3 8.2 + - - -
51B ASN* 3.0 33.2 + - - +
129B SER 4.2 1.7 - - - +
131B ILE* 4.1 2.9 - - + -
132B GLY* 3.2 33.0 + - - -
137B GLY* 3.6 26.2 - - - +
140B SER* 3.5 13.2 - - - +
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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* 3.0 27.9 + - + +
45B LEU* 4.0 3.6 - - - +
47B GLU* 1.3 76.1 - - - +
49B ILE* 1.3 58.3 + - - +
51B ASN* 3.2 4.0 + - - +
52B SER* 2.9 30.4 + - - -
91B ILE* 3.8 37.7 - - + -
137B GLY 5.2 0.7 - - - +
138B PHE* 4.0 29.4 - - + +
141B ALA* 4.5 4.9 - - + +
186B VAL* 4.2 9.9 - - + -
188B LEU* 3.9 27.1 - - + -
901B 3RQ 3.2 29.2 - - + +
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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
----------------------------------------------------------
45B LEU* 3.0 44.1 + - + +
46B ARG 4.0 2.5 - - - +
48B LEU* 1.3 72.6 - - - +
50B SER* 1.3 62.5 + - - +
52B SER* 3.2 8.1 + - - -
53B SER* 2.8 27.2 + - - -
78B ILE* 4.0 19.2 - - + +
80B LEU* 4.3 17.3 - - + -
91B ILE* 4.9 2.9 - - + -
207B VAL* 4.2 17.5 - - + -
211B SER* 3.9 18.6 - - - +
214B ILE* 3.8 26.7 - - + -
218B ILE* 4.3 12.3 - - + -
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Residues in contact with SER 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ARG* 2.9 22.6 + - - -
47B GLU* 3.4 11.4 - - - -
49B ILE* 1.3 78.4 - - - +
51B ASN* 1.3 59.8 + - - +
53B SER* 3.3 7.5 + - - -
54B ASP* 3.0 38.4 + - - +
214B ILE* 4.6 8.3 - - - -
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Residues in contact with ASN 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLU 3.0 17.2 + - - +
48B LEU 3.6 2.5 - - - +
50B SER* 1.3 78.4 + - - +
52B SER* 1.3 62.4 + - - +
54B ASP* 3.4 13.1 + - - +
55B ALA* 3.0 22.5 + - - +
137B GLY* 4.7 3.5 + - - +
138B PHE* 3.8 26.1 - - - +
901B 3RQ 3.4 70.1 + - + +
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Residues in contact with SER 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU 2.9 12.4 + - - -
49B ILE* 3.2 9.4 + - - -
51B ASN* 1.3 74.9 - - - +
53B SER* 1.3 60.9 + - - +
55B ALA* 3.1 2.9 + - - +
56B LEU* 2.9 34.0 + - - +
78B ILE* 3.8 13.9 - - - -
91B ILE* 3.9 15.1 - - - +
93B ASP* 2.9 36.5 + - - +
901B 3RQ 3.2 12.7 - - - -
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Residues in contact with SER 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ILE 2.8 16.6 + - - -
50B SER 3.5 8.3 - - - -
52B SER* 1.3 72.2 - - - +
54B ASP* 1.3 61.6 + - - +
56B LEU* 3.2 12.8 + - - +
57B ASP* 2.8 35.7 + - - +
78B ILE* 4.2 1.3 - - - +
214B ILE* 4.0 31.1 - - - +
215B GLY 4.8 2.1 + - - -
216B TYR* 3.8 15.2 - - - -
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Residues in contact with ASP 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B SER* 3.0 27.3 + - - +
51B ASN* 3.6 16.0 - - - +
52B SER 3.2 0.2 - - - -
53B SER* 1.3 78.2 + - - +
55B ALA* 1.3 62.8 + - - +
57B ASP* 3.2 15.2 + - - +
58B LYS* 3.0 36.7 + - - +
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ASN 3.0 8.2 + - - +
52B SER 3.1 7.8 + - - +
54B ASP* 1.3 79.3 - - - +
56B LEU* 1.3 60.5 + - - +
58B LYS* 3.3 14.8 + - - +
59B ILE 3.3 5.0 + - - -
93B ASP* 4.3 1.3 - - - +
95B GLY* 3.8 6.3 - - - -
96B ILE* 3.1 30.6 + - - +
901B 3RQ 3.2 43.7 - - + +
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Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B SER 2.9 19.8 + - - +
53B SER 3.6 2.9 - - - +
55B ALA* 1.3 72.7 - - - +
57B ASP* 1.3 66.3 + - - +
59B ILE* 3.3 4.2 - - - +
60B ARG* 3.0 24.8 + - - +
76B LEU* 4.0 11.0 - - + +
77B HIS 3.8 11.7 - - - +
78B ILE* 3.6 30.3 - - + -
93B ASP* 4.3 2.7 - - + -
94B THR* 3.4 24.9 - - - +
95B GLY* 3.3 27.6 - - - +
216B TYR* 3.5 40.1 + - + -
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Residues in contact with ASP 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B SER* 2.8 17.9 + - - +
54B ASP* 3.2 18.5 + - - +
56B LEU* 1.3 76.8 - - - +
58B LYS* 1.3 57.8 + - + +
60B ARG* 3.3 17.2 + - - +
61B TYR* 2.9 53.8 + - + -
216B TYR* 2.6 33.5 + - - -
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Residues in contact with LYS 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ASP* 3.0 22.9 + - - +
55B ALA* 3.6 9.4 - - - +
56B LEU 3.2 0.6 - - - -
57B ASP* 1.3 77.9 - - + +
59B ILE* 1.3 57.4 + - - +
61B TYR* 3.5 5.8 + - - +
62B GLU* 2.9 34.1 + - - +
96B ILE* 4.1 29.2 - - + -
901B 3RQ 5.8 5.0 - - + +
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Residues in contact with ILE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ALA 3.3 7.6 + - - +
56B LEU 3.3 11.4 - - - +
58B LYS* 1.3 76.0 - - - +
60B ARG* 1.3 68.8 + - - +
62B GLU* 3.4 21.4 + - - +
63B SER* 3.0 22.9 + - - -
69B LYS* 3.9 20.6 - - + +
70B LEU* 3.8 13.6 - - + +
76B LEU* 3.7 23.6 - - + -
94B THR 4.0 0.7 - - - +
95B GLY* 4.0 12.3 - - - -
96B ILE* 3.8 22.4 - - + +
155B ASN* 4.0 7.6 - - - +
182B ARG* 3.7 25.1 - - - +
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Residues in contact with ARG 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU 3.0 17.7 + - - +
57B ASP* 3.3 24.1 + - - +
59B ILE* 1.3 80.4 - - - +
61B TYR* 1.3 96.4 + - + +
63B SER* 2.6 26.2 + - - +
64B LEU* 3.5 11.4 + - + +
70B LEU* 5.4 0.9 - - + -
76B LEU* 4.0 24.9 - - + -
216B TYR* 2.9 24.3 + - - -
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Residues in contact with TYR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ASP* 2.9 45.3 + - + +
58B LYS* 4.0 4.9 - - - +
60B ARG* 1.3 111.8 + - + +
62B GLU* 1.3 65.5 - - - +
64B LEU* 3.1 43.3 - - + +
65B THR* 4.0 4.0 + - - +
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LYS* 2.9 22.0 + - + +
59B ILE* 3.6 16.1 - - - +
61B TYR* 1.3 76.8 - - - +
63B SER* 1.3 61.9 + - - +
64B LEU 3.0 1.6 + - - -
65B THR* 3.2 10.2 + - - -
66B ASP* 3.1 22.7 + - - +
69B LYS* 3.7 32.4 - - + +
96B ILE* 3.6 23.5 - - + +
154B HIS* 5.7 2.1 + - - -
155B ASN* 5.2 0.5 + - - -
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Residues in contact with SER 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ILE 3.0 12.5 + - - -
60B ARG* 2.6 24.2 + - - +
62B GLU* 1.3 75.5 - - - +
64B LEU* 1.3 64.3 + - - +
65B THR 3.3 0.4 - - - -
66B ASP 3.4 13.9 - - - -
67B PRO* 3.4 25.4 - - - +
69B LYS* 4.4 2.2 - - - +
70B LEU* 3.4 38.9 - - - +
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Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ARG* 3.7 14.8 - - + +
61B TYR* 3.1 43.0 + - + +
62B GLU 3.0 0.6 - - - -
63B SER* 1.3 81.9 + - - +
65B THR* 1.3 64.3 + - + +
67B PRO* 5.1 2.9 - - - +
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Residues in contact with THR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B TYR 4.7 2.8 + - - +
62B GLU* 3.2 10.0 + - - -
64B LEU* 1.3 85.2 - - + +
66B ASP* 1.3 64.5 + - - +
67B PRO* 4.0 5.8 - - - +
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Residues in contact with ASP 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLU 3.1 9.0 + - - +
63B SER* 3.4 7.4 - - - -
65B THR* 1.3 84.6 - - - +
67B PRO* 1.3 67.9 - - - +
68B SER* 2.7 28.5 + - - -
69B LYS* 3.0 50.3 + - + +
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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