Contacts of the helix formed by residues 103 - 123 (chain B) in PDB entry 3QLD
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 ASN 103 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PRO* 3.9 5.3 - - - +
57A GLU* 3.0 29.7 + - - +
62A THR* 5.2 1.9 - - - +
57B GLU* 4.7 5.1 + - - -
58B GLU* 3.3 24.5 - - - +
62B THR* 6.0 0.5 - - - -
66B MSE 3.6 43.5 - - + +
71B LEU* 5.1 0.2 - - + -
100B VAL* 4.1 9.3 - - + +
101B ARG 3.0 21.4 + - - +
102B GLY* 1.3 70.6 - - - +
104B ARG* 1.3 65.3 + - - +
105B MSE 3.3 2.0 - - - -
106B SER* 3.3 2.8 + - - -
107B VAL* 3.0 22.7 + - + +
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Residues in contact with ARG 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLU* 5.4 0.6 + - - -
58B GLU* 3.3 6.1 + - - +
102B GLY* 3.9 17.7 - - - +
103B ASN* 1.3 79.6 - - - +
105B MSE 1.3 52.4 + - - +
107B VAL* 3.6 6.2 - - + +
108B ALA* 2.7 35.7 + - - +
249B ARG* 4.1 5.9 + - - +
250B SER* 3.4 28.8 - - - -
271B GLY 3.3 2.7 - - - +
272B ARG 3.3 22.2 - - - +
273B LEU 3.3 23.4 + - - -
274B GLY* 3.4 10.2 - - - -
278B ALA* 5.3 0.2 - - - +
281B ARG* 4.9 3.0 - - - +
401B SO4 2.8 42.8 + - - -
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Residues in contact with MSE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B CYS* 3.7 16.6 - - - -
48B VAL* 3.7 19.4 + - + +
49B ALA* 3.6 36.6 - - + +
50B LEU 5.1 0.2 - - - -
55B TYR* 5.2 0.7 - - + -
56B THR* 3.4 34.1 - - + +
58B GLU* 2.9 22.5 + - - +
104B ARG* 1.3 78.0 - - - +
106B SER* 1.4 54.4 + - - +
108B ALA* 3.5 2.9 + - - +
109B ALA* 3.2 21.0 + - - +
271B GLY* 3.3 18.8 - - - +
272B ARG* 3.6 32.8 - - + +
298B MSE 4.0 19.3 - - + -
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Residues in contact with SER 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B CYS* 4.3 5.8 - - - -
58B GLU* 3.2 9.8 + - - -
63B ALA* 3.4 35.0 + - - +
66B MSE 3.7 15.0 - - - +
67B LEU* 3.7 17.1 - - - +
71B LEU* 3.4 22.7 - - - +
103B ASN* 3.7 6.0 + - - -
105B MSE 1.4 70.2 - - - +
107B VAL* 1.3 67.3 + - - +
109B ALA* 3.1 14.3 + - - +
110B ILE* 3.3 7.8 + - - +
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 4.0 20.0 - - + -
94B CYS* 3.9 27.6 - - + -
97B LEU* 4.0 30.8 - - + +
100B VAL* 4.7 7.4 - - + +
102B GLY 4.3 7.2 - - - +
103B ASN 3.0 19.5 + - - +
104B ARG* 3.6 10.1 - - + +
106B SER* 1.3 76.5 - - - +
108B ALA* 1.3 62.1 + - - +
110B ILE* 3.1 6.6 + - - +
111B GLU* 3.0 18.9 + - - +
274B GLY* 4.0 10.8 - - - +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLU 6.2 0.2 - - - +
104B ARG 2.7 21.8 + - - +
105B MSE 3.6 5.2 - - - +
106B SER 3.3 0.2 - - - -
107B VAL* 1.3 74.1 - - - +
109B ALA* 1.3 54.6 - - - +
111B GLU* 4.4 0.7 - - - -
112B MSE 2.8 44.0 + - - +
271B GLY* 3.5 23.6 - - - +
274B GLY 3.6 10.5 - - - -
275B GLY* 3.4 22.9 - - - +
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 3.8 23.2 - - + +
45B SER* 2.6 27.0 + - - +
46B GLU 4.7 5.1 + - - -
47B CYS* 3.8 23.1 - - + -
67B LEU* 4.8 4.0 - - + -
105B MSE 3.2 12.2 + - - +
106B SER* 3.1 12.4 + - - +
108B ALA* 1.3 75.0 - - - +
110B ILE* 1.3 63.5 + - - +
112B MSE 5.5 0.2 - - - -
113B ALA* 3.2 13.0 + - - +
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LEU* 6.4 0.2 - - + -
33B VAL* 5.0 9.0 - - + -
35B LEU* 4.4 2.9 - - + +
67B LEU* 3.8 19.7 - - + -
71B LEU* 3.6 43.7 - - + +
72B VAL* 4.2 11.2 - - + +
75B PHE* 3.9 42.0 - - + -
93B VAL* 4.2 8.5 - - + -
97B LEU* 4.4 11.2 - - + -
106B SER 3.3 3.1 + - - +
107B VAL 3.1 6.9 + - - +
109B ALA* 1.3 76.0 - - + +
111B GLU* 1.3 66.0 + - - +
113B ALA* 3.3 6.6 + - - +
114B VAL* 3.1 22.4 + - + +
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B PRO 4.5 5.0 - - - +
91B ARG* 5.8 0.3 - - - -
93B VAL* 4.2 22.9 - - + +
94B CYS* 3.8 27.8 - - - +
97B LEU* 6.4 0.2 - - + -
107B VAL 3.0 15.5 + - - +
108B ALA 3.9 1.8 - - - +
110B ILE* 1.3 76.5 - - - +
112B MSE 1.3 68.9 + - - +
114B VAL* 3.2 4.5 + - - +
115B TRP* 3.0 40.6 + - + +
274B GLY 4.2 4.9 - - - +
275B GLY* 3.3 5.9 - - - -
276B PHE 2.7 25.0 + - - -
277B GLY* 2.8 28.6 + - - -
278B ALA 5.4 0.2 - - - -
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Residues in contact with MSE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B SER* 4.0 13.7 - - - -
46B GLU 5.3 8.7 - - - +
48B VAL* 6.6 0.2 - - - -
108B ALA* 2.8 36.0 + - - +
109B ALA* 5.5 0.2 - - - -
111B GLU* 1.3 85.8 - - - +
113B ALA* 1.3 62.3 + - - +
115B TRP* 3.4 2.4 + - - +
116B ASP* 2.9 28.9 + - - +
270B PRO* 4.3 12.3 - - + -
271B GLY* 4.5 11.4 - - - +
275B GLY* 3.8 17.0 - - - -
276B PHE* 3.7 30.3 - - + -
304B GLY* 5.8 0.9 - - - +
307B HIS* 3.5 38.4 - - + +
308B GLY 5.4 0.4 - - - +
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 3.9 14.8 - - + +
35B LEU* 3.7 19.7 - - + +
43B GLY* 3.8 4.2 - - - +
44B TRP 3.9 13.2 - - - -
45B SER* 3.5 16.0 - - - +
109B ALA 3.2 19.9 + - - +
110B ILE 3.7 3.8 - - - +
112B MSE 1.3 76.0 - - - +
114B VAL* 1.3 60.1 + - - +
116B ASP* 3.6 1.0 - - - +
117B TRP* 2.8 31.4 + - - +
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LEU* 4.6 1.6 - - + -
35B LEU* 3.6 10.5 - - + -
75B PHE* 3.5 36.1 - - + -
88B VAL* 3.9 23.8 - - + -
90B PRO* 4.0 10.8 - - + -
93B VAL* 3.5 27.6 - - + -
110B ILE 3.1 15.8 + - - +
111B GLU 3.6 7.2 - - - +
112B MSE 3.2 0.4 - - - -
113B ALA* 1.3 74.8 - - - +
115B TRP* 1.3 67.1 + - - +
117B TRP* 3.6 8.5 - - + -
118B TYR* 2.9 21.5 + - - +
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Residues in contact with TRP 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B PRO* 3.6 32.0 + - + -
91B ARG* 3.7 39.2 - - + +
111B GLU* 3.0 55.4 + - + -
112B MSE 3.4 5.8 + - - +
114B VAL* 1.3 77.9 - - - +
116B ASP* 1.3 64.7 + - - +
118B TYR* 3.2 6.9 + + - +
119B ALA* 3.0 23.7 + - - +
126B LEU* 3.7 17.8 - - + +
129B LEU* 4.3 24.2 - - + +
130B LEU* 3.9 29.6 - - + -
276B PHE* 3.6 23.4 - + + +
277B GLY* 4.2 4.4 - - - +
280B LEU* 4.9 11.2 - - + -
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Residues in contact with ASP 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLU 4.4 0.5 - - - +
43B GLY* 3.3 7.3 - - - -
44B TRP 2.9 37.5 + - - +
112B MSE 2.9 19.0 + - - +
113B ALA 3.6 3.1 - - - +
114B VAL 3.2 0.2 - - - -
115B TRP* 1.3 77.4 - - - +
117B TRP* 1.3 63.2 + - - +
119B ALA 3.3 1.9 + - - -
120B ALA* 3.1 18.5 + - - +
126B LEU* 4.0 10.5 - - - +
307B HIS* 2.8 21.3 + - - +
354B GLY* 3.3 15.5 - - - -
355B VAL* 2.9 34.5 + - - +
356B ALA 4.1 2.6 + - - -
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Residues in contact with TRP 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B SER 5.1 8.5 - - - -
2B LEU* 3.6 30.7 - - + -
35B LEU* 4.9 4.3 - - + -
37B ASP* 2.9 33.5 + - + +
41B ILE* 3.6 28.6 - - + +
42B GLU 3.9 4.9 - - - -
43B GLY* 3.4 16.7 - - - +
87B ASP* 6.1 0.9 - - + -
88B VAL* 3.5 45.5 - - + -
113B ALA 2.8 21.8 + - - +
114B VAL* 3.6 13.9 - - + +
116B ASP* 1.3 74.4 - - - +
118B TYR* 1.3 82.8 + + + +
120B ALA* 3.1 2.9 + - - +
121B ARG* 2.8 49.8 + - + +
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Residues in contact with TYR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ASP* 6.6 0.2 - - + -
88B VAL 3.8 13.7 - - - -
89B ASP* 5.5 0.2 - - - -
90B PRO* 3.6 36.6 - - + -
114B VAL 2.9 17.9 + - - +
115B TRP* 3.2 8.7 + + - +
117B TRP* 1.3 94.3 - + + +
119B ALA* 1.3 57.7 + - - +
121B ARG* 3.3 3.5 + - + +
122B THR* 2.9 63.5 + - + +
124B GLN* 4.1 6.7 + - - -
129B LEU* 4.0 21.3 - - + -
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Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B TRP 3.0 13.3 + - - +
116B ASP 3.6 4.9 - - - +
117B TRP 3.2 0.2 - - - -
118B TYR* 1.3 77.1 - - - +
120B ALA* 1.3 56.5 - - - +
122B THR* 3.9 4.0 - - - -
123B GLY* 2.8 26.5 + - - -
124B GLN 3.1 28.3 + - - +
126B LEU* 3.8 20.9 - - + -
129B LEU* 3.9 7.2 - - + -
353B ALA* 3.6 3.3 - - - +
354B GLY* 3.5 19.1 - - - +
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ILE* 3.7 16.4 - - + +
42B GLU 3.5 23.8 - - - +
116B ASP 3.1 9.8 + - - +
117B TRP 3.1 8.7 + - - +
119B ALA* 1.3 76.0 - - - +
121B ARG* 1.3 62.0 + - - +
123B GLY* 3.4 10.2 + - - -
353B ALA* 3.1 18.1 + - - +
354B GLY* 4.6 2.0 - - - -
356B ALA* 5.6 2.9 - - + -
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Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B SER* 4.8 5.9 + - - -
37B ASP* 2.8 32.1 + - - -
39B ASP* 2.8 34.1 + - - +
41B ILE* 3.8 15.5 - - - +
117B TRP* 2.8 44.6 + - + +
118B TYR* 3.6 7.4 - - + +
120B ALA* 1.3 74.2 - - - +
122B THR* 1.3 65.3 + - + +
123B GLY 3.7 0.2 + - - -
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Residues in contact with THR 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B TYR* 2.9 56.0 + - + +
119B ALA* 3.4 7.4 + - - -
121B ARG* 1.3 82.8 - - + +
123B GLY* 1.3 61.5 + - - +
124B GLN* 2.9 35.3 + - - +
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Residues in contact with GLY 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ALA 2.8 9.8 + - - -
120B ALA 3.4 7.0 + - - -
121B ARG 3.3 3.8 + - - -
122B THR* 1.3 80.3 - - - +
124B GLN* 1.3 57.3 + - - +
125B PRO* 4.2 3.6 - - - +
353B ALA* 3.6 14.5 - - - +
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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
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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