Contacts of the helix formed by residues 103 - 124 (chain X) in PDB entry 2DQ7
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 LYS 103 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101X ALA 4.1 8.1 - - - +
102X LEU* 1.3 75.1 - - - +
104X LEU* 1.3 54.5 + - - +
105X PRO* 3.4 14.4 - - + -
106X ASN* 2.6 39.9 + - + +
107X LEU* 3.3 3.6 + - - -
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Residues in contact with LEU 104 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103X LYS* 1.3 68.0 - - - +
105X PRO* 1.3 63.5 - - + +
106X ASN 2.6 2.3 + - - -
107X LEU* 2.6 42.6 + - + +
108X VAL* 2.7 34.7 + - + +
200X VAL* 4.7 12.6 - - + -
230X ASP* 5.1 7.9 - - - +
232X PRO* 3.6 33.9 - - + -
235X LEU* 4.6 11.7 - - + -
263X TYR* 5.7 5.2 - - + -
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Residues in contact with PRO 105 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103X LYS* 3.4 17.9 - - + +
104X LEU* 1.3 96.6 - - + +
106X ASN* 1.3 62.1 + - + +
108X VAL* 3.9 9.6 - - + +
109X ASP* 3.3 18.7 + - - +
263X TYR* 6.4 1.1 - - + -
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Residues in contact with ASN 106 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102X LEU* 2.9 27.1 - - + +
103X LYS* 2.6 24.0 + - + +
105X PRO* 1.3 74.7 - - + +
107X LEU* 1.3 61.1 + - - +
108X VAL 3.3 0.2 - - - -
109X ASP* 3.1 22.5 + - - +
110X MET* 3.3 14.5 + - - +
142X LEU* 2.6 38.5 - - - +
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Residues in contact with LEU 107 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94X LEU* 3.9 12.1 - - + -
99X GLY 4.6 0.4 - - - +
102X LEU* 3.6 34.3 - - + +
103X LYS 4.0 2.5 - - - +
104X LEU* 2.6 31.3 + - + +
106X ASN* 1.3 70.0 - - - +
108X VAL* 1.3 64.9 + - - +
109X ASP 3.3 0.2 + - - -
110X MET* 3.3 23.9 + - + +
111X ALA 3.1 16.6 + - - -
199X LEU* 3.2 49.4 - - + +
200X VAL* 4.9 9.6 - - + +
202X LYS* 3.9 13.0 - - - +
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Residues in contact with VAL 108 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104X LEU* 2.7 42.0 + - + +
105X PRO* 3.9 8.5 - - + +
107X LEU* 1.3 76.9 - - - +
109X ASP* 1.3 63.2 + - - +
111X ALA* 3.2 8.8 + - - +
112X ALA* 3.0 20.6 + - - +
235X LEU* 4.4 9.9 - - + -
260X LEU* 3.5 39.6 - - + +
263X TYR* 4.1 31.9 - - + -
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Residues in contact with ASP 109 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105X PRO 3.3 12.2 + - - +
106X ASN* 3.1 17.2 + - - +
108X VAL* 1.3 79.2 - - - +
110X MET* 1.3 65.6 + - - +
112X ALA* 2.9 19.2 + - - +
113X GLN* 3.0 25.9 + - - +
142X LEU* 4.9 12.0 - - - +
260X LEU 5.6 0.9 - - - -
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Residues in contact with MET 110 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90X LEU* 4.4 15.5 - - + -
93X PHE* 4.9 4.5 - - - -
94X LEU* 5.1 0.7 - - + -
102X LEU* 3.1 37.0 - - + -
106X ASN* 3.3 9.8 + - - +
107X LEU* 3.3 39.0 + - + +
109X ASP* 1.3 76.7 - - + +
111X ALA* 1.3 62.3 + - - +
113X GLN* 3.0 19.1 + - - +
114X VAL* 3.0 25.2 + - - +
138X VAL* 5.5 0.9 - - - -
142X LEU* 4.3 20.4 - - + +
144X CYS* 3.5 29.0 - - - +
199X LEU* 4.3 11.2 - - + -
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Residues in contact with ALA 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107X LEU 3.1 7.4 + - - +
108X VAL* 3.3 14.1 - - - +
109X ASP 3.1 0.6 - - - -
110X MET* 1.3 77.3 - - - +
112X ALA* 1.3 62.4 + - - +
114X VAL* 3.1 9.7 + - - +
115X ALA* 3.0 17.8 + - - +
192X PHE* 3.7 10.4 - - + -
195X LEU* 5.8 1.1 - - + -
196X LEU* 4.1 15.7 - - + -
199X LEU* 3.6 22.8 - - + +
260X LEU* 3.6 19.3 - - + -
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Residues in contact with ALA 112 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108X VAL 3.0 11.0 + - - +
109X ASP* 2.9 15.1 + - - +
111X ALA* 1.3 76.8 - - - +
113X GLN* 1.3 64.5 + - + +
115X ALA* 3.3 5.4 + - - +
116X ALA* 3.0 22.2 + - - +
257X GLN* 4.0 8.9 - - - +
260X LEU* 3.9 31.8 - - + +
261X GLU* 4.2 13.0 - - + +
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Residues in contact with GLN 113 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65X LYS* 2.6 53.7 - - + +
109X ASP* 3.0 23.1 + - - +
110X MET* 3.0 24.8 + - - +
112X ALA* 1.3 78.4 - - + +
114X VAL* 1.3 63.2 + - - +
116X ALA* 3.1 17.5 + - - +
117X GLY 3.1 10.2 + - - -
142X LEU 2.9 19.7 - - - +
143X ILE* 3.5 10.5 - - - +
144X CYS* 3.2 30.8 + - + +
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Residues in contact with VAL 114 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65X LYS* 5.7 1.1 - - - -
90X LEU* 5.1 4.3 - - + -
110X MET 3.0 15.0 + - - +
111X ALA* 3.1 8.9 + - - +
113X GLN* 1.3 75.0 - - - +
115X ALA* 1.3 57.1 + - - +
117X GLY* 3.5 0.6 + - - +
118X MET* 3.0 26.3 + - + +
131X LEU* 4.2 14.1 - - + -
136X ILE* 3.8 47.6 - - + -
144X CYS* 4.4 8.3 - - + -
146X ILE* 3.9 9.6 - - + +
192X PHE* 3.9 22.0 - - + -
195X LEU* 4.5 10.3 - - + -
199X LEU* 6.1 0.2 - - + -
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Residues in contact with ALA 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111X ALA 3.0 11.9 + - - +
112X ALA* 3.6 7.6 - - - +
113X GLN 3.1 0.2 - - - -
114X VAL* 1.3 74.5 - - - +
116X ALA* 1.3 56.2 + - - +
118X MET* 3.2 6.3 + - - +
119X ALA* 2.7 36.2 + - - +
192X PHE* 4.1 15.5 - - + -
253X PHE* 4.0 7.7 - - + +
256X LEU* 4.2 7.6 - - + +
257X GLN* 3.5 32.3 - - - +
260X LEU* 4.6 0.7 - - + -
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Residues in contact with ALA 116 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63X HIS* 3.9 12.8 + - + +
65X LYS* 4.5 11.0 - - + -
112X ALA 3.0 12.2 + - - +
113X GLN* 3.4 11.4 - - - +
115X ALA* 1.3 76.7 - - - +
117X GLY* 1.3 62.5 + - - +
119X ALA* 3.1 4.2 + - - +
120X TYR* 3.0 21.5 + - - +
257X GLN* 3.0 32.5 - - - +
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Residues in contact with GLY 117 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63X HIS* 4.4 4.5 - - - -
65X LYS* 4.1 13.1 - - - +
66X LEU* 3.6 21.0 - - - +
113X GLN 3.1 7.7 + - - -
114X VAL 3.9 2.2 - - - -
116X ALA* 1.3 77.6 - - - +
118X MET* 1.3 61.3 + - - +
120X TYR* 3.2 5.7 + - - +
121X ILE* 3.2 23.7 + - - +
146X ILE* 3.9 10.1 - - - -
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Residues in contact with MET 118 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114X VAL* 3.0 23.3 + - + +
115X ALA 3.6 2.0 - - - +
117X GLY* 1.3 74.3 - - - +
119X ALA* 1.3 59.9 + - - +
121X ILE* 3.1 20.5 + - + +
122X GLU* 2.7 28.6 + - - +
128X HIS* 4.6 6.3 - - + -
131X LEU* 3.9 21.3 - - + -
146X ILE* 3.5 21.7 - - + +
185X ILE* 4.0 8.5 - - + -
188X ASP* 3.5 30.7 - - + +
253X PHE* 3.2 56.8 - - + -
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Residues in contact with ALA 119 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115X ALA 2.7 21.6 + - - +
116X ALA 3.3 6.5 - - - +
118X MET* 1.3 72.3 - - - +
120X TYR* 1.3 60.1 + - - +
122X GLU* 2.8 24.1 - - - +
123X ARG* 2.9 16.1 + - - +
253X PHE* 3.7 22.1 - - + +
254X GLU* 3.6 21.8 - - - +
257X GLN* 4.1 12.6 - - - +
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Residues in contact with TYR 120 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60X LYS 3.7 3.3 + - - -
61X LEU* 3.5 20.0 - - + -
62X LYS* 3.1 40.1 + - - +
63X HIS* 3.1 43.1 - + + +
66X LEU* 3.9 11.4 - - + -
116X ALA 3.0 6.8 + - - +
117X GLY 3.3 7.0 - - - +
118X MET 3.1 0.2 - - - -
119X ALA* 1.3 73.8 - - - +
121X ILE* 1.3 68.1 - - - +
123X ARG* 2.9 37.8 + - - +
124X MET* 2.9 61.4 + - + +
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Residues in contact with ILE 121 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61X LEU* 4.9 4.5 - - + -
66X LEU* 4.2 15.9 - - + -
117X GLY 3.2 10.3 + - - +
118X MET* 3.1 33.2 + - + +
120X TYR* 1.3 81.1 - - + +
122X GLU* 1.3 62.3 + - - +
124X MET* 3.2 8.1 + - - -
125X ASN 3.1 3.5 + - - -
126X TYR* 3.0 61.2 + - + +
127X ILE* 4.0 7.9 - - - +
128X HIS* 4.4 7.0 - - + -
146X ILE* 4.2 9.4 - - + -
149X PHE* 3.9 27.8 - - + -
185X ILE* 4.7 5.6 - - + -
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Residues in contact with GLU 122 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118X MET 2.7 13.9 + - - +
119X ALA 2.8 15.7 - - - +
121X ILE* 1.3 75.9 - - - +
123X ARG* 1.3 57.2 + - + +
125X ASN* 2.9 26.2 + - - +
126X TYR 4.8 0.8 - - - +
185X ILE* 3.8 37.8 - - + +
186X LYS* 5.5 0.5 + - - -
189X VAL* 5.4 1.0 - - - +
252X THR* 3.7 14.1 - - - +
253X PHE* 3.0 28.3 + - - +
254X GLU* 3.5 33.1 + - - +
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Residues in contact with ARG 123 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63X HIS* 4.8 5.3 + - - -
119X ALA* 2.9 12.8 + - - +
120X TYR* 2.9 45.2 + - - +
122X GLU* 1.3 78.8 - - + +
124X MET* 1.3 71.2 + - + +
125X ASN* 3.0 13.7 + - - +
254X GLU* 4.4 17.7 + - + +
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Residues in contact with MET 124 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60X LYS* 4.9 14.4 - - - +
61X LEU* 3.7 11.9 - - + -
120X TYR* 2.9 57.4 + - + +
121X ILE 3.6 7.0 - - - +
122X GLU 3.1 0.2 - - - -
123X ARG* 1.3 94.1 - - + +
125X ASN* 1.3 64.9 + - - +
126X TYR* 2.8 37.0 - - + -
154X LEU* 3.8 2.8 - - - +
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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
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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