Contacts of the helix formed by residues 126 - 148 (chain X) in PDB entry 2BOD
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 MET 126 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125X CYS* 1.3 77.8 - - - +
127X GLN* 1.3 71.8 + - + +
128X HIS* 3.2 4.3 - - + +
129X VAL* 3.2 17.1 + - + +
130X GLN* 3.0 19.6 + - - +
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Residues in contact with GLN 127 (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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126X MET* 1.3 78.4 - - + +
128X HIS* 1.3 58.2 + - - +
130X GLN* 3.4 13.4 + - - +
131X GLN* 3.1 38.8 + - + +
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Residues in contact with HIS 128 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126X MET* 3.2 3.8 - - + +
127X GLN* 1.3 76.3 - - - +
129X VAL* 1.3 65.5 + - + +
131X GLN* 3.1 13.1 + - + +
132X GLU* 2.9 59.0 + - + +
135X GLU* 5.6 3.0 + - - -
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Residues in contact with VAL 129 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77X GLY* 4.8 9.2 - - - -
80X CYS* 3.7 9.4 - - + -
91X HIS* 4.6 5.3 + - - +
125X CYS* 3.5 31.2 - - + -
126X MET* 3.2 24.2 + - + +
128X HIS* 1.3 80.3 - - + +
130X GLN* 1.3 57.6 + - - +
132X GLU* 3.2 18.3 + - - +
133X VAL* 2.9 27.6 + - + +
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Residues in contact with GLN 130 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122X MET* 3.3 51.5 + - + +
123X SER* 3.7 19.7 + - - +
125X CYS* 3.0 20.3 + - + +
126X MET 3.0 16.0 + - - +
127X GLN* 3.5 13.3 - - - +
129X VAL* 1.3 74.3 - - - +
131X GLN* 1.3 70.5 + - - +
133X VAL* 3.2 5.7 + - - +
134X LEU* 3.1 27.4 + - - +
171X TRP* 4.4 8.0 + - - -
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Residues in contact with GLN 131 (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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127X GLN* 3.1 33.7 + - + +
128X HIS* 3.1 16.4 + - + +
130X GLN* 1.3 81.5 - - - +
132X GLU* 1.3 57.5 + - - +
134X LEU* 3.3 12.2 + - - +
135X GLU* 2.9 42.5 + - - +
174X GLN* 3.4 27.5 + - - +
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Residues in contact with GLU 132 (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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91X HIS* 3.6 34.3 + - + +
95X ARG* 4.5 0.7 + - - +
128X HIS* 2.9 44.6 + - + +
129X VAL* 3.2 22.2 + - - +
131X GLN* 1.3 76.0 - - - +
133X VAL* 1.3 60.1 + - - +
135X GLU* 3.6 18.0 - - - +
136X THR* 2.9 33.8 + - - -
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Residues in contact with VAL 133 (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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76X PRO 4.0 7.9 - - - +
77X GLY* 4.0 27.4 - - - -
91X HIS* 4.1 8.1 - - + +
118X LEU* 3.8 26.2 - - + +
119X ILE* 4.3 8.7 - - + -
122X MET* 3.6 32.1 - - + -
129X VAL* 2.9 19.0 + - + +
130X GLN 3.2 8.5 + - - +
132X GLU* 1.3 76.3 - - - +
134X LEU* 1.3 63.3 + - + +
136X THR* 3.1 5.7 + - - +
137X MET* 3.0 26.7 + - + +
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Residues in contact with LEU 134 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119X ILE* 3.9 27.1 - - + -
122X MET* 3.8 29.6 - - + -
130X GLN* 3.1 14.0 + - + +
131X GLN* 3.3 15.2 + - - +
133X VAL* 1.3 75.6 - - - +
135X GLU* 1.3 61.3 + - + +
137X MET* 3.3 1.8 + - - -
138X ALA* 3.1 18.7 + - - +
171X TRP* 3.8 20.9 - - + +
174X GLN* 3.5 43.1 - - + +
175X ALA* 3.5 25.7 - - + +
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Residues in contact with GLU 135 (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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95X ARG* 3.2 19.4 + - - +
128X HIS* 5.6 2.6 + - - -
131X GLN* 2.9 31.5 + - + +
132X GLU* 3.6 20.2 - - - +
134X LEU* 1.3 76.7 - - - +
136X THR* 1.3 58.0 + - - +
138X ALA* 3.4 7.5 + - - +
139X TYR* 3.0 23.6 + - - +
174X GLN 5.8 0.4 - - - -
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Residues in contact with THR 136 (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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75X ALA* 4.3 11.7 - - + -
91X HIS* 2.7 32.2 + - + +
94X TYR* 3.4 36.1 - - + -
95X ARG* 3.0 21.6 + - + +
115X GLU* 6.0 0.2 - - + -
118X LEU* 5.1 3.6 - - + -
132X GLU 2.9 15.9 + - - -
133X VAL* 3.1 6.0 + - - -
135X GLU* 1.3 74.9 - - - +
137X MET* 1.3 61.1 + - - +
139X TYR* 3.4 1.8 + - - +
140X ALA* 2.9 27.9 + - + +
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Residues in contact with MET 137 (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* 3.5 32.8 - - + +
115X GLU* 3.8 15.0 - - + +
118X LEU* 3.8 25.1 - - + -
119X ILE* 4.2 28.3 - - + -
133X VAL 3.0 18.3 + - - +
134X LEU* 3.6 7.4 - - - +
136X THR* 1.3 78.6 - - - +
138X ALA* 1.3 63.6 + - - +
140X ALA* 3.2 4.9 + - - +
141X GLY 3.0 19.6 + - - -
155X PHE* 3.2 42.9 - - + -
156X ASP 4.2 4.3 - - - +
175X ALA* 4.0 12.3 - - + -
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Residues in contact with ALA 138 (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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134X LEU 3.1 14.5 + - - +
135X GLU* 3.6 8.1 - - - +
137X MET* 1.3 76.1 - - - +
139X TYR* 1.3 61.8 + - - +
141X GLY 3.5 0.3 + - - -
142X LYS* 3.2 45.8 + - - +
174X GLN 5.3 1.3 - - - +
175X ALA 3.2 28.2 + - - +
176X ASP* 4.0 3.4 - - + -
180X SER* 3.5 6.6 + - - -
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Residues in contact with TYR 139 (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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94X TYR* 6.2 0.4 - + - -
95X ARG* 3.6 57.6 + - + +
98X ILE* 4.1 9.2 - - + -
99X ASP* 2.5 37.9 + - - -
135X GLU 3.0 17.5 + - - +
136X THR 3.8 3.8 - - - +
138X ALA* 1.3 77.4 - - - +
140X ALA* 1.3 57.9 + - - +
142X LYS* 3.4 7.3 + - + +
143X ALA* 2.8 26.9 + - + +
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Residues in contact with ALA 140 (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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94X TYR* 4.2 13.2 - - + +
98X ILE* 4.0 26.7 - - + -
114X VAL* 4.2 21.1 - - + -
136X THR* 2.9 19.4 + - + +
137X MET* 3.7 4.5 - - - +
139X TYR* 1.3 77.1 - - - +
141X GLY* 1.3 62.3 + - - +
143X ALA* 3.5 0.9 - - - +
144X LEU* 3.0 31.7 + - + +
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Residues in contact with GLY 141 (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* 5.4 0.2 - - - +
137X MET 3.0 14.1 + - - -
138X ALA 4.0 1.1 - - - -
140X ALA* 1.3 77.2 - - - +
142X LYS* 1.3 61.7 + - - +
144X LEU* 3.4 2.7 + - - +
145X LYS* 3.0 27.4 + - - +
153X ILE* 3.8 9.5 - - - +
155X PHE* 4.0 10.0 - - - -
180X SER 3.0 25.1 - - - +
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Residues in contact with LYS 142 (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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138X ALA* 3.2 28.7 + - - +
139X TYR* 3.8 6.5 - - + +
141X GLY* 1.3 75.5 - - - +
143X ALA* 1.3 62.4 + - - +
145X LYS* 3.4 8.8 + - - +
146X ALA* 3.0 24.1 + - - +
176X ASP* 2.8 28.5 + - - +
179X ASN* 4.0 17.7 - - - +
180X SER* 2.9 21.5 + - - +
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Residues in contact with ALA 143 (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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98X ILE* 4.0 23.8 - - + +
99X ASP* 3.4 25.2 - - - +
102X ALA* 3.2 11.1 - - - +
139X TYR* 2.8 22.1 + - + +
140X ALA 3.5 4.7 - - - +
141X GLY 3.2 0.2 - - - -
142X LYS* 1.3 77.2 - - - +
144X LEU* 1.3 62.7 + - - +
146X ALA* 3.3 8.5 + - - +
147X GLY 3.1 16.1 + - - -
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Residues in contact with LEU 144 (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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72X VAL* 4.8 1.1 - - + -
98X ILE* 4.1 22.9 - - + -
101X PHE* 3.6 35.4 - - + -
102X ALA* 4.0 8.3 - - + -
105X LEU* 3.7 16.4 - - + +
112X ILE* 3.9 20.6 - - + -
114X VAL* 3.9 28.0 - - + -
140X ALA* 3.0 23.3 + - + +
141X GLY 3.8 2.9 - - - +
143X ALA* 1.3 74.5 - - - +
145X LYS* 1.3 65.2 + - - +
147X GLY* 3.1 3.5 + - - -
148X SER 3.0 19.6 + - - +
151X ALA* 4.6 0.7 - - - +
153X ILE* 4.0 17.5 - - + -
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Residues in contact with LYS 145 (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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141X GLY 3.0 13.3 + - - +
142X LYS* 3.7 7.6 - - - +
144X LEU* 1.3 75.0 - - - +
146X ALA* 1.3 62.6 + - - +
148X SER 3.1 26.4 - - - +
149X SER* 3.5 5.4 + - - -
151X ALA 5.5 1.3 - - - +
153X ILE* 3.1 23.1 - - + +
178X SER 5.4 1.4 + - - -
179X ASN* 3.6 23.7 + - - +
180X SER* 3.8 24.8 - - - +
181X ALA* 4.3 6.5 + - - +
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Residues in contact with ALA 146 (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 ASN* 4.8 4.3 + - - -
142X LYS 3.0 17.4 + - - +
143X ALA* 3.6 7.4 - - - +
144X LEU 3.2 0.2 - - - -
145X LYS* 1.3 77.0 - - - +
147X GLY* 1.3 60.7 + - - +
148X SER* 3.6 0.3 + - - -
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Residues in contact with GLY 147 (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 ALA* 3.4 25.8 - - - -
103X ALA* 5.4 1.3 - - - -
105X LEU* 4.0 1.3 - - - -
106X LYS* 3.6 8.8 + - - -
107X ASN* 3.1 23.4 + - - -
143X ALA 3.1 9.8 + - - -
144X LEU 3.1 8.7 + - - -
146X ALA* 1.3 76.2 - - - +
148X SER* 1.3 59.3 + - - +
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Residues in contact with SER 148 (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 LEU* 3.8 12.3 - - - -
107X ASN* 3.3 14.2 - - - +
108X ARG 2.7 34.0 + - - -
144X LEU 3.0 6.7 + - - +
145X LYS* 3.1 14.5 + - - +
146X ALA 3.4 0.2 - - - -
147X GLY* 1.3 80.4 - - - +
149X SER* 1.3 62.2 + - - +
150X GLN 3.0 13.9 + - - -
151X ALA* 3.2 24.3 + - - +
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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
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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