Contacts of the helix formed by residues 109 - 130 (chain B) in PDB entry 2B2V
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 SER 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107B ASN 3.5 4.5 + - - -
108B ALA* 1.3 78.0 - - - +
110B PRO* 1.3 74.5 - - - +
111B GLU* 3.5 11.8 + - - +
112B ASP* 2.9 41.5 + - - +
113B VAL 3.0 8.0 + - - -
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Residues in contact with PRO 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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108B ALA 3.5 2.2 - - - +
109B SER* 1.3 81.8 - - - +
111B GLU* 1.3 66.9 + - + +
113B VAL* 4.3 8.7 - - + +
114B GLU* 2.9 32.2 + - - +
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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
----------------------------------------------------------
135A ARG* 4.4 10.9 + - - +
185A ARG* 3.3 39.8 - - - +
109B SER* 3.1 11.2 + - - +
110B PRO* 1.3 84.5 - - + +
112B ASP* 1.3 64.1 + - - +
114B GLU* 3.4 5.9 + - - +
115B TYR* 3.3 18.6 + - - +
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Residues in contact with ASP 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ARG* 4.2 14.0 + - - +
137A ILE* 5.8 1.9 - - - +
160A TYR* 4.7 0.5 + - - -
185A ARG* 4.1 20.3 + - - -
104B TRP* 3.9 29.9 + - + -
108B ALA* 4.0 7.1 - - + +
109B SER* 2.9 28.3 + - - +
111B GLU* 1.3 81.2 - - - +
113B VAL* 1.3 56.9 + - - +
115B TYR* 3.5 6.8 + - - +
116B TYR* 3.1 27.4 + - - +
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B TRP* 5.3 0.4 - - - -
105B LEU* 4.5 20.6 - - + +
108B ALA* 3.3 39.5 - - + +
109B SER 3.0 4.1 + - - +
110B PRO* 3.1 9.4 + - + +
112B ASP* 1.3 75.4 - - - +
114B GLU* 1.3 59.5 + - - +
116B TYR* 3.4 5.4 - - + +
117B ASN* 2.6 58.9 + - - +
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PRO* 2.9 15.3 + - - +
111B GLU* 3.6 9.0 - - - +
113B VAL* 1.3 77.8 - - - +
115B TYR* 1.3 66.6 + - - +
117B ASN* 2.8 19.4 + - + +
118B CYS* 2.8 32.0 + - - -
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Residues in contact with TYR 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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134A GLY* 3.0 32.7 + - - -
135A ARG* 2.6 52.3 - - + +
154A LYS* 4.8 7.5 - - + +
156A GLN* 4.3 6.4 + - - -
160A TYR* 3.0 25.1 - + - -
111B GLU 3.3 7.9 + - - +
112B ASP* 3.7 8.5 - - - +
113B VAL 3.4 0.2 - - - -
114B GLU* 1.3 76.1 - - - +
116B TYR* 1.3 64.3 + - - +
118B CYS* 2.9 18.2 + - + +
119B GLN* 3.1 45.1 + - + +
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Residues in contact with TYR 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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160A TYR* 3.4 51.4 + + + +
101B THR* 4.1 19.0 + - - -
102B LYS* 4.5 11.3 + - - -
104B TRP* 3.8 22.4 - + + -
105B LEU* 4.6 20.0 - - + -
112B ASP 3.1 12.2 + - - +
113B VAL* 3.4 10.8 - - + +
115B TYR* 1.3 78.2 - - - +
117B ASN* 1.3 79.4 + - - +
119B GLN* 4.1 0.3 - - - +
120B GLN* 3.0 51.3 + - + +
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Residues in contact with ASN 117 (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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113B VAL* 2.6 47.2 + - - +
114B GLU* 2.8 28.6 + - - +
116B TYR* 1.3 89.3 - - - +
118B CYS* 1.3 62.9 + - - +
120B GLN* 3.9 2.6 - - - +
121B GLU* 3.1 31.9 + - + +
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Residues in contact with CYS 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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114B GLU* 2.8 26.8 + - - -
115B TYR* 3.6 9.0 - - + +
117B ASN* 1.3 74.1 - - - +
119B GLN* 1.3 65.8 + - + +
121B GLU* 3.0 31.0 + - - +
122B LEU* 3.1 16.3 + - + +
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Residues in contact with GLN 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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154A LYS* 3.6 28.3 - - - +
156A GLN* 5.3 6.2 + - - +
157A GLY* 5.5 3.4 - - - +
160A TYR* 4.2 8.7 - - + -
115B TYR* 3.3 54.3 + - + +
116B TYR 4.1 2.0 - - - +
118B CYS* 1.3 77.8 - - + +
120B GLN* 1.3 66.6 + - - +
122B LEU* 3.0 22.5 + - - +
123B THR* 2.8 31.0 + - - +
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Residues in contact with GLN 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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159A PRO* 3.5 18.9 - - - +
160A TYR* 2.8 41.8 + - + +
116B TYR* 3.0 50.9 + - + +
117B ASN* 4.2 3.4 - - - +
119B GLN* 1.3 76.2 - - - +
121B GLU* 1.3 55.0 + - - +
123B THR* 4.2 6.1 - - - +
124B ASP* 2.5 44.8 + - - +
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Residues in contact with GLU 121 (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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117B ASN* 3.1 20.2 + - + +
118B CYS* 3.0 18.4 + - - +
120B GLN* 1.3 77.2 - - - +
122B LEU* 1.3 54.3 + - + +
124B ASP* 3.2 6.1 + - - +
125B ASP* 2.7 36.7 + - - +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B CYS* 3.6 13.9 - - + +
119B GLN* 3.0 30.9 + - - +
121B GLU* 1.3 73.3 - - + +
123B THR* 1.3 70.4 + - - +
124B ASP 2.8 0.7 - - - -
125B ASP* 2.5 22.8 + - + +
126B LEU* 3.0 15.4 + - + +
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Residues in contact with THR 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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154A LYS* 5.0 3.1 + - - -
157A GLY 4.8 5.9 + - - -
158A LEU* 4.2 4.2 + - - -
159A PRO* 3.7 37.2 - - + +
119B GLN* 2.8 19.0 + - - +
120B GLN* 4.0 9.8 + - - +
122B LEU* 1.3 77.7 - - - +
124B ASP* 1.3 70.4 + - - +
126B LEU* 3.1 12.1 - - - +
127B HIS* 3.0 51.9 + - + +
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Residues in contact with ASP 124 (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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20B MET 5.2 4.2 - - - +
21B ASP* 4.9 10.8 - - - +
120B GLN* 2.5 34.2 + - - +
121B GLU* 3.4 7.4 - - - +
122B LEU 2.6 5.3 + - - -
123B THR* 1.3 87.0 - - - +
125B ASP* 1.3 62.0 - - - +
127B HIS* 3.4 19.5 + - - +
128B LYS* 3.4 23.1 + - - +
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Residues in contact with ASP 125 (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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121B GLU* 2.7 17.5 - - - +
122B LEU* 2.5 17.6 + - + +
124B ASP* 1.3 72.9 - - - +
126B LEU* 1.3 64.2 + - - +
128B LYS* 2.9 30.6 + - - +
129B GLN* 3.2 18.9 + - - +
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Residues in contact with LEU 126 (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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126A LEU* 5.6 14.6 - - + -
130A TYR* 5.8 3.1 - - - +
157A GLY 5.3 10.5 - - - +
122B LEU* 3.0 12.0 + - + +
123B THR* 3.1 17.5 - - - +
125B ASP* 1.3 68.8 - - - +
127B HIS* 1.3 64.8 + - + +
128B LYS 2.7 11.5 + - - -
129B GLN* 3.1 26.5 + - + +
130B TYR* 3.1 45.8 - - + +
157B GLY* 5.2 7.9 - - - +
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Residues in contact with HIS 127 (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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159A PRO* 4.3 11.6 - - + +
18B ARG* 4.0 21.3 + - - -
20B MET* 3.4 43.0 + - + +
69B HIS* 4.8 3.3 - - - -
72B ASN* 5.6 1.0 + - - -
123B THR* 3.0 42.1 + - + +
124B ASP* 3.7 14.6 + - - +
125B ASP 3.2 0.8 - - - -
126B LEU* 1.3 84.1 - - + +
128B LYS* 1.3 58.1 + - + +
130B TYR* 3.5 42.3 + + - +
131B GLN* 4.4 8.3 - - - +
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Residues in contact with LYS 128 (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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124B ASP* 3.4 18.9 + - - +
125B ASP* 2.9 26.2 + - - +
126B LEU 2.7 2.8 + - - -
127B HIS* 1.3 79.8 - - + +
129B GLN* 1.3 64.6 + - - +
130B TYR 3.2 1.3 - - - -
131B GLN* 3.3 24.7 + - - +
132B ILE* 3.5 13.1 - - - +
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Residues in contact with GLN 129 (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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125B ASP* 3.2 14.4 + - - +
126B LEU* 3.3 26.3 - - + +
128B LYS* 1.3 67.2 - - - +
130B TYR* 1.3 55.0 + - + +
131B GLN 2.5 5.5 + - - -
132B ILE* 2.3 50.3 + - - +
156B GLN* 2.8 48.2 - - + +
157B GLY* 4.6 4.9 - - - +
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Residues in contact with TYR 130 (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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130A TYR* 5.2 4.9 + - - -
18B ARG* 4.0 14.4 + - - -
20B MET* 4.6 0.2 - - + -
69B HIS* 3.1 57.7 + + + +
70B ILE 4.8 0.7 + - - -
126B LEU* 3.1 46.5 - - + +
127B HIS* 3.5 36.3 + + - +
129B GLN* 1.3 79.1 - - + +
131B GLN* 1.3 58.4 + - - +
132B ILE 3.2 1.2 + - - -
155B TRP* 3.5 24.8 - - - +
156B GLN 3.8 11.0 - - - -
157B GLY* 4.0 7.6 + - - -
158B LEU* 3.8 35.8 - - + +
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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