Contacts of the helix formed by residues 106 - 125 (chain B) in PDB entry 4BT9
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 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A MET* 5.6 0.2 - - - +
75A ASN* 3.6 16.9 + - - +
104B PHE 5.3 0.7 - - - +
105B PRO* 1.3 75.9 - - - +
107B ASP* 1.3 65.7 + - - +
108B GLU* 2.8 42.9 + - - +
109B ASP* 2.9 25.6 + - - +
110B GLN* 3.2 9.5 + - - +
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Residues in contact with ASP 107 (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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75A ASN* 2.7 34.4 + - - +
106B ASN* 1.3 77.7 - - - +
108B GLU* 1.3 62.7 + - - +
110B GLN* 3.2 3.6 + - - +
111B VAL* 3.1 24.7 + - - +
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Residues in contact with GLU 108 (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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106B ASN* 2.8 38.7 + - - +
107B ASP* 1.3 78.5 - - - +
109B ASP* 1.3 65.4 + - - +
111B VAL* 3.3 12.0 - - + +
112B GLY* 2.9 25.1 + - - -
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Residues in contact with ASP 109 (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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71A MET* 3.7 4.9 - - - +
4B PHE* 3.6 27.6 - - + -
105B PRO* 3.2 24.5 - - + +
106B ASN* 2.9 37.4 + - - +
108B GLU* 1.3 81.4 - - - +
110B GLN* 1.3 59.9 + - - +
112B GLY* 3.6 0.3 - - - -
113B ALA* 2.8 31.5 + - - +
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Residues in contact with GLN 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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68A PHE* 4.1 10.2 - - + -
71A MET* 3.8 15.0 - - + +
72A LYS* 3.5 50.0 - - + +
75A ASN* 3.0 24.3 + - - +
76A THR* 3.3 14.4 + - - -
106B ASN 3.2 10.2 + - - +
107B ASP* 3.2 9.2 + - - +
109B ASP* 1.3 77.1 - - - +
111B VAL* 1.3 61.8 + - - +
113B ALA* 3.4 2.4 + - - +
114B ALA* 3.1 22.5 + - - +
152B GLU* 4.0 13.5 + - - -
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Residues in contact with VAL 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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107B ASP 3.1 14.2 + - - +
108B GLU* 3.3 19.3 - - + +
110B GLN* 1.3 76.0 - - - +
112B GLY* 1.3 61.0 + - - +
114B ALA* 3.2 6.6 + - - +
115B LYS* 2.9 54.4 + - + +
156B VAL* 4.8 13.5 - - + -
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Residues in contact with GLY 112 (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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4B PHE* 3.7 13.6 - - - -
108B GLU 2.9 20.3 + - - -
109B ASP 3.6 1.8 - - - -
110B GLN 3.2 0.2 - - - -
111B VAL* 1.3 78.1 - - - +
113B ALA* 1.3 56.8 + - - +
115B LYS* 3.4 9.1 + - - +
116B ALA* 3.0 26.7 + - - +
119B ARG* 4.8 1.9 + - - -
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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
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64A PRO* 4.8 2.1 - - - +
67A ALA* 3.8 11.4 - - + +
68A PHE* 3.7 29.8 - - - +
71A MET* 3.8 9.2 - - + -
4B PHE* 3.6 21.7 - - + +
109B ASP 2.8 19.5 + - - +
110B GLN 4.0 2.7 - - - +
112B GLY* 1.3 70.0 - - - +
114B ALA* 1.3 65.5 + - - +
116B ALA* 3.4 2.3 + - - +
117B LEU* 3.1 23.2 + - - +
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Residues in contact with ALA 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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68A PHE* 3.8 25.5 - - + -
110B GLN 3.1 14.5 + - - +
111B VAL* 3.4 10.3 - - - +
113B ALA* 1.3 77.3 - - - +
115B LYS* 1.3 61.9 + - - +
117B LEU* 3.3 5.0 + - - +
118B LEU* 3.1 27.4 + - - +
152B GLU 6.2 0.2 - - - -
153B LEU* 4.0 13.9 - - + +
156B VAL* 4.2 20.0 - - + -
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Residues in contact with LYS 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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111B VAL* 2.9 39.9 + - + +
112B GLY* 3.8 7.2 - - - +
113B ALA 3.4 0.2 - - - -
114B ALA* 1.3 73.7 - - - +
116B ALA* 1.3 58.3 + - - +
118B LEU* 3.4 6.5 + - - +
119B ARG* 2.9 60.5 + - - +
156B VAL* 3.8 22.0 - - + -
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Residues in contact with ALA 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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64A PRO* 4.7 3.1 - - + -
3B GLY* 4.2 7.4 - - - -
4B PHE* 3.9 32.1 - - + +
112B GLY 3.0 17.5 + - - +
113B ALA 3.7 5.4 - - - +
114B ALA 3.3 0.2 - - - -
115B LYS* 1.3 72.5 - - - +
117B LEU* 1.3 66.3 + - - +
119B ARG* 3.4 16.2 + - - +
120B LEU* 3.1 29.7 + - - +
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Residues in contact with LEU 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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64A PRO* 3.6 26.4 - - + +
65A VAL* 3.8 29.6 - - + -
68A PHE* 4.1 13.7 - - + -
113B ALA 3.1 12.8 + - - +
114B ALA* 3.5 7.9 - - - +
116B ALA* 1.3 77.4 - - - +
118B LEU* 1.3 61.9 - - + +
120B LEU* 3.3 2.1 + - - +
121B GLN* 2.8 46.7 + - - +
131B ILE* 3.9 26.2 - - + -
153B LEU* 4.1 31.6 - - + -
169B TRP* 4.2 0.9 - - + -
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Residues in contact with LEU 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 ALA 3.1 15.1 + - - +
115B LYS* 3.8 7.6 - - - +
117B LEU* 1.3 80.7 - - + +
119B ARG* 1.3 56.5 + - + +
121B GLN* 3.6 20.8 - - - +
122B ASP* 2.9 31.5 + - - +
153B LEU* 3.6 20.9 - - + +
156B VAL* 3.5 32.8 - - + -
157B ALA* 3.8 11.2 - - + +
162B ASP* 5.7 3.1 - - - +
165B HIS* 4.2 20.0 - - + +
169B TRP* 3.8 20.6 - - + +
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Residues in contact with ARG 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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112B GLY 4.8 2.0 + - - -
115B LYS* 2.9 63.1 + - + +
116B ALA* 3.8 15.4 - - - +
117B LEU 3.3 0.2 - - - -
118B LEU* 1.3 72.2 - - + +
120B LEU* 1.3 60.6 + - + +
122B ASP* 3.4 5.7 + - - +
123B THR* 2.8 36.0 + - - +
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Residues in contact with LEU 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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62A GLY 5.1 3.4 - - - +
64A PRO* 3.8 37.2 - - + -
2B PRO* 3.6 42.4 - - + +
3B GLY* 4.1 8.7 - - - +
116B ALA 3.1 15.9 + - - +
117B LEU 3.8 3.4 - - - +
119B ARG* 1.3 75.0 - - + +
121B GLN* 1.3 65.9 + - - +
123B THR* 4.4 3.4 - - - -
124B TYR* 3.0 55.2 + - + +
126B LEU* 4.0 7.5 - - + +
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Residues in contact with GLN 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 LEU* 2.8 20.1 + - - +
118B LEU* 3.6 14.6 - - - +
120B LEU* 1.3 76.5 - - - +
122B ASP* 1.3 57.4 + - - +
125B ASN* 3.0 24.9 + - - -
126B LEU* 3.1 47.5 + - + +
127B ASP 4.3 0.6 - - - -
128B THR* 4.1 14.8 - - - +
131B ILE* 4.2 11.0 - - + +
165B HIS* 3.7 23.1 + - - +
168B LEU* 4.3 5.5 - - - +
169B TRP* 2.9 44.5 + - - +
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Residues in contact with ASP 122 (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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118B LEU 2.9 18.1 + - - +
119B ARG* 3.7 5.8 - - - +
121B GLN* 1.3 77.4 - - - +
123B THR* 1.3 66.8 + - - +
124B TYR 3.5 0.2 + - - -
125B ASN* 3.6 7.2 + - - +
162B ASP* 4.8 4.7 - - - +
164B TYR* 5.5 0.2 - - - -
165B HIS* 3.3 28.0 + - + -
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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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119B ARG* 2.8 28.4 + - - +
120B LEU* 4.0 3.8 - - - -
122B ASP* 1.3 77.4 + - - +
124B TYR* 1.3 94.7 + - + +
125B ASN* 3.8 0.5 + - - +
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Residues in contact with TYR 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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2B PRO* 4.7 11.9 - - + +
120B LEU* 3.0 44.1 + - + +
123B THR* 1.3 100.5 - - + +
125B ASN* 1.3 71.8 + - - +
126B LEU* 3.4 23.1 + - + +
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Residues in contact with ASN 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 GLN 3.0 10.1 + - - -
122B ASP 3.6 5.6 + - - +
123B THR 3.5 3.2 - - - +
124B TYR* 1.3 80.3 - - - +
126B LEU* 1.3 62.7 + - - +
127B ASP 3.8 1.0 + - - -
164B TYR* 4.3 15.8 + - - -
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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