Contacts of the helix formed by residues 132 - 145 (chain B) in PDB entry 4BSX
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 ARG 132 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94B TRP* 3.4 33.9 - - + -
98B ARG* 4.6 9.1 - - - +
125B LEU* 4.1 3.4 - - + -
130B ASP* 2.8 15.7 + - - +
131B HIS* 1.3 103.7 - - + +
133B LEU* 1.3 65.3 + - - +
134B GLY 3.4 2.2 - - - -
135B GLU* 3.2 44.2 + - - +
136B LEU* 3.1 20.4 + - - +
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Residues in contact with LEU 133 (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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122B VAL* 3.7 13.5 - - + +
125B LEU* 3.7 28.8 - - + +
126B SER* 3.4 31.9 - - - +
129B ASP* 5.8 4.3 - - - +
130B ASP* 3.1 20.9 + - + +
131B HIS 3.2 1.2 - - - -
132B ARG* 1.3 78.4 - - - +
134B GLY* 1.3 64.4 + - - +
136B LEU* 3.0 7.0 + - + +
137B GLN* 3.0 49.6 + - + +
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Residues in contact with GLY 134 (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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131B HIS 4.7 3.2 + - - -
132B ARG 3.4 0.2 - - - -
133B LEU* 1.3 77.1 - - - +
135B GLU* 1.3 53.0 + - - +
137B GLN* 3.2 16.6 + - - +
138B ASP* 2.8 44.7 + - - +
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Residues in contact with GLU 135 (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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94B TRP* 3.8 11.6 - - + -
98B ARG* 4.7 4.9 + - - -
131B HIS 5.4 0.6 + - - -
132B ARG* 3.2 55.7 + - - +
134B GLY* 1.3 75.7 - - - +
136B LEU* 1.3 57.5 + - - +
138B ASP* 3.3 10.4 + - - +
139B GLU* 2.9 29.2 + - + +
35D PRO* 3.6 35.6 - - + +
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Residues in contact with LEU 136 (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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94B TRP* 3.4 45.5 - - + +
118B TYR* 3.9 20.4 - - + -
121B ALA* 3.4 40.8 - - + +
122B VAL* 3.7 15.9 - - + -
125B LEU* 3.7 20.0 - - + -
132B ARG 3.1 7.6 + - - +
133B LEU* 3.0 10.5 + - + +
135B GLU* 1.3 76.9 - - - +
137B GLN* 1.3 56.3 + - - +
139B GLU* 3.1 4.7 + - - +
140B ALA* 2.6 34.0 + - - +
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Residues in contact with GLN 137 (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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122B VAL* 4.5 18.7 - - + +
126B SER* 5.3 0.6 + - - -
133B LEU* 3.0 43.5 + - + +
134B GLY* 3.5 19.3 - - - +
136B LEU* 1.3 75.5 - - - +
138B ASP* 1.3 66.0 - - - +
140B ALA* 3.7 8.0 - - - +
141B ARG* 3.0 24.6 + - - +
148B ILE 5.7 0.9 + - - -
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Residues in contact with ASP 138 (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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134B GLY* 2.8 26.7 + - - +
135B GLU* 3.5 10.9 + - - +
137B GLN* 1.3 73.7 - - - +
139B GLU* 1.3 63.0 + - - +
141B ARG* 3.1 21.6 + - - +
142B ASN* 3.1 24.4 + - - +
34D ARG* 6.0 2.9 - - - +
35D PRO 5.8 4.5 - - - +
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Residues in contact with GLU 139 (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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38B GLN* 5.1 0.9 - - - +
94B TRP* 3.0 19.0 + - - -
98B ARG* 2.9 44.0 + - - +
118B TYR* 2.4 33.6 + - + +
135B GLU* 2.9 14.6 + - - +
136B LEU* 3.4 7.9 - - - +
138B ASP* 1.3 72.8 - - - +
140B ALA* 1.3 66.5 + - - +
142B ASN* 3.4 5.5 + - - +
143B ARG* 3.0 41.0 + - + +
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Residues in contact with ALA 140 (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 TYR* 3.7 36.3 - - + -
122B VAL* 4.5 8.3 - - + -
136B LEU 2.6 20.0 + - - +
137B GLN* 3.7 9.4 - - - +
138B ASP 3.3 0.2 - - - -
139B GLU* 1.3 74.4 - - - +
141B ARG* 1.3 57.3 + - - +
144B CYS* 2.9 37.2 + - - +
148B ILE* 3.8 16.2 - - - +
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Residues in contact with ARG 141 (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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137B GLN 3.0 17.0 + - - +
138B ASP* 3.1 19.7 + - - +
140B ALA* 1.3 75.3 - - - +
142B ASN* 1.3 68.3 + - - +
145B GLY* 3.2 19.4 + - - -
146B TRP* 3.3 33.0 + - - +
147B ASP* 4.3 20.4 - - - +
148B ILE 4.6 3.1 - - - +
105D GLU* 2.8 37.9 + - - -
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Residues in contact with ASN 142 (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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138B ASP 3.1 13.3 + - - +
139B GLU* 3.8 6.3 - - - +
141B ARG* 1.3 87.3 - - - +
143B ARG* 1.3 72.1 + - + +
145B GLY* 4.1 5.4 + - - -
101D HIS* 6.0 1.4 - - - -
142D ASN* 2.7 60.5 + - - +
143D ARG* 4.7 11.3 - - - +
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Residues in contact with ARG 143 (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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36B GLY* 3.4 21.1 + - - -
37B CYS* 5.2 0.4 - - - +
38B GLN* 2.6 38.6 + - - +
98B ARG* 4.2 8.9 - - - +
101B HIS* 3.3 53.8 + - - +
114B ARG* 3.3 21.3 + - - -
118B TYR* 3.2 40.1 + - + +
139B GLU* 3.0 36.9 + - + +
142B ASN* 1.3 88.3 + - + +
144B CYS* 1.3 63.0 + - - +
145B GLY 3.3 0.4 + - - -
142D ASN* 4.9 6.1 - - - +
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Residues in contact with CYS 144 (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 ARG* 3.7 21.3 + - - +
115B ASP* 3.3 26.2 - - - +
118B TYR* 3.5 39.0 - - - -
140B ALA 2.9 20.1 + - - +
143B ARG* 1.3 77.8 - - - +
145B GLY* 1.3 52.9 + - - +
146B TRP* 2.7 40.9 + - + +
148B ILE 4.3 8.7 - - - -
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Residues in contact with GLY 145 (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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141B ARG 3.2 9.7 + - - -
142B ASN 4.1 4.4 + - - -
143B ARG 3.3 3.2 - - - -
144B CYS* 1.3 75.4 - - - +
146B TRP* 1.3 64.3 + - - +
145D GLY* 6.5 0.7 - - - -
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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