Contacts of the helix formed by residues 137 - 153 (chain A) in PDB entry 4BIT
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 GLU 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A VAL* 4.3 4.0 - - + -
136A ALA* 1.3 81.0 - - + +
138A LYS* 1.3 85.7 + - + +
139A THR* 2.6 35.5 + - - +
140A ASP* 2.8 28.7 + - + +
141A TYR* 2.8 18.8 + - - -
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Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LEU 6.0 0.4 - - - +
114A ARG 5.9 1.6 - - - +
116A MET* 3.7 21.8 - - + +
117A ARG* 5.4 5.8 - - - +
118A VAL* 3.2 40.4 - - + +
121A LEU* 3.3 12.4 - - + +
137A GLU* 1.3 100.8 + - + +
139A THR* 1.3 63.5 + - - +
141A TYR* 3.1 7.4 + - - -
142A VAL* 2.7 41.5 + - + +
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Residues in contact with THR 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLU* 2.6 31.5 + - - +
138A LYS* 1.3 88.8 + - - +
140A ASP* 1.3 62.0 + - - +
142A VAL* 3.4 9.8 + - + +
143A ASN* 3.1 24.1 + - - +
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Residues in contact with ASP 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ALA 4.6 0.2 - - - +
135A CYS* 3.0 18.3 - - - +
136A ALA* 2.7 29.4 + - + -
137A GLU* 2.8 27.0 + - + +
139A THR* 1.3 76.7 - - - +
141A TYR* 1.3 62.5 + - - -
143A ASN* 3.4 11.2 + - - +
144A LEU* 3.1 25.9 + - - +
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Residues in contact with TYR 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A VAL* 4.3 10.3 - - + -
121A LEU* 3.4 25.4 - - + -
122A LYS* 3.0 34.8 + - + -
125A LEU* 3.5 21.5 - - + -
132A CYS* 3.3 22.8 - - + -
135A CYS* 3.0 25.5 - - + -
136A ALA 3.4 27.7 + - - -
137A GLU 2.8 30.0 + - - -
138A LYS* 3.3 8.5 - - - +
140A ASP* 1.3 80.2 - - - +
142A VAL* 1.3 52.0 + - - +
144A LEU* 3.1 10.0 + - + +
145A ILE* 2.7 45.5 + - + +
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Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LEU* 3.1 43.3 - - + +
116A MET* 4.4 0.9 - - + -
121A LEU* 3.6 14.8 - - + +
138A LYS* 2.7 27.2 + - + +
139A THR* 3.5 11.9 - - + +
140A ASP 3.3 0.2 - - - -
141A TYR* 1.3 71.5 - - - +
143A ASN* 1.3 58.3 + - - +
145A ILE* 3.2 5.7 + - - +
146A GLN* 2.9 59.2 + - + +
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Residues in contact with ASN 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A THR 3.1 10.6 + - - +
140A ASP* 3.5 12.9 + - - +
142A VAL* 1.3 79.3 - - - +
144A LEU* 1.3 63.8 + - - +
146A GLN* 3.7 20.9 + - - +
147A GLU* 3.8 12.0 + - - +
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLU* 4.5 9.4 - - - +
132A CYS* 4.8 10.8 - - + -
134A ALA 4.7 14.8 - - - +
135A CYS* 5.2 4.7 - - + -
140A ASP* 3.1 16.4 + - - +
141A TYR* 3.5 12.3 - - + +
143A ASN* 1.3 77.5 - - - +
145A ILE* 1.3 66.2 + - + +
147A GLU* 3.0 26.1 + - + +
148A LEU* 3.1 39.8 + - + +
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Residues in contact with ILE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 4.1 18.4 - - + -
113A LEU* 5.7 4.7 - - + -
116A MET* 5.8 0.7 - - - -
121A LEU* 3.7 45.1 - - + +
124A ILE* 3.9 16.8 - - + -
125A LEU* 5.0 7.2 - - + +
128A TRP* 3.5 30.8 - - + -
130A GLU* 5.7 2.5 - - - +
141A TYR* 2.7 31.2 + - + +
142A VAL* 3.6 5.2 - - - +
144A LEU* 1.3 76.0 - - + +
146A GLN* 1.3 56.1 + - + +
148A LEU* 4.5 2.2 - - + -
149A ALA* 2.7 37.2 + - - +
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Residues in contact with GLN 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 5.7 2.2 - - + -
113A LEU* 4.7 16.1 - - + +
142A VAL* 2.9 40.1 + - + +
143A ASN* 3.7 20.1 + - - +
144A LEU 3.2 0.2 - - - -
145A ILE* 1.3 81.3 - - + +
147A GLU* 1.3 59.7 + - - +
149A ALA* 3.6 14.7 - - - +
150A PRO* 3.7 6.2 - - - +
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Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ASN 3.8 7.9 + - - +
144A LEU* 3.0 22.3 + - + +
146A GLN* 1.3 77.3 - - - +
148A LEU* 1.3 81.6 + - + +
149A ALA 3.2 0.8 + - - -
150A PRO* 3.5 13.6 - - - +
151A LYS* 2.6 53.7 + - - +
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Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A TRP* 4.0 6.7 - - + -
130A GLU* 3.5 25.1 - - - +
144A LEU* 3.1 45.1 + - + +
145A ILE* 3.9 4.5 - - + +
147A GLU* 1.3 98.0 - - - +
149A ALA* 1.3 68.1 + - - +
150A PRO 3.6 0.2 - - - -
151A LYS* 3.1 26.3 + - - +
152A TYR* 3.1 41.2 + - + +
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Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LYS 4.5 0.7 - - - +
105A THR* 5.7 3.1 - - - +
108A LEU* 3.8 17.9 - - + -
128A TRP* 3.4 18.4 - - + -
145A ILE 2.7 18.5 + - - +
146A GLN* 3.6 9.0 - - - +
147A GLU 3.2 0.6 - - - -
148A LEU* 1.3 77.2 - - - +
150A PRO* 1.4 63.9 - - + +
153A ALA* 2.7 37.0 + - + +
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Residues in contact with PRO 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LYS* 6.1 6.5 - - + -
50A GLY 5.5 0.7 + - - -
54A ARG* 3.0 26.8 + - - -
104A LYS* 3.3 27.9 - - + +
146A GLN 3.7 7.9 - - - +
147A GLU 3.5 13.9 - - - +
149A ALA* 1.4 93.5 - - + +
151A LYS* 1.3 60.6 + - + +
152A TYR 3.4 0.2 - - - -
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Residues in contact with LYS 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ARG* 3.6 13.5 + - - +
147A GLU* 2.6 62.0 + - - +
148A LEU* 3.1 20.1 + - - +
149A ALA 3.0 0.2 + - - -
150A PRO* 1.3 84.1 - - + +
152A TYR* 1.3 71.2 + - + +
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Residues in contact with TYR 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ARG* 3.0 17.2 + - - -
102A TYR* 4.4 4.9 - - - +
128A TRP* 3.7 49.1 - + + -
130A GLU* 3.6 25.9 - - + +
148A LEU* 3.1 40.2 + - + +
149A ALA 3.1 2.4 + - - -
151A LYS* 1.3 89.2 - - + +
153A ALA* 1.3 69.3 + - - +
154A ALA* 3.3 4.8 + - + +
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Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A TYR 3.7 4.2 - - - -
103A GLU 3.2 16.2 - - - +
104A LYS 4.2 0.2 - - - +
105A THR* 3.4 12.6 - - - +
106A LEU* 3.1 32.5 - - + +
128A TRP* 3.4 13.3 - - + +
149A ALA* 2.7 24.4 + - + +
152A TYR* 1.3 75.4 - - - +
154A ALA* 1.3 59.3 + - - +
155A THR* 3.0 11.1 + - - -
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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