Contacts of the helix formed by residues 138 - 152 (chain A) in PDB entry 4B92
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 ALA 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A TRP* 3.7 22.9 - - + -
137A TRP* 1.3 91.9 - - - +
139A PRO* 1.3 79.7 - - + +
140A LYS* 3.2 7.2 - - + +
141A VAL* 3.3 14.1 + - - +
142A LYS 3.5 7.4 + - - -
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Residues in contact with PRO 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 TRP* 5.3 2.2 - - + +
138A ALA* 1.3 90.4 - - + +
140A LYS* 1.3 60.8 + - - +
142A LYS* 3.2 16.9 + - + +
143A ALA* 3.1 19.2 + - - +
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Residues in contact with LYS 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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108A SER* 5.2 4.9 - - - +
136A TRP* 4.6 22.4 - - + -
138A ALA* 3.2 4.2 - - + +
139A PRO* 1.3 79.0 - - - +
141A VAL* 1.3 56.3 + - - +
143A ALA* 3.0 11.1 + - + +
144A GLU* 2.9 47.6 + - + +
182B LYS* 5.0 8.0 - - - +
240B HIS* 4.8 5.7 - - - -
479B GLU* 3.1 38.5 + - - +
482B LEU* 4.8 22.9 - - + +
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Residues in contact with VAL 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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109A LEU* 4.2 18.1 - - + +
134A ILE* 3.9 12.6 - - + -
136A TRP* 3.2 72.7 - - + +
137A TRP* 3.7 15.7 - - + -
138A ALA 3.3 10.5 + - - +
139A PRO 3.2 0.4 - - - -
140A LYS* 1.3 73.1 - - - +
142A LYS* 1.3 68.1 + - - +
144A GLU* 3.2 8.7 + - - +
145A MET* 2.9 24.7 + - + +
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Residues in contact with LYS 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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137A TRP* 3.6 31.5 - - + -
138A ALA 3.5 3.4 + - - -
139A PRO* 3.2 19.0 + - + +
141A VAL* 1.3 79.5 - - - +
143A ALA* 1.3 63.4 + - - +
145A MET* 3.3 7.7 + - - +
146A GLU* 3.1 48.7 + - + +
176A GLN* 5.9 0.8 + - - -
179A HIS* 4.9 14.8 - - - -
180A ALA* 4.6 15.0 - - + +
183A ASP* 5.1 4.6 + - - +
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Residues in contact with ALA 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 PRO 3.1 8.8 + - - +
140A LYS* 3.0 15.9 + - + +
142A LYS* 1.3 80.6 - - - +
144A GLU* 1.3 64.4 + - + +
146A GLU* 3.1 18.3 + - - +
147A THR* 3.0 24.4 + - - -
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Residues in contact with GLU 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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107A THR 4.3 0.7 - - - +
108A SER* 2.6 34.2 + - - -
109A LEU* 3.0 39.8 + - + +
110A VAL* 3.7 19.1 + - + +
136A TRP* 4.8 2.4 - - - -
140A LYS* 2.9 34.2 + - + +
141A VAL* 3.7 10.0 - - - +
143A ALA* 1.3 77.7 - - + +
145A MET* 1.3 61.2 + - - +
147A THR* 3.2 10.4 + - - -
148A LEU* 2.9 29.8 + - - +
182B LYS* 5.1 2.9 + - - -
183B ASP* 5.5 0.2 - - - +
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Residues in contact with MET 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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109A LEU* 4.4 4.0 - - + +
134A ILE* 3.5 35.2 - - + -
137A TRP* 3.8 26.7 - - - -
141A VAL* 2.9 18.8 + - + +
142A LYS* 3.3 9.4 - - - +
144A GLU* 1.3 75.6 - - - +
146A GLU* 1.3 62.8 + - + +
148A LEU* 3.2 5.1 + - - +
149A VAL* 3.1 27.2 + - - +
157A PHE* 3.7 25.4 - - + -
177A VAL* 4.1 2.0 - - - +
180A ALA* 3.8 22.0 - - + -
181A CYS* 3.8 27.4 - - - +
184A ILE* 4.0 11.2 - - + -
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Residues in contact with GLU 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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142A LYS* 3.3 37.0 - - + +
143A ALA* 3.1 16.8 + - - +
145A MET* 1.3 79.5 - - - +
147A THR* 1.3 56.6 + - - +
149A VAL* 3.9 1.1 - - - +
150A ARG* 2.9 46.8 + - - +
184A ILE* 3.8 30.8 - - + +
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Residues in contact with THR 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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110A VAL* 4.4 15.0 - - + -
143A ALA 3.0 14.4 + - - -
144A GLU* 3.2 13.7 + - - -
146A GLU* 1.3 76.2 - - - +
148A LEU* 1.3 54.6 + - - +
150A ARG* 4.1 14.5 + - - +
151A GLU* 2.8 61.5 + - + +
152A LYS* 3.6 11.1 + - - +
142B LYS* 5.6 1.1 - - - +
183B ASP* 5.2 0.7 - - - +
1483B ZN 4.6 11.7 - - - -
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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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109A LEU* 3.9 27.8 - - + -
110A VAL* 4.1 14.4 - - + -
113A TYR* 3.7 39.7 - - + -
132A VAL* 4.1 8.3 - - + -
144A GLU 2.9 21.4 + - - +
145A MET 3.6 3.8 - - - +
147A THR* 1.3 73.7 - - - +
149A VAL* 1.3 61.6 + - - +
152A LYS* 2.9 43.7 + - + +
153A GLY 3.3 5.5 + - - -
154A VAL* 3.3 18.1 + - + -
157A PHE* 4.1 19.5 - - + -
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Residues in contact with VAL 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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145A MET 3.1 17.3 + - - +
146A GLU* 3.9 2.7 - - - +
148A LEU* 1.3 78.0 - - - +
150A ARG* 1.3 63.5 + - - +
153A GLY* 4.3 7.4 + - - -
154A VAL 3.2 22.6 + - - +
155A ASN* 5.3 0.4 - - - -
157A PHE* 3.8 14.1 - - + -
184A ILE* 3.4 49.4 - - + +
185A GLY 5.6 0.4 - - - -
186A ALA* 4.6 4.7 - - + -
464A LEU 5.2 2.1 - - - +
466A SER* 3.6 22.0 + - - +
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Residues in contact with ARG 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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146A GLU* 2.9 43.6 + - - +
147A THR* 4.1 9.8 + - - +
149A VAL* 1.3 80.9 - - - +
151A GLU* 1.3 92.8 + - + +
153A GLY 5.4 0.2 - - - -
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Residues in contact with GLU 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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147A THR* 2.8 31.3 + - + +
150A ARG* 1.3 113.7 + - + +
152A LYS* 1.3 71.6 + - + +
153A GLY 3.8 1.6 - - - -
142B LYS* 3.0 37.3 + - - -
146B GLU* 5.3 3.5 - - - +
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Residues in contact with LYS 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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110A VAL* 4.7 12.3 - - - +
113A TYR* 2.7 40.9 + - + -
114A GLU* 2.9 28.8 + - - +
117A ARG* 5.5 0.2 - - - -
147A THR* 3.9 13.9 - - + +
148A LEU* 2.9 39.5 + - + +
151A GLU* 1.3 96.9 - - - +
153A GLY* 1.3 65.2 + - - +
154A VAL* 3.4 1.8 + - + +
461A PHE* 3.4 8.5 - - - -
463A PRO* 5.6 0.2 - - - -
142B LYS* 4.7 4.8 - - - +
146B GLU* 2.4 33.3 + - - +
150B ARG* 4.0 5.2 - - - +
183B ASP* 5.4 5.3 + - - +
184B ILE* 4.8 3.6 - - - +
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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