Contacts of the helix formed by residues 140 - 154 (chain D) in PDB entry 4BUR
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 GLY 140 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D GLY 3.4 6.1 + - - -
139D GLY* 1.3 80.6 - - - +
141D THR* 1.3 66.1 + - - -
142D ALA 3.4 2.5 - - - -
143D ALA* 3.4 2.1 + - - +
144D PHE* 3.2 22.3 + - - +
169D PRO* 4.4 0.7 - - - +
170D TYR 5.0 4.7 - - - -
172D ARG* 4.8 4.0 - - - -
205D PHE* 4.7 5.2 - - - -
259D ALA 5.1 0.2 + - - -
1612D FAD 3.5 27.6 + - - -
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Residues in contact with THR 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D GLY* 1.3 71.4 - - - -
142D ALA* 1.3 63.6 + - - +
144D PHE* 3.3 1.4 + - - +
145D ALA* 2.9 24.6 + - + +
170D TYR 4.0 7.4 + - - -
171D MET* 4.6 1.0 - - - -
172D ARG* 5.1 1.2 + - - +
205D PHE* 3.8 26.1 - - + -
455D HIS* 3.7 24.4 - - + +
458D ALA* 3.8 18.8 - - + -
459D VAL* 3.7 31.6 - - + +
1612D FAD 3.1 17.7 + - - -
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Residues in contact with ALA 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D THR* 1.3 72.8 - - - +
143D ALA* 1.3 57.2 - - - +
146D ALA* 2.9 32.1 + - - +
257D LEU* 4.8 0.9 - - - -
259D ALA* 3.7 19.1 - - + -
436D ALA* 4.1 6.5 - - + -
437D GLY* 4.0 15.9 - - - +
458D ALA* 3.4 21.5 + - + +
462D GLY* 3.6 5.0 - - - -
1612D FAD 2.8 28.8 + - - +
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Residues in contact with ALA 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D LEU* 3.2 21.3 - - + +
137D ILE 5.2 0.2 - - - +
138D GLY 2.7 31.6 - - - +
139D GLY* 4.2 3.1 - - - -
140D GLY 3.4 10.6 + - - +
141D THR 3.3 0.2 - - - -
142D ALA* 1.3 77.8 - - - +
144D PHE* 1.3 58.3 + - - +
146D ALA 3.1 1.7 + - - -
147D ALA* 2.9 24.9 + - - +
161D ILE* 4.3 13.0 - - + -
169D PRO* 5.9 0.2 - - + -
257D LEU* 4.4 7.2 - - - -
259D ALA* 4.0 6.8 - - + +
1612D FAD 4.5 0.2 + - - -
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Residues in contact with PHE 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D GLY 3.2 10.9 + - - +
141D THR 3.3 4.9 + - - +
143D ALA* 1.3 77.5 - - - +
145D ALA* 1.3 65.8 + - + +
147D ALA* 3.0 11.6 + - + +
148D ARG* 2.8 63.5 + - + -
161D ILE* 4.5 6.4 - - + +
169D PRO* 4.3 6.9 - - + +
205D PHE* 3.5 52.3 - + + -
206D GLN* 4.2 29.2 - - + -
211D TYR* 3.7 26.5 - + - -
225D VAL* 6.5 0.2 - - + -
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Residues in contact with ALA 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D THR* 2.9 18.4 + - + +
142D ALA 4.0 2.5 - - - +
144D PHE* 1.3 86.5 - - + +
146D ALA* 1.3 60.9 + - - +
148D ARG* 4.1 4.6 - - - +
149D SER* 3.3 22.0 + - - -
458D ALA 4.4 0.4 - - - +
459D VAL* 3.9 42.8 - - + +
463D ARG* 3.8 15.1 + - - +
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Residues in contact with ALA 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D LEU* 4.3 2.7 - - + -
142D ALA 2.9 17.9 + - - +
143D ALA 3.5 4.0 - - - +
144D PHE 3.1 0.2 - - - -
145D ALA* 1.3 74.8 - - - +
147D ALA* 1.3 59.9 + - - +
149D SER* 3.1 4.3 + - - -
150D ILE* 2.9 36.1 + - + +
257D LEU* 3.7 24.0 - - + -
462D GLY 3.2 24.9 - - - +
463D ARG 4.2 0.2 - - - +
466D GLY* 3.8 7.0 - - - +
469D MET* 5.5 0.9 - - - -
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Residues in contact with ALA 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D LEU* 3.8 5.5 - - + +
143D ALA 2.9 12.9 + - - +
144D PHE* 3.0 11.6 + - + +
146D ALA* 1.3 74.6 - - - +
148D ARG* 1.3 59.5 + - - +
150D ILE* 2.8 31.4 + - - +
151D ARG* 3.1 17.6 + - - +
159D VAL* 4.3 6.0 - - + +
161D ILE* 3.9 21.5 - - + -
225D VAL* 4.1 18.6 - - + -
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Residues in contact with ARG 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D PHE* 2.8 50.5 + - + +
145D ALA* 4.1 5.6 - - - +
147D ALA* 1.3 72.1 - - - +
149D SER* 1.3 59.8 + - - +
151D ARG* 4.2 6.2 - - - +
152D ALA* 3.3 23.9 + - - +
206D GLN* 6.1 2.2 - - - +
225D VAL* 6.2 0.4 - - - -
463D ARG* 5.0 19.1 - - - +
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Residues in contact with SER 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D ALA 3.3 18.3 + - - -
146D ALA 3.1 5.8 + - - -
147D ALA 3.0 0.8 - - - -
148D ARG* 1.3 78.4 - - - +
150D ILE* 1.3 65.5 + - - +
152D ALA* 3.5 7.0 + - - +
153D ARG* 3.4 23.7 + - - +
463D ARG* 2.9 41.6 + - - +
466D GLY* 4.2 3.1 - - - -
467D GLU* 3.5 16.6 + - - +
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Residues in contact with ILE 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D PHE* 4.0 18.4 - - + -
136D LEU* 3.9 26.2 - - + -
146D ALA* 2.9 27.2 + - + +
147D ALA* 2.8 9.7 + - - +
149D SER* 1.3 77.4 - - - +
151D ARG* 1.3 56.2 + - - +
153D ARG* 3.2 3.8 + - - +
154D ASP* 3.0 27.4 + - - +
157D ALA* 3.9 21.5 - - + -
159D VAL* 4.0 11.0 - - + -
466D GLY* 3.8 22.0 - - - +
469D MET* 4.5 12.3 - - + -
470D THR* 3.7 21.2 - - + +
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Residues in contact with ARG 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ALA 3.1 14.1 + - - +
148D ARG* 4.2 5.6 - - - +
150D ILE* 1.3 72.0 - - - +
152D ALA* 1.3 62.3 + - - +
153D ARG 2.9 6.2 + - - -
154D ASP 3.2 21.5 + - - -
155D PRO* 2.6 40.3 + - + +
157D ALA* 3.3 27.0 + - - -
159D VAL* 4.5 6.5 - - + -
222D ASN* 2.9 22.0 + - - +
223D GLY 4.4 0.4 - - - -
224D GLY* 3.5 21.5 - - - -
225D VAL* 4.0 23.7 - - + +
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Residues in contact with ALA 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D ARG 3.3 17.6 + - - +
149D SER* 3.8 7.4 - - - +
150D ILE 3.4 0.4 - - - -
151D ARG* 1.3 77.8 - - - +
153D ARG* 1.3 61.0 + - + +
155D PRO* 5.1 5.2 - - - +
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Residues in contact with ARG 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D SER 3.4 11.4 + - - +
150D ILE 3.2 2.6 + - - +
151D ARG 3.0 0.6 - - - -
152D ALA* 1.3 82.7 - - + +
154D ASP* 1.3 60.0 + - - +
155D PRO* 4.1 5.6 - - - +
467D GLU* 3.7 32.8 + - + +
470D THR* 2.9 48.9 + - - +
471D GLY 4.0 1.6 - - - -
472D ALA* 3.5 30.9 - - - +
474D LYS* 6.3 0.2 - - - +
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Residues in contact with ASP 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D PHE* 4.0 15.2 - - - -
150D ILE 3.0 11.0 + - - +
151D ARG* 3.3 6.3 - - - +
153D ARG* 1.3 79.3 - - - +
155D PRO* 1.4 62.7 - - - +
156D GLY* 3.4 7.3 + - - -
157D ALA* 3.0 43.8 + - + +
470D THR* 4.5 13.3 - - + +
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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