Contacts of the helix formed by residues 143 - 158 (chain D) in PDB entry 4WLU
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 PRO 143 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110D ARG* 3.5 33.7 - - + +
111D ASP* 3.9 15.0 - - + +
114D PHE* 3.9 27.6 - - + +
117D ASN* 4.9 0.2 - - + -
142D ASN* 1.3 86.5 - - + +
144D VAL* 1.3 61.9 + - - +
145D ASN* 3.2 7.0 - - + +
146D SER* 3.0 21.1 + - - +
147D THR* 2.9 32.5 + - + +
200D HIS 5.7 1.1 - - - +
326D SER* 6.0 0.7 - - - +
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Residues in contact with VAL 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D VAL 4.3 6.7 - - - +
140D ILE 3.6 20.6 - - - +
141D ALA 3.7 3.4 - - - +
142D ASN* 3.1 18.0 + - - +
143D PRO* 1.3 70.3 - - - +
145D ASN* 1.3 61.9 + - - +
146D SER 3.1 1.2 + - - -
147D THR* 3.2 8.3 - - - +
148D ILE* 3.2 24.5 + - + +
168D GLY* 3.9 28.7 - - - -
169D VAL 4.4 3.8 - - - +
170D THR* 4.9 1.6 - - + -
200D HIS* 4.2 20.2 + - + -
277D PHE* 3.8 17.7 - - + -
402D NAD 3.6 13.9 - - - +
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Residues in contact with ASN 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D PRO* 3.2 5.3 - - + -
144D VAL* 1.3 76.2 - - - +
146D SER* 1.3 57.4 + - - +
149D PRO* 3.3 18.2 - - - +
199D GLY* 3.4 6.4 - - - -
200D HIS* 2.9 25.9 + - - +
201D ALA* 3.5 19.1 - - + +
204D THR* 3.3 26.7 + - - +
277D PHE* 3.8 17.8 - - + -
322D GLU* 5.1 1.0 + - - -
323D LEU* 3.6 17.9 - - + +
326D SER* 3.7 21.2 + - - +
327D ILE* 3.8 14.0 + - - +
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Residues in contact with SER 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D ASP* 4.6 1.6 + - - -
114D PHE* 3.6 34.4 - - - -
143D PRO* 3.0 14.8 + - - +
145D ASN* 1.3 77.0 - - - +
147D THR* 1.3 59.5 + - - +
148D ILE 3.4 2.2 - - - -
149D PRO* 3.3 7.3 - - - +
150D ILE* 3.1 29.9 + - - +
326D SER* 2.7 35.2 + - - -
329D LYS* 4.2 3.5 - - - +
330D GLY* 3.7 1.5 - - - -
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Residues in contact with THR 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D PHE* 5.9 0.7 - - + -
117D ASN* 4.8 5.8 - - + +
118D ALA* 5.2 0.7 - - - +
121D VAL* 3.8 23.2 - - + +
139D VAL* 3.5 14.4 - - - +
141D ALA 3.0 26.0 + - - +
142D ASN 3.9 14.1 - - - +
143D PRO* 2.9 25.0 + - + +
144D VAL* 3.2 9.4 - - - -
146D SER* 1.3 74.3 - - - +
148D ILE* 1.3 61.9 + - - +
150D ILE* 3.5 15.7 + - + +
151D THR* 2.8 30.0 + - - -
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Residues in contact with ILE 148 (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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139D VAL* 3.7 19.5 - - + -
144D VAL* 3.2 14.7 + - + +
147D THR* 1.3 75.0 + - - +
149D PRO* 1.3 76.4 - - + +
151D THR* 3.0 5.0 + - - +
152D ALA* 3.0 20.6 + - - +
166D ILE* 3.7 23.9 - - + +
167D PHE 3.3 11.9 - - - +
168D GLY* 3.2 39.3 - - - +
277D PHE* 3.9 18.4 - - + +
278D VAL* 5.0 1.8 - - - -
279D LYS 5.4 0.2 - - - +
287D TYR* 3.9 22.9 - - + -
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Residues in contact with PRO 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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144D VAL 4.0 0.2 - - - +
145D ASN 3.3 22.7 - - - +
146D SER 3.3 14.1 - - - +
148D ILE* 1.3 96.8 - - + +
150D ILE* 1.3 60.8 + - - +
152D ALA* 3.4 1.6 + - - +
153D GLU* 3.1 30.4 + - - +
277D PHE* 4.1 3.4 - - + -
287D TYR* 3.9 36.3 + - + -
327D ILE* 3.9 26.0 - - + +
330D GLY 4.9 1.3 - - - -
331D GLU* 4.4 7.6 - - + +
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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
----------------------------------------------------------
114D PHE* 4.0 8.3 - - + -
118D ALA* 3.8 33.9 - - + +
121D VAL* 4.5 3.6 - - + -
122D ALA* 4.0 33.4 - - + +
146D SER 3.1 17.3 + - - +
147D THR* 3.6 16.4 - - + +
149D PRO* 1.3 76.1 - - - +
151D THR* 1.3 57.2 + - - +
153D GLU 3.4 0.7 + - - -
154D VAL* 2.9 34.2 + - + +
330D GLY* 3.3 28.0 - - - +
333D PHE* 4.2 5.6 - - + -
334D VAL* 3.6 20.6 - - + +
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Residues in contact with THR 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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121D VAL* 3.6 2.6 - - - +
125D THR* 3.5 39.9 - - + +
137D ILE* 4.1 18.4 - - + -
139D VAL* 3.5 12.8 - - + +
147D THR 2.8 19.5 + - - -
148D ILE* 3.0 11.3 + - - -
150D ILE* 1.3 76.8 - - - +
152D ALA* 1.3 56.3 + - - +
154D VAL* 3.3 1.9 + - - +
155D PHE* 2.9 39.6 + - + -
166D ILE* 4.1 17.9 - - + -
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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 ILE 3.0 11.2 + - - +
149D PRO 3.7 3.4 - - - +
150D ILE 3.3 0.2 - - - -
151D THR* 1.3 75.4 - - - +
153D GLU* 1.3 57.2 + - - +
155D PHE* 3.2 4.3 + - - +
156D LYS* 2.8 35.5 + - - +
161D TYR* 3.4 32.3 - - + +
166D ILE* 4.1 7.5 - - + +
287D TYR* 3.1 30.7 - - + +
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Residues in contact with GLU 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 PRO 3.1 16.1 + - - +
150D ILE 3.9 2.0 - - - +
152D ALA* 1.3 79.9 - - + +
154D VAL* 1.3 56.7 + - - +
156D LYS* 3.3 36.5 + - - +
157D LYS* 3.0 34.5 + - - +
287D TYR* 4.6 4.5 + - - +
331D GLU* 4.2 35.0 - - + +
334D VAL* 3.8 23.7 - - + +
335D LYS* 5.1 14.0 + - + +
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Residues in contact with VAL 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D ALA* 4.1 17.7 - - + +
125D THR* 3.6 16.6 - - - +
126D ALA* 3.5 40.6 - - + +
150D ILE 2.9 27.4 + - - +
151D THR 3.6 4.5 - - - +
153D GLU* 1.3 76.8 - - - +
155D PHE* 1.3 58.6 + - + +
157D LYS* 3.3 12.2 + - + +
158D HIS* 2.7 35.8 + - + +
334D VAL* 4.1 18.6 - - + -
337D LEU* 5.3 3.1 - - + -
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Residues in contact with PHE 155 (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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125D THR* 3.4 23.1 - - - -
128D CYS* 4.0 5.4 - - + -
129D ALA* 3.7 26.2 - - + -
133D PRO* 3.8 22.7 - - + -
135D ALA 5.4 0.4 - - - -
137D ILE* 3.6 35.7 - - + -
151D THR* 2.9 33.9 + - + +
152D ALA 3.6 4.3 - - - +
154D VAL* 1.3 75.5 - - - +
156D LYS* 1.3 60.2 + - - +
158D HIS 3.3 2.1 + - - -
159D GLY 3.2 3.8 + - - -
160D VAL* 3.0 54.3 + - + +
161D TYR* 4.0 17.0 - - + -
162D ASN 5.0 0.9 - - - -
166D ILE* 4.2 11.0 - - + -
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Residues in contact with LYS 156 (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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152D ALA* 2.8 18.9 + - - +
153D GLU* 3.3 40.2 + - - +
155D PHE* 1.3 76.1 - - - +
157D LYS* 1.3 57.0 + - + +
159D GLY* 2.9 21.0 + - - +
161D TYR* 3.6 48.0 - - + +
279D LYS* 5.7 5.9 - - - +
287D TYR* 4.6 6.3 + - - -
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Residues in contact with LYS 157 (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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153D GLU* 3.0 15.3 + - - +
154D VAL* 3.3 12.1 + - + +
156D LYS* 1.3 76.7 - - + +
158D HIS* 1.3 67.6 + - + +
159D GLY 3.3 0.6 + - - -
334D VAL* 3.5 35.3 + - + -
335D LYS* 5.6 1.6 - - - +
337D LEU* 3.7 28.0 + - + -
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Residues in contact with HIS 158 (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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126D ALA* 3.9 12.5 + - + +
129D ALA* 3.8 18.6 - - + +
130D GLN* 3.4 40.4 + - + -
154D VAL* 2.7 41.0 + - + -
155D PHE 3.3 6.9 + - - +
156D LYS 3.1 1.0 - - - -
157D LYS* 1.3 83.6 - - + +
159D GLY* 1.3 62.5 + - - +
160D VAL* 3.3 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