Contacts of the helix formed by residues 141 - 159 (chain B) in PDB entry 4DTZ
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 VAL 141 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B TRP* 5.5 0.9 - - + -
139B ILE* 4.0 14.8 - - + +
140B GLU* 1.3 71.0 - - - +
142B PRO* 1.3 71.2 - - + +
143B GLU 3.2 0.3 + - - -
144B ASP* 3.2 2.7 + - - +
145B MET* 2.9 39.8 + - + +
273B LEU 5.2 0.2 - - - +
274B SER* 3.9 15.5 - - - +
277B LEU* 4.0 15.7 - - + -
444B PHE* 3.0 49.9 + - + +
446B VAL* 3.9 27.1 - - + -
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Residues in contact with PRO 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B VAL* 1.3 97.0 - - + +
143B GLU* 1.3 68.8 + - - +
145B MET* 3.8 0.7 - - - +
146B THR* 2.9 36.1 + - - -
270B SER* 4.7 1.3 - - - -
274B SER* 3.3 22.2 - - - +
440B LYS* 3.9 26.5 - - + -
441B PRO 3.4 24.9 - - - +
442B GLU* 4.8 0.7 - - - -
443B GLY 4.5 4.7 - - - +
444B PHE* 3.3 16.6 - - + +
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Residues in contact with GLU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLU* 3.3 44.4 - - + +
141B VAL 3.1 0.2 - - - -
142B PRO* 1.3 93.5 - - - +
144B ASP* 1.3 58.0 + - - +
146B THR* 3.4 5.2 + - - -
147B ARG* 3.0 47.3 + - - +
443B GLY* 5.1 8.4 + - - -
444B PHE 4.8 0.7 - - - +
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Residues in contact with ASP 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 3.9 14.8 - - + -
129B LYS* 2.8 37.5 + - - +
130B TRP* 2.9 31.6 + - + +
139B ILE* 4.0 7.6 - - - +
140B GLU* 3.0 19.3 + - - +
141B VAL 4.1 1.3 - - - +
143B GLU* 1.3 73.9 - - - +
145B MET* 1.3 69.7 + - - +
147B ARG* 2.9 22.2 + - - +
148B LEU* 3.0 22.3 + - - +
165B PHE* 3.8 6.4 - - + -
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Residues in contact with MET 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 3.7 22.9 - - + -
130B TRP* 3.7 35.9 - - + -
141B VAL* 2.9 30.3 + - + +
142B PRO 3.9 2.7 - - - +
144B ASP* 1.3 77.2 - - + +
146B THR* 1.3 58.1 + - - +
148B LEU* 3.2 6.1 + - + +
149B THR* 2.9 31.9 + - - +
270B SER* 3.5 23.3 - - - +
273B LEU* 3.6 34.3 - - + -
274B SER* 3.7 12.1 - - - +
413B VAL* 4.6 2.9 - - - -
417B MET* 4.3 13.5 - - - +
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Residues in contact with THR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B PRO 2.9 20.0 + - - -
143B GLU* 3.8 6.5 - - - +
145B MET* 1.3 73.2 - - - +
147B ARG* 1.3 69.4 + - + +
148B LEU 3.1 0.2 - - - -
149B THR* 3.8 2.0 - - - -
150B LEU* 3.0 46.0 + - + +
178B VAL* 6.1 2.2 - - + -
266B HIS* 4.0 13.9 + - + +
267B GLU* 5.1 1.1 - - + +
270B SER* 2.8 24.7 + - - -
440B LYS* 4.6 10.6 - - - -
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Residues in contact with ARG 147 (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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166A TYR 5.4 2.0 + - - -
129B LYS* 3.7 11.9 - - - +
140B GLU* 5.2 5.7 + - - +
143B GLU* 3.0 39.3 + - - +
144B ASP* 2.9 34.0 + - - +
146B THR* 1.3 78.1 - - + +
148B LEU* 1.3 63.8 + - - +
150B LEU* 4.1 2.2 - - - +
151B ASP* 3.2 29.6 + - - +
164B SER* 3.4 39.4 + - - -
165B PHE* 3.7 22.3 - - + +
167B ARG 3.3 18.4 + - - -
168B ASP* 4.3 19.4 + - - +
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE* 3.6 18.4 - - + +
123B ALA* 3.9 20.6 - - - +
126B LEU* 3.9 31.6 - - + -
144B ASP 3.0 13.6 + - - +
145B MET* 3.4 9.2 - - - +
147B ARG* 1.3 78.9 - - - +
149B THR* 1.4 67.7 + - + +
151B ASP 3.4 0.3 + - - -
152B THR* 2.8 33.9 + - - +
165B PHE* 3.8 6.3 - - + -
273B LEU* 4.1 11.0 - - + -
409B GLU* 3.1 33.2 - - - +
413B VAL* 3.9 20.0 - - + -
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Residues in contact with THR 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B MET 2.9 24.1 + - - +
146B THR* 3.6 4.9 + - - -
148B LEU* 1.4 85.4 - - + +
150B LEU* 1.3 59.3 + - - +
152B THR* 3.3 0.7 + - - -
153B ILE* 2.9 40.3 + - - +
266B HIS* 2.7 30.3 + - - +
269B THR* 3.8 20.4 - - + -
270B SER* 3.6 24.7 - - - +
273B LEU* 4.4 3.1 - - + -
409B GLU* 3.9 9.4 - - - +
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B THR* 3.0 38.6 + - + +
147B ARG* 4.1 3.8 - - - +
149B THR* 1.3 79.5 + - - +
151B ASP* 1.3 60.3 + - - +
153B ILE 3.7 0.2 - - - -
154B GLY* 2.7 27.4 + - - -
162B PHE* 3.7 7.9 - - + -
164B SER* 4.7 1.6 - - - +
174B ILE* 3.7 45.3 - - + -
177B MET* 3.8 20.6 - - + -
178B VAL* 5.3 1.8 - - + -
262B LEU* 3.9 17.2 - - + +
266B HIS* 3.5 34.1 - - + +
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Residues in contact with ASP 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE* 3.8 29.2 - - + +
125B GLN* 5.3 2.6 + - - +
147B ARG 3.2 14.5 + - - +
150B LEU* 1.3 76.3 - - - +
152B THR* 1.4 58.3 + - - +
154B GLY* 3.3 0.5 + - - -
155B LEU* 2.9 30.5 + - - +
160B TYR 4.6 1.7 - - - +
161B ARG* 5.9 1.0 - - - -
162B PHE* 3.4 17.7 - - - +
163B ASN* 3.3 13.3 + - - -
164B SER* 2.5 48.9 + - - -
165B PHE* 4.2 6.7 + - - -
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Residues in contact with THR 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B MET 5.0 0.4 - - - +
119B MET* 3.6 37.8 + - + -
122B ILE* 3.3 23.2 - - - +
148B LEU* 2.8 20.9 + - - +
149B THR 3.9 2.0 - - - -
150B LEU 3.2 0.2 - - - -
151B ASP* 1.4 77.8 - - - +
153B ILE* 1.3 58.2 + - - +
155B LEU* 3.3 2.2 + - - +
156B CYS* 2.9 31.8 + - - -
405B PHE* 4.2 10.8 - - + -
409B GLU* 3.2 29.9 + - - +
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Residues in contact with ILE 153 (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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149B THR* 2.9 24.8 + - - +
152B THR* 1.3 72.5 - - - +
154B GLY* 1.4 58.0 + - - +
157B GLY* 2.6 38.8 + - - +
158B PHE* 4.9 0.5 - - - -
233B LEU* 6.1 1.3 - - + -
261B PHE* 3.7 33.4 - - + +
262B LEU* 3.8 20.4 - - + +
265B GLY* 3.7 8.7 - - - +
266B HIS* 3.6 36.6 - - + +
269B THR* 5.4 1.3 - - - +
405B PHE* 3.9 25.4 - - + -
500B HEM 4.5 12.3 - - + -
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Residues in contact with GLY 154 (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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150B LEU 2.7 18.9 + - - -
151B ASP 3.7 1.6 - - - -
153B ILE* 1.4 75.7 - - - +
155B LEU* 1.3 56.7 + - - +
158B PHE* 3.0 34.1 + - - -
159B ASN 3.2 5.4 + - - -
160B TYR 3.2 14.6 + - - -
162B PHE* 3.8 21.3 - - - -
262B LEU* 3.8 2.3 - - - +
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Residues in contact with LEU 155 (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 MET* 3.5 55.2 - - + +
121B ASP* 4.2 2.0 - - + -
122B ILE* 3.9 19.7 - - + -
151B ASP 2.9 15.9 + - - +
152B THR* 3.9 3.4 - - - +
154B GLY* 1.3 75.2 - - - +
156B CYS* 1.4 60.3 + - - +
159B ASN* 2.9 49.4 + - - +
160B TYR 3.5 5.7 + - - +
161B ARG* 3.8 43.7 - - + +
232B ASP* 4.0 4.3 - - - +
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Residues in contact with CYS 156 (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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115B TYR* 3.8 44.9 - - + -
118B MET* 4.2 14.1 - - - -
119B MET* 4.2 8.5 - - - -
152B THR* 2.9 21.2 + - - +
153B ILE* 4.4 0.7 - - - +
155B LEU* 1.4 72.9 - - - +
157B GLY* 1.3 60.8 + - - +
231B ASP 5.3 0.9 - - - -
232B ASP* 3.2 7.8 - - - +
233B LEU* 3.0 29.8 + - + +
405B PHE* 3.8 29.4 - - + -
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Residues in contact with GLY 157 (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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153B ILE* 2.6 28.2 + - - +
156B CYS* 1.3 74.9 - - - +
158B PHE* 1.4 64.1 + - - +
232B ASP* 3.9 0.9 - - - -
233B LEU* 3.4 18.0 + - - +
234B LEU* 2.9 28.6 + - - +
258B ILE* 4.9 6.6 - - - +
261B PHE* 5.1 6.1 - - - -
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Residues in contact with PHE 158 (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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154B GLY* 3.0 20.9 + - - -
157B GLY* 1.4 79.9 - - - +
159B ASN* 1.3 69.4 + - - +
160B TYR* 3.2 27.6 + + + +
162B PHE* 4.0 24.0 - + - -
173B PHE* 5.7 0.2 - + - -
215B LEU* 4.4 8.5 - - + -
216B VAL* 4.2 20.4 - - + -
219B ILE* 3.6 49.7 - - + +
223B ARG* 3.4 9.1 + - - -
232B ASP* 3.1 12.3 - - - -
234B LEU* 4.0 14.8 - - + -
258B ILE* 4.0 32.8 - - + -
262B LEU* 4.1 12.6 - - + -
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Residues in contact with ASN 159 (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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134A ASN* 4.6 2.8 - - - +
118B MET* 5.4 5.2 - - - +
155B LEU* 2.9 38.0 + - - +
158B PHE* 1.3 79.1 - - - +
160B TYR* 1.3 58.9 + - - +
161B ARG* 4.2 1.4 + - - +
223B ARG* 3.6 9.7 - - - +
228B GLU* 5.0 9.5 + - - -
230B SER* 3.9 17.1 + - - +
232B ASP* 3.3 15.7 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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