Contacts of the helix formed by residues 170 - 185 (chain B) 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 ARG 170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B MET* 4.4 8.5 + - + -
169B LEU* 1.3 76.9 - - - +
171B ASP* 1.3 62.1 + - - +
172B SER* 3.1 24.4 + - - +
173B GLU* 2.9 39.0 + - + +
174B LEU* 2.9 25.9 + - - +
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Residues in contact with ASP 171 (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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169B LEU 5.1 0.9 - - - +
170B ARG* 1.3 73.4 - - - +
172B SER* 1.3 63.3 + - - +
174B LEU* 3.5 10.0 + - - +
175B TYR* 3.0 25.1 + - - +
231B ARG* 2.4 48.9 + - - +
235B ILE* 4.0 17.2 - - + +
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Residues in contact with SER 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ARG* 3.1 35.6 + - - +
171B ASP* 1.3 77.9 - - - +
173B GLU* 1.3 62.9 + - - +
175B TYR* 3.7 6.6 - - - +
176B GLN* 3.3 27.8 + - - +
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Residues in contact with GLU 173 (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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136B TRP* 5.3 0.5 - - - -
137B TRP* 3.7 41.5 + - + +
168B MET 4.6 1.6 - - - +
169B LEU* 3.4 25.0 - - + +
170B ARG* 2.9 60.5 + - + +
172B SER* 1.3 86.1 - - - +
174B LEU* 1.3 54.7 + - - +
176B GLN* 3.0 4.7 + - - +
177B VAL* 2.7 40.2 + - - +
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Residues in contact with LEU 174 (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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159B MET* 4.2 19.1 - - + -
160B PHE 5.4 0.7 - - - +
161B MET* 3.6 42.8 - - + -
169B LEU* 4.2 30.2 - - + +
170B ARG 2.9 14.1 + - - +
171B ASP* 3.8 13.9 - - - +
173B GLU* 1.3 75.0 - - - +
175B TYR* 1.3 54.5 + - - +
177B VAL* 4.2 3.8 - - - -
178B LEU* 2.7 45.9 + - + +
190B VAL* 4.9 10.5 - - + -
231B ARG* 5.0 0.4 - - - +
232B VAL* 4.5 5.6 - - + -
235B ILE* 4.0 20.9 - - + -
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Residues in contact with TYR 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ASP 3.0 18.1 + - - +
172B SER* 3.7 7.4 - - - +
173B GLU 3.2 0.2 - - - -
174B LEU* 1.3 74.4 - - - +
176B GLN* 1.3 77.6 + - - +
179B HIS* 3.0 40.9 + + + +
235B ILE* 3.8 19.9 - - + +
238B ARG* 4.3 21.8 + - + +
239B THR* 3.0 38.5 - - + +
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Residues in contact with GLN 176 (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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137B TRP* 3.3 37.2 - - + +
142B LYS* 5.9 0.9 + - - -
172B SER 3.3 13.9 + - - +
173B GLU 3.0 5.0 + - - +
175B TYR* 1.3 95.5 - - - +
177B VAL* 1.3 61.1 + - - +
179B HIS* 3.3 12.3 + - - +
180B ALA* 2.9 29.3 + - - +
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Residues in contact with VAL 177 (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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134B ILE* 3.8 30.7 - - + -
137B TRP* 3.6 29.8 - - + -
145B MET* 4.7 0.9 - - + -
159B MET* 3.8 26.9 - - + -
169B LEU* 3.9 19.3 - - + -
173B GLU 2.7 24.8 + - - +
174B LEU* 3.7 7.0 - - - +
176B GLN* 1.3 69.8 - - - +
178B LEU* 1.3 64.3 + - + +
180B ALA* 3.1 8.5 + - - +
181B CYS* 2.8 29.7 + - - -
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Residues in contact with LEU 178 (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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159B MET* 4.1 13.9 - - + -
174B LEU* 2.7 29.5 + - + +
175B TYR 4.1 1.3 - - - +
177B VAL* 1.3 73.8 - - + +
179B HIS* 1.3 62.7 + - - +
181B CYS* 3.2 1.6 + - - -
182B LYS* 3.0 19.9 + - - +
188B ALA* 3.4 30.5 - - + -
190B VAL* 4.8 3.1 - - + -
232B VAL* 4.3 7.6 - - + +
235B ILE* 3.8 11.4 - - + -
236B ALA* 3.6 39.5 - - + +
239B THR* 3.5 13.9 - - + +
241B CYS* 3.4 18.7 - - + +
243B ILE* 4.0 12.1 - - + -
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Residues in contact with HIS 179 (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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142B LYS* 4.9 9.4 - - - -
175B TYR* 3.0 30.4 + + + +
176B GLN* 3.5 14.6 - - - +
178B LEU* 1.3 76.9 - - - +
180B ALA* 1.3 64.9 + - - +
182B LYS* 3.4 21.4 + - - +
183B ASP* 3.1 24.7 + - - +
239B THR* 4.2 20.4 + - + +
1483B ZN 2.2 35.7 - - - -
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Residues in contact with ALA 180 (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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137B TRP* 4.0 17.5 - - + -
142B LYS* 4.7 17.0 - - + +
145B MET* 3.8 18.6 - - + -
176B GLN 2.9 14.5 + - - +
177B VAL 3.2 10.1 - - - +
179B HIS* 1.3 79.9 - - - +
181B CYS* 1.3 61.8 + - - +
183B ASP* 3.3 8.3 + - - +
184B ILE* 3.3 25.7 + - + +
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Residues in contact with CYS 181 (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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145B MET* 3.9 15.9 - - - +
157B PHE* 3.9 24.2 - - - -
159B MET* 4.6 0.7 - - - -
177B VAL* 2.8 26.4 + - - -
178B LEU 3.2 7.8 + - - +
180B ALA* 1.3 74.3 - - - +
182B LYS* 1.3 57.1 + - - +
184B ILE* 3.3 8.8 + - - +
185B GLY 2.9 10.2 + - - -
186B ALA* 2.8 37.4 + - + +
188B ALA* 4.1 20.6 - - + -
241B CYS* 3.9 12.6 - - - -
472B TYR* 4.2 0.4 - - - -
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Residues in contact with LYS 182 (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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108A SER* 4.5 7.3 + - - -
111A ASP* 3.5 27.9 + - - +
140A LYS* 5.0 6.8 - - - +
144A GLU* 5.1 2.2 + - - -
178B LEU 3.0 15.3 + - - +
179B HIS* 3.8 19.5 - - - +
181B CYS* 1.3 77.2 - - - +
183B ASP* 1.3 86.7 + - - +
185B GLY* 3.4 9.9 + - - -
239B THR 3.2 22.9 - - - +
240B HIS* 3.8 20.0 - - + +
241B CYS* 4.0 15.9 - - + -
467B PHE* 4.0 5.2 - - - -
472B TYR* 3.7 19.4 - - + +
479B GLU* 4.1 20.6 + - - +
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Residues in contact with ASP 183 (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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110A VAL* 3.8 24.1 - - + +
111A ASP* 3.4 16.0 - - - +
114A GLU* 3.2 19.7 - - + +
144A GLU* 5.5 0.3 - - - +
147A THR* 5.2 1.0 - - - +
152A LYS* 5.4 5.8 + - - +
142B LYS* 4.8 7.2 + - - +
179B HIS* 3.1 20.5 + - - +
180B ALA* 3.6 7.4 - - - +
181B CYS 3.2 0.2 - - - -
182B LYS* 1.3 102.3 + - - +
184B ILE* 1.3 63.0 + - + +
467B PHE* 3.8 2.6 - - - -
1483B ZN 2.0 37.2 - - - -
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Residues in contact with ILE 184 (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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114A GLU* 3.7 30.7 - - - +
152A LYS* 4.8 1.8 - - - +
145B MET* 3.9 28.5 - - + +
146B GLU* 3.8 23.3 - - + -
149B VAL* 3.4 50.1 - - + +
157B PHE* 4.0 10.8 - - + -
180B ALA* 3.4 17.9 - - + +
181B CYS* 3.5 8.3 - - - +
183B ASP* 1.3 79.5 - - + +
185B GLY* 1.3 59.4 + - - +
186B ALA* 4.2 3.1 - - + -
466B SER* 3.6 6.6 + - - -
467B PHE* 3.8 7.3 - - - -
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Residues in contact with GLY 185 (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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155B ASN 4.6 0.3 - - - +
181B CYS 2.9 4.5 + - - -
182B LYS 3.4 0.8 + - - -
183B ASP 3.4 3.8 - - - -
184B ILE* 1.3 79.6 - - - +
186B ALA* 1.3 61.3 + - - +
466B SER* 3.7 4.1 - - - -
467B PHE* 2.7 53.9 + - - -
468B PRO* 3.4 11.1 - - - +
472B TYR* 3.5 8.1 - - - -
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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