Contacts of the helix formed by residues 170 - 188 (chain B) in PDB entry 1DSB
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 ASN 170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B ASP* 3.9 3.2 + - - +
169B SER* 1.3 82.9 + - - +
171B MET* 1.3 62.9 + - - +
172B ASP* 2.9 20.7 + - - +
173B VAL* 2.8 47.4 + - + +
174B PHE* 2.9 26.3 + - - +
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Residues in contact with MET 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A THR 5.2 9.4 - - - +
101A THR* 6.2 3.6 - - + -
103A ARG* 5.2 6.5 - - - +
32B HIS* 6.1 3.4 - - + -
35B GLN* 6.1 0.9 - - - +
40B LEU* 4.1 34.3 - - + -
168B THR* 3.7 28.9 - - + +
169B SER 4.1 1.7 + - - +
170B ASN* 1.3 70.4 + - - +
172B ASP* 1.3 66.0 + - - +
174B PHE* 3.6 35.1 - - + +
175B VAL* 3.0 29.2 + - - +
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Residues in contact with ASP 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ASN* 2.9 13.6 + - - +
171B MET* 1.3 79.1 - - - +
173B VAL* 1.3 64.4 + - + +
175B VAL* 3.6 5.4 + - - +
176B GLN* 3.3 28.6 + - - +
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Residues in contact with VAL 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ASP* 3.5 22.4 - - + +
170B ASN* 2.8 31.8 + - + +
172B ASP* 1.3 77.9 - - + +
174B PHE* 1.3 59.0 + - - +
176B GLN* 3.2 6.5 + - - +
177B GLN* 2.9 32.3 + - + +
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Residues in contact with PHE 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B HIS* 6.1 0.7 - + - -
36B PHE* 4.8 7.9 - + - -
40B LEU* 4.6 6.1 - - + -
42B ILE* 4.1 20.0 - - + -
163B PRO* 3.8 23.6 - - + -
166B MET* 3.8 30.1 - - + -
167B ASP 3.3 19.0 + - - +
168B THR* 3.4 29.2 - - + -
170B ASN 2.9 14.6 + - - +
171B MET* 3.6 34.3 - - + +
173B VAL* 1.3 74.7 - - - +
175B VAL* 1.3 66.3 + - + +
177B GLN* 3.0 6.3 + - - +
178B TYR* 2.8 39.4 + + - +
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Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 4.0 35.4 - - + +
42B ILE* 4.1 17.8 - - + +
45B ASN* 3.5 41.2 - - + +
46B VAL* 5.9 0.2 - - - +
171B MET* 3.0 23.2 + - + +
172B ASP* 3.9 5.8 - - - +
174B PHE* 1.3 80.2 - - + +
176B GLN* 1.3 64.6 + - - +
178B TYR* 3.3 2.9 + - - +
179B ALA* 3.0 26.5 + - - +
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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
----------------------------------------------------------
45B ASN* 3.4 25.8 + - - +
49B LYS* 2.7 40.2 + - - +
172B ASP* 3.3 13.5 + - + +
173B VAL* 3.2 9.7 + - - +
175B VAL* 1.3 82.4 - - - +
177B GLN* 1.3 60.6 + - - +
179B ALA* 3.3 5.0 + - - +
180B ASP* 2.8 40.5 + - - +
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Residues in contact with GLN 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ALA 6.1 2.5 - - - +
2B GLN 5.6 0.6 + - - -
3B TYR* 4.8 7.2 - - + +
8B GLN* 3.5 36.6 - - - +
166B MET* 3.5 15.6 - - - +
167B ASP* 2.9 37.9 + - - +
173B VAL* 2.9 17.6 + - + +
174B PHE* 3.4 8.2 - - - +
176B GLN* 1.3 74.3 - - - +
178B TYR* 1.3 60.6 + - - +
180B ASP* 3.3 6.9 + - - +
181B THR* 2.7 38.6 + - - +
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Residues in contact with TYR 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PHE* 4.1 19.2 - + - -
42B ILE* 3.8 30.5 - - + -
46B VAL* 4.0 12.8 - - + -
151B PRO 6.1 0.2 - - - -
152B ALA* 4.9 2.1 - - - -
153B MET* 3.4 43.3 + - + +
161B LEU* 3.8 21.3 - - + +
163B PRO* 4.1 25.2 - - + +
166B MET* 3.7 29.5 - - + -
174B PHE* 2.8 26.3 + + + +
175B VAL 3.6 8.7 - - - +
177B GLN* 1.3 77.2 - - - +
179B ALA* 1.3 62.3 + - - +
181B THR* 3.3 2.8 + - - -
182B VAL* 3.1 26.4 + - + +
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Residues in contact with ALA 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASN* 3.6 31.4 - - + +
46B VAL* 4.0 16.2 - - + +
49B LYS* 3.8 18.8 - - + +
50B LEU* 5.9 0.2 - - - +
175B VAL 3.0 17.4 + - - +
176B GLN* 3.6 9.0 - - - +
178B TYR* 1.3 78.4 - - - +
180B ASP* 1.3 58.7 + - - +
182B VAL* 3.3 4.7 + - - +
183B LYS* 3.0 26.9 + - - +
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Residues in contact with ASP 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ALA 4.7 6.1 + - - +
3B TYR* 3.2 19.4 + - - +
49B LYS* 2.9 33.9 + - - +
176B GLN* 2.8 27.6 + - - +
177B GLN* 3.7 6.7 - - - +
179B ALA* 1.3 69.6 - - - +
181B THR* 1.3 60.4 + - - +
183B LYS* 3.3 10.8 + - - +
184B TYR* 2.8 30.8 + - - +
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Residues in contact with THR 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B TYR* 3.3 27.2 + - + -
8B GLN* 4.0 33.1 - - + +
9B TYR* 4.6 3.4 - - + -
161B LEU* 4.3 5.8 - - + -
166B MET* 3.9 10.5 - - - +
177B GLN* 2.7 26.2 + - - +
178B TYR 3.5 4.9 - - - -
180B ASP* 1.3 73.6 - - - +
182B VAL* 1.3 65.3 + - - +
184B TYR* 3.2 2.3 + - + +
185B LEU* 2.9 46.7 + - + +
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Residues in contact with VAL 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B VAL* 4.2 19.1 - - + -
46B VAL* 3.7 30.7 - - + -
50B LEU* 3.7 15.7 - - + -
153B MET* 4.0 18.4 - - - -
155B VAL* 4.4 11.5 - - + +
161B LEU* 3.4 24.5 - - + -
178B TYR* 3.1 16.1 + - + +
179B ALA 3.3 6.7 + - - +
181B THR* 1.3 75.6 - - - +
183B LYS* 1.3 57.9 + - - +
185B LEU* 3.8 1.4 - - - +
186B SER* 2.9 27.9 + - - -
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Residues in contact with LYS 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LYS* 3.5 33.3 + - + +
50B LEU* 4.9 4.2 - - + +
51B PRO* 3.9 18.0 - - + +
179B ALA 3.0 14.1 + - - +
180B ASP* 3.5 13.9 - - - +
182B VAL* 1.3 78.2 - - - +
184B TYR* 1.3 64.7 + - - +
186B SER* 2.8 22.0 + - - -
187B GLU* 2.9 41.2 + - - +
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Residues in contact with TYR 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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3B TYR* 3.3 62.1 + + + +
9B TYR* 4.4 7.5 + + - -
180B ASP 2.8 21.1 + - - +
181B THR* 3.5 3.8 - - + +
183B LYS* 1.3 75.8 - - - +
185B LEU* 1.3 78.5 + - + +
187B GLU* 3.4 16.3 + - - +
188B LYS* 3.6 47.4 - - + +
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Residues in contact with LEU 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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9B TYR* 3.7 46.4 - - + -
155B VAL* 3.8 24.4 - - + +
156B ASN* 3.4 6.2 + - - -
159B TYR* 3.7 29.0 - - + -
161B LEU* 4.4 6.7 - - + -
181B THR* 2.9 28.1 + - + +
182B VAL 3.9 0.9 - - - +
184B TYR* 1.3 91.7 - - + +
186B SER* 1.3 65.5 + - - +
188B LYS* 3.0 38.2 + - - +
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Residues in contact with SER 186 (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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21B GLN* 3.7 31.2 + - - +
22B VAL* 5.0 1.3 - - - -
50B LEU* 4.8 4.0 - - - -
51B PRO* 3.9 13.1 - - - +
54B VAL* 4.6 9.0 - - - -
155B VAL* 3.6 12.0 - - - +
156B ASN* 3.8 9.8 + - - +
182B VAL 2.9 14.8 + - - -
183B LYS* 2.8 22.4 + - - -
185B LEU* 1.3 77.5 - - - +
187B GLU* 1.3 62.0 + - - +
188B LYS 3.1 3.7 + - - -
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Residues in contact with GLU 187 (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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51B PRO* 3.9 16.9 - - + +
183B LYS* 2.9 52.3 + - - +
184B TYR* 3.7 7.8 - - - +
185B LEU 3.2 0.6 - - - -
186B SER* 1.3 80.9 - - - +
188B LYS* 1.3 58.3 + - - +
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Residues in contact with LYS 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B TYR* 3.9 11.9 + - - -
156B ASN* 3.5 5.2 + - - -
158B LYS* 3.4 16.3 + - - -
159B TYR* 3.3 46.6 + - - +
184B TYR* 3.6 38.4 - - + +
185B LEU* 3.0 45.3 + - - +
186B SER 3.1 2.4 + - - -
187B GLU* 1.3 79.9 - - - +
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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
------------------------------------------------------------
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