Contacts of the helix formed by residues 184 - 194 (chain B) in PDB entry 3U44
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 GLU 184 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B THR* 3.9 21.5 + - + +
131B LYS* 4.2 14.9 - - + +
132B ARG* 2.9 40.5 + - + +
182B HIS* 2.9 25.5 + - + +
183B SER* 1.3 93.7 - - - +
185B ASP* 1.3 60.4 + - - +
186B TYR 3.4 1.3 - - - -
187B LEU* 4.1 2.3 + - - -
188B THR* 4.1 0.2 + - - -
216B GLN* 2.5 43.8 + - - +
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Residues in contact with ASP 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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131B LYS* 5.1 14.0 - - - +
176B LEU* 6.1 0.2 - - - +
180B TYR 4.7 3.3 - - - +
181B LEU* 3.6 21.0 - - + +
182B HIS* 2.8 43.2 + - - +
184B GLU* 1.3 80.8 - - - +
186B TYR* 1.3 63.6 + - - +
187B LEU 3.3 0.2 - - - -
188B THR* 2.7 25.5 + - - -
189B LEU* 3.0 14.2 + - - +
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Residues in contact with TYR 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B SER* 5.7 4.7 - - - -
72B ALA* 4.1 15.8 - - + +
73B TRP* 3.0 44.6 + + - -
76B LEU* 4.5 14.6 - - + +
82B MET* 5.1 10.6 + - - +
84B ARG 5.0 1.7 + - - -
86B PHE* 3.5 42.6 - + - +
181B LEU* 3.2 38.5 - - + +
182B HIS 4.4 3.1 - - - -
183B SER 4.1 12.3 - - - +
184B GLU 3.4 0.8 - - - -
185B ASP* 1.3 80.0 - - - +
187B LEU* 1.3 56.6 + - + +
189B LEU* 3.1 6.1 + - + +
190B LEU* 2.6 38.4 + - - +
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Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 3.7 38.8 - - + +
69B SER* 4.7 3.4 - - - +
72B ALA* 4.8 2.7 - - + -
184B GLU* 4.1 2.5 + - - +
185B ASP 3.3 0.6 - - - -
186B TYR* 1.3 81.8 - - + +
188B THR* 1.3 59.0 + - - +
190B LEU* 3.6 4.4 - - + +
191B ALA* 3.0 28.8 + - - +
216B GLN* 3.5 33.9 - - + +
217B GLU* 3.3 42.4 - - + +
220B VAL* 3.6 19.7 - - + +
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Residues in contact with THR 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LYS* 5.0 5.4 - - + +
134B CYS* 5.2 10.1 - - - -
185B ASP* 2.7 33.8 + - - -
187B LEU* 1.3 74.8 - - - +
189B LEU* 1.3 61.3 + - - +
191B ALA* 3.5 6.9 + - - +
192B GLU* 3.1 33.9 + - - +
216B GLN* 3.4 26.3 + - + +
219B ARG* 6.2 3.6 - - + -
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Residues in contact with LEU 189 (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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76B LEU* 4.2 19.7 - - + -
81B GLY* 4.7 15.9 - - - -
84B ARG* 5.3 4.3 - - - +
181B LEU* 4.4 30.7 - - + -
185B ASP 3.0 17.5 + - - +
186B TYR* 3.4 7.4 - - + +
188B THR* 1.3 76.2 + - - +
190B LEU* 1.3 64.6 + - - +
192B GLU* 3.3 19.6 - - - +
193B HIS* 3.1 54.3 + - + +
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Residues in contact with LEU 190 (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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68B PHE* 4.1 7.9 - - + +
71B LEU* 4.2 11.7 - - + -
72B ALA* 3.7 34.3 - - + +
75B VAL* 3.6 36.8 - - + -
76B LEU* 4.5 7.4 - - - +
186B TYR 2.6 20.7 + - - +
187B LEU* 3.6 6.3 - - + +
189B LEU* 1.3 70.1 - - - +
191B ALA* 1.3 61.3 + - - +
193B HIS* 2.9 2.2 + - - -
194B ILE* 2.8 50.4 + - + +
220B VAL* 3.7 27.1 - - + -
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Residues in contact with ALA 191 (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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187B LEU 3.0 17.9 + - - +
188B THR* 3.8 7.6 - - - +
189B LEU 3.4 0.2 - - - -
190B LEU* 1.3 77.3 - - - +
192B GLU* 1.3 58.8 + - - +
194B ILE* 4.1 11.7 - - - -
195B PRO* 3.5 5.0 - - - +
219B ARG* 3.5 37.5 - - + +
220B VAL* 4.1 2.0 - - + -
223B GLN* 3.2 27.6 - - - +
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Residues in contact with GLU 192 (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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188B THR* 3.1 22.6 - - - +
189B LEU* 3.3 29.7 - - - +
191B ALA* 1.3 79.2 - - + +
193B HIS* 1.3 71.3 + - + +
194B ILE 3.5 0.2 - - - -
195B PRO* 3.8 12.5 - - - +
196B LEU* 5.2 6.2 - - - +
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Residues in contact with HIS 193 (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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75B VAL* 4.5 4.9 - - + -
76B LEU* 3.3 15.2 - - + +
79B THR* 2.8 40.2 + - - +
80B GLY 3.1 23.8 - - - -
81B GLY* 5.3 0.4 - - - -
189B LEU* 3.1 37.2 + - + +
190B LEU 2.9 3.4 + - - +
192B GLU* 1.3 90.9 + - + +
194B ILE* 1.3 67.0 + - - +
195B PRO* 3.3 2.7 - - - -
196B LEU* 3.4 12.3 + - + +
197B ALA* 3.2 20.1 + - - +
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Residues in contact with ILE 194 (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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75B VAL* 4.7 3.8 - - + -
190B LEU* 2.8 39.2 + - + +
191B ALA* 4.0 6.1 - - - +
193B HIS* 1.3 77.4 - - - +
195B PRO* 1.3 71.3 - - + +
197B ALA* 2.9 28.0 + - - +
200B ILE* 3.8 22.8 - - + +
220B VAL* 3.7 37.9 - - + +
223B GLN* 3.5 30.1 - - + +
224B LEU* 3.7 19.3 - - + -
227B HIS* 4.5 2.0 - - + -
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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