Contacts of the helix formed by residues 182 - 191 (chain B) in PDB entry 4WB7
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 182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104B LEU 5.1 0.3 - - - +
181B GLY* 1.3 72.1 - - - -
183B MET* 1.3 65.6 + - - +
184B PHE* 3.2 26.4 + - + +
185B SER* 3.2 17.7 + - - +
186B HIS* 3.0 18.8 - - - -
224B PRO 3.9 6.3 - - - +
225B GLU* 3.7 18.4 - - - +
227B LEU 3.4 5.8 - - - +
228B LEU* 4.0 7.2 - - + +
381B ASN 4.6 0.6 + - - -
382B PHE* 4.3 6.5 - - + -
385B TYR* 4.4 2.1 + - - -
501B ATP 2.6 30.3 + - - +
18J ARG* 2.8 42.4 + - - +
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Residues in contact with MET 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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181B GLY 3.8 1.2 + - - -
182B GLU* 1.3 70.7 - - - +
184B PHE* 1.3 57.3 + - - +
186B HIS* 3.2 11.5 + - - +
187B LEU* 2.9 28.8 + - + +
193B PHE* 3.8 18.2 - - + -
201B TYR* 3.7 22.0 - - + -
205B ILE* 6.2 0.2 - - + -
224B PRO* 3.8 17.5 - - + +
227B LEU* 2.8 42.7 + - + +
229B ILE* 4.2 12.7 - - + +
235B ILE* 3.6 27.6 - - + -
282B LEU* 4.3 2.9 - - + -
286B MET* 3.7 32.3 - - - +
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Residues in contact with PHE 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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182B GLU* 3.6 15.5 - - - +
183B MET* 1.3 79.3 - - - +
185B SER* 1.3 69.2 + - - +
187B LEU* 3.7 3.8 - - + +
188B ARG* 3.0 61.5 + - + +
224B PRO* 3.3 26.0 + - + +
225B GLU* 3.4 32.5 - - + +
383B ASP* 6.1 0.4 - - - -
16J THR 3.4 12.3 - - - -
17J GLY* 3.3 28.3 - - - -
18J ARG* 3.4 27.8 - - + -
19J ARG* 3.9 6.5 - - - -
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Residues in contact with SER 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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182B GLU* 3.2 20.8 + - - +
184B PHE* 1.3 87.4 - - - +
186B HIS* 1.3 69.4 + - - +
188B ARG* 3.5 3.7 + - - +
189B ARG* 3.0 34.0 + - - +
381B ASN 3.9 17.7 + - - -
383B ASP* 4.9 16.4 - - - -
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Residues in contact with HIS 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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180B GLY 2.7 28.8 + - - -
181B GLY* 4.3 1.4 - - - -
182B GLU 3.0 29.0 + - - -
183B MET* 3.2 5.3 + - - +
185B SER* 1.3 79.0 + - - +
187B LEU* 1.3 64.8 + - - +
189B ARG* 2.9 36.4 + - - +
190B ILE* 3.0 39.9 + - + +
193B PHE* 4.4 8.3 - - + -
229B ILE* 4.1 10.7 - - + +
369B PHE* 3.3 37.2 - + + -
381B ASN* 4.2 17.0 - - + -
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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
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183B MET* 2.9 18.8 + - - +
184B PHE* 3.7 5.2 - - - +
186B HIS* 1.3 77.4 - - - +
188B ARG* 1.3 71.4 + - - +
190B ILE* 3.9 0.6 - - - -
191B GLY 2.8 49.7 + - - +
192B ARG* 3.8 6.5 - - - -
193B PHE* 3.8 26.2 - - + -
224B PRO* 4.4 15.7 - - + -
285B GLU* 3.9 34.3 - - + +
286B MET* 3.7 33.2 - - + +
289B GLY* 5.1 0.2 - - - -
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Residues in contact with ARG 188 (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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184B PHE* 3.0 50.9 + - + +
185B SER* 4.1 4.3 - - - +
187B LEU* 1.3 93.5 - - - +
189B ARG* 1.3 63.7 + - - +
191B GLY* 3.7 8.2 + - - -
285B GLU* 2.6 30.9 + - - -
289B GLY 3.7 17.9 + - - -
7J TYR* 4.7 12.4 + - - -
10J PHE* 3.7 27.1 - - - -
11J ILE* 6.5 0.9 - - - -
15J ARG 4.7 2.0 + - - -
16J THR* 3.0 25.4 + - - +
19J ARG* 3.5 16.4 - - - +
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Residues in contact with ARG 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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185B SER* 3.0 30.9 + - - +
186B HIS* 2.9 43.4 + - - +
188B ARG* 1.3 79.8 - - - +
190B ILE* 1.3 72.0 + - + +
369B PHE* 4.5 9.1 - - - -
381B ASN* 5.9 1.0 - - - +
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Residues in contact with ILE 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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186B HIS* 3.0 28.5 + - + +
187B LEU* 4.3 1.8 - - - +
189B ARG* 1.3 93.5 - - + +
191B GLY* 1.3 58.3 + - - +
192B ARG* 3.6 25.3 + - - +
193B PHE* 4.2 17.0 - - + -
197B HIS* 5.5 5.2 - - + -
369B PHE* 5.7 9.0 - - + -
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Residues in contact with GLY 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* 2.8 22.0 + - - +
188B ARG* 3.7 6.5 + - - -
189B ARG 3.4 2.4 - - - -
190B ILE* 1.3 76.7 - - - +
192B ARG* 1.3 73.5 + - - -
289B GLY* 3.0 25.4 - - - +
7J TYR* 4.9 11.5 - - - -
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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