Contacts of the helix formed by residues 187 - 200 (chain B) in PDB entry 4ACR
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 ASP 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185B PRO* 3.7 18.8 - - + +
186B ASP* 1.3 81.0 - - - +
188B TYR* 1.3 66.8 + - - +
189B LEU 3.0 0.9 - - - -
190B ASP* 3.1 21.5 + - - +
191B CYS* 3.7 4.7 + - - +
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Residues in contact with TYR 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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175B PHE* 5.3 2.2 - + - -
184B LEU* 3.5 31.6 - - + -
185B PRO* 3.8 21.6 - - + +
187B ASP* 1.3 82.6 + - - +
189B LEU* 1.3 57.5 + - - +
191B CYS* 3.3 2.2 + - - -
192B LEU* 2.9 28.6 + - + -
339B VAL* 2.9 43.7 + - + +
340B ILE* 3.3 5.5 - - - +
343B CYS* 3.1 44.1 - - + -
344B GLY 4.4 0.9 - - - -
345B ASN 4.3 0.2 - - - -
346B PRO* 3.2 42.2 - - + +
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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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172B GLU* 3.8 45.6 - - + +
176B LYS* 5.0 11.2 - - + -
184B LEU* 3.6 42.8 - - + +
186B ASP* 3.6 40.4 - - + +
187B ASP 3.0 1.2 - - - +
188B TYR* 1.3 79.9 - - - +
190B ASP* 1.3 56.6 + - - +
192B LEU* 3.2 21.8 - - + +
193B GLY* 2.9 23.6 + - - -
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Residues in contact with ASP 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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172B GLU* 5.5 1.4 - - - +
186B ASP* 3.5 29.2 - - - +
187B ASP* 3.1 10.9 + - - +
189B LEU* 1.3 72.4 - - - +
191B CYS* 1.3 61.3 + - - +
193B GLY* 3.2 4.0 + - - -
194B LYS* 2.9 45.7 + - - +
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Residues in contact with CYS 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 ASP 3.7 4.5 + - - +
188B TYR* 3.3 2.8 + - - +
190B ASP* 1.3 74.9 - - - +
192B LEU* 1.3 58.7 + - - +
194B LYS* 3.3 12.3 + - + +
195B GLN* 2.9 35.6 + - - +
342B GLY 4.1 6.1 - - - -
343B CYS* 2.0 59.7 - - - -
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Residues in contact with LEU 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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171B LEU* 4.4 20.9 - - + +
172B GLU* 4.9 3.4 - - + -
175B PHE* 3.9 42.2 - - + -
184B LEU* 4.8 1.1 - - + -
188B TYR* 2.9 19.7 + - + +
189B LEU* 3.2 33.4 - - + +
191B CYS* 1.3 77.8 - - - +
193B GLY* 1.3 57.3 - - - +
195B GLN* 3.4 4.6 + - - +
196B ALA* 2.9 29.7 + - + +
335B LEU* 5.8 1.3 - - + -
339B VAL* 3.7 38.9 - - + +
343B CYS* 3.7 2.4 - - - -
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Residues in contact with GLY 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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171B LEU* 5.4 2.7 - - - -
189B LEU 2.9 14.0 + - - -
190B ASP* 3.6 4.0 - - - -
192B LEU* 1.3 78.0 - - - +
194B LYS* 1.3 61.9 + - - +
196B ALA* 3.6 16.5 + - - +
197B GLU* 3.7 10.2 + - - +
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Residues in contact with LYS 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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190B ASP* 2.9 32.5 + - - +
191B CYS* 3.7 10.1 - - - +
192B LEU 3.3 0.2 - - - -
193B GLY* 1.3 78.0 - - - +
195B GLN* 1.3 65.0 + - + +
197B GLU* 4.1 9.3 + - - +
198B ALA* 4.4 7.3 + - - +
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Residues in contact with GLN 195 (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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191B CYS* 2.9 32.4 + - - +
192B LEU* 3.8 5.8 - - - +
194B LYS* 1.3 75.8 - - + +
196B ALA* 1.3 66.2 + - - +
198B ALA* 3.4 7.1 + - - +
199B LEU* 2.9 31.8 + - + +
338B LYS* 4.2 16.9 - - - +
339B VAL* 4.7 15.7 - - + -
342B GLY* 3.8 28.7 + - - -
343B CYS* 4.9 1.6 - - + +
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Residues in contact with ALA 196 (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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171B LEU* 3.5 28.7 - - + -
192B LEU* 2.9 19.4 + - + +
193B GLY* 3.6 10.1 - - - +
194B LYS 3.3 0.4 - - - -
195B GLN* 1.3 76.0 - - - +
197B GLU* 1.3 57.0 + - - +
199B LEU* 2.9 4.5 + - - -
200B ARG 2.7 32.4 + - - -
201B PRO* 3.1 17.5 - - + +
335B LEU* 6.0 0.2 - - - -
339B VAL* 6.0 1.3 - - - +
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Residues in contact with GLU 197 (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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193B GLY 3.7 10.6 + - - +
194B LYS* 4.5 6.5 - - - +
195B GLN 3.4 0.6 - - - -
196B ALA* 1.3 78.9 - - - +
198B ALA* 1.3 61.4 + - - +
200B ARG* 4.0 13.2 + - - +
201B PRO* 5.4 0.4 - - - -
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Residues in contact with ALA 198 (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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194B LYS 4.4 5.3 + - - +
195B GLN* 3.4 7.2 + - - +
196B ALA 3.2 0.6 - - - -
197B GLU* 1.3 79.5 - - - +
199B LEU* 1.3 62.3 + - - +
200B ARG* 3.4 8.2 + - - +
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Residues in contact with LEU 199 (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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195B GLN* 2.9 26.5 + - - +
196B ALA* 2.9 6.1 + - - +
198B ALA* 1.3 77.8 - - - +
200B ARG* 1.3 71.7 + - - +
335B LEU* 3.6 37.4 - - + +
338B LYS* 3.6 56.3 - - + +
339B VAL* 4.5 9.0 - - + -
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Residues in contact with ARG 200 (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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196B ALA 2.7 13.8 + - - -
197B GLU* 4.1 13.0 - - - +
198B ALA 4.1 6.7 - - - +
199B LEU* 1.3 77.7 - - - +
201B PRO* 1.3 69.7 - - - +
202B PHE 3.4 1.8 - - - -
203B GLY* 3.5 23.5 + - - +
204B GLU* 3.8 39.0 - - - +
331B ASN* 4.3 7.4 + - - -
335B LEU* 5.1 0.2 - - - +
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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