Contacts of the helix formed by residues 167 - 175 (chain B) in PDB entry 4AOR
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 SER 167 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135B ALA* 3.9 19.6 - - - +
166B LEU* 1.3 76.7 - - - +
168B ASP* 1.3 63.8 + - - +
169B SER* 3.2 12.7 + - - -
170B SER* 3.0 24.9 + - - -
171B CYS* 3.0 18.9 + - - +
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Residues in contact with ASP 168 (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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135B ALA* 5.4 0.4 - - - +
166B LEU 3.5 3.7 + - - +
167B SER* 1.3 71.9 - - - +
169B SER* 1.3 58.2 + - - +
171B CYS* 3.6 7.2 - - - +
172B LYS* 2.9 48.4 + - - +
179B ILE* 6.5 0.4 - - - -
183B MET 4.8 9.2 - - - +
184B PHE* 4.9 9.4 - - - +
231B LYS* 5.2 10.7 + - - -
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Residues in contact with SER 169 (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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167B SER* 3.1 12.2 + - - -
168B ASP* 1.3 80.0 - - - +
170B SER* 1.3 58.0 + - - +
172B LYS* 3.9 5.5 - - - +
173B SER* 3.0 32.2 + - - -
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Residues in contact with SER 170 (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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166B LEU* 4.6 4.5 - - - +
167B SER* 3.0 22.4 + - - -
169B SER* 1.3 78.9 + - - +
171B CYS* 1.3 66.4 + - - +
173B SER* 3.3 7.7 + - - -
174B ALA* 3.0 23.4 + - - +
189B LEU* 3.4 22.6 - - - +
226B PRO* 6.3 0.2 - - - -
1253B CA 3.1 24.9 - - - -
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Residues in contact with CYS 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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166B LEU* 5.2 0.4 - - - +
167B SER 3.0 12.7 + - - +
168B ASP* 3.6 13.7 - - - +
170B SER* 1.3 77.9 - - - +
172B LYS* 1.3 62.1 + - - +
174B ALA* 3.0 14.3 + - - +
175B TYR* 3.1 11.6 + - - -
179B ILE* 3.7 32.3 - - + +
184B PHE* 4.0 4.3 - - - -
185B CYS* 2.0 65.4 - - + +
226B PRO* 5.5 0.4 - - - -
228B VAL* 5.0 0.2 - - - -
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Residues in contact with LYS 172 (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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168B ASP* 2.9 31.9 + - + +
169B SER* 4.0 6.1 - - - +
171B CYS* 1.3 76.2 - - - +
173B SER* 1.3 60.4 + - - +
175B TYR 4.5 0.7 - - - -
176B PRO* 3.3 28.2 - - + +
177B GLY 6.2 0.4 - - - +
179B ILE* 4.1 41.4 + - + +
180B THR 5.6 2.9 - - - -
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Residues in contact with SER 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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169B SER 3.0 18.2 + - - -
170B SER* 3.7 8.0 - - - -
171B CYS 3.3 0.2 - - - -
172B LYS* 1.3 77.4 - - - +
174B ALA* 1.3 62.4 + - - +
176B PRO* 3.8 13.0 - - - +
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Residues in contact with ALA 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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170B SER 3.0 13.9 + - - +
171B CYS 3.0 9.2 + - - +
173B SER* 1.3 78.2 - - - +
175B TYR* 1.3 61.5 + - + +
176B PRO* 3.5 3.4 - - - +
189B LEU* 5.0 4.0 - - + -
224B ASN* 3.5 22.4 - - + +
225B LYS* 2.7 32.6 + - - -
226B PRO* 3.7 23.1 - - + -
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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
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171B CYS 3.1 9.8 + - - +
172B LYS* 3.4 5.4 - - - +
174B ALA* 1.3 85.9 - - + +
176B PRO* 1.3 69.0 - - - +
177B GLY 3.3 0.5 + - - -
178B GLN* 3.1 24.7 + - + +
179B ILE* 3.9 20.7 - - + +
185B CYS* 4.2 4.5 - - - -
216B TRP* 3.6 13.5 - + - -
217B GLY* 3.5 1.3 - - - -
218B SER* 3.1 23.6 + - - -
225B LYS* 3.3 32.2 - - + +
226B PRO* 2.7 43.7 + - + -
228B VAL* 3.6 20.4 - - + -
1247B GOL 3.1 27.8 - - - -
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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