Contacts of the helix formed by residues 228 - 232 (chain B) in PDB entry 3QI2
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 228 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B ASP* 3.9 5.8 + - - -
227B LEU* 1.3 77.6 - - - +
229B ASP* 1.3 62.8 + - - +
230B TYR* 3.1 10.9 + - - -
231B ASP* 3.0 22.3 - - - +
270B LYS* 3.3 30.3 + - - +
273B LEU* 3.9 25.5 - - - +
274B PHE* 4.3 5.6 - - - +
277B LYS* 3.0 27.3 + - - +
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Residues in contact with ASP 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ALA* 5.8 0.7 - - - +
42B ARG 4.7 4.2 - - - +
43B GLU* 4.8 3.4 - - - +
150B ASP* 5.5 0.3 - - - +
226B ALA* 3.1 30.6 + - - +
227B LEU 2.9 2.2 + - - -
228B SER* 1.3 81.6 + - - +
230B TYR* 1.3 62.0 - - - +
231B ASP 3.2 2.8 + - - -
232B LEU* 3.5 40.8 + - + +
241B ASN* 6.1 0.5 - - - +
242B ARG* 3.8 35.5 + - + +
243B MET* 4.1 11.4 + - + +
270B LYS* 4.8 5.0 + - - -
277B LYS* 5.5 0.5 + - - -
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Residues in contact with TYR 230 (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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227B LEU 3.1 25.1 + - - +
228B SER* 3.1 6.1 - - - -
229B ASP* 1.3 79.1 - - - +
231B ASP* 1.3 76.7 + - + +
232B LEU 4.7 1.4 - - - +
241B ASN* 5.1 1.6 + - - +
243B MET* 3.7 15.2 - - + +
274B PHE* 3.5 23.6 - + + -
277B LYS* 3.1 24.5 + - + +
278B ILE* 3.1 26.6 + - + -
281B SER* 2.6 33.3 + - - -
282B PRO 3.6 13.9 - - - -
283B LEU* 3.8 26.5 - - + -
285B ILE* 3.6 8.5 - - + +
286B CYS* 3.1 36.7 - - + +
303B ILE* 4.9 0.9 - - + -
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Residues in contact with ASP 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ARG* 3.1 41.6 + - - +
228B SER 3.0 14.1 - - - +
230B TYR* 1.3 96.9 - - + +
232B LEU* 1.3 73.7 + - - +
277B LYS* 3.2 37.3 + - - +
281B SER* 3.8 21.3 + - - +
285B ILE* 3.8 13.5 - - + +
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Residues in contact with LEU 232 (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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143B SER 4.8 4.5 - - - +
144B ARG* 3.7 17.3 - - - +
146B TYR 5.0 4.9 - - - +
147B GLN* 6.4 0.4 - - - -
228B SER 4.7 1.1 - - - +
229B ASP* 3.5 46.8 - - + +
230B TYR 3.4 4.2 - - - +
231B ASP* 1.3 89.8 + - - +
233B VAL* 1.3 67.9 + - - +
234B LEU 3.6 1.9 + - - -
241B ASN* 5.2 9.0 - - - +
242B ARG* 3.6 39.8 + - + +
277B LYS* 4.8 5.6 - - - +
285B ILE* 4.7 5.2 - - - +
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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