Contacts of the helix formed by residues 229 - 236 (chain A) in PDB entry 3B3S
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 229 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A HIS* 3.4 7.1 - - - +
148A TYR* 3.2 26.3 - - + +
151A GLU* 3.3 30.1 - - - +
155A LEU* 4.2 6.0 - - - -
158A SER* 2.6 33.7 + - - +
177A GLN* 3.0 31.0 + - - +
228A SER* 1.3 74.3 + - - +
230A HIS* 1.3 64.3 + - - +
231A ALA 3.0 2.2 - - - -
232A SER* 3.0 20.2 + - - -
233A TRP* 3.5 11.2 - - - -
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Residues in contact with HIS 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ALA 5.3 1.1 - - - +
177A GLN* 3.9 21.4 - - + +
193A ILE* 4.4 4.4 - - - +
195A ASP* 4.0 7.9 + - - -
196A TYR* 3.4 28.0 - - + +
197A THR* 3.6 13.9 - - + -
225A TYR 5.3 0.6 + - - -
227A CYS* 3.7 16.1 + - - -
228A SER* 3.5 31.3 + - - -
229A ASP* 1.3 77.5 - - - +
231A ALA* 1.3 63.8 + - - +
233A TRP* 3.1 7.5 + - - -
234A HIS* 2.9 27.7 + - - +
240A ALA* 3.5 22.2 - - + +
241A ALA 4.2 7.4 - - - +
242A MET* 3.6 33.5 - - + -
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Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A LEU* 3.9 5.2 - - + -
196A TYR* 3.6 28.5 - - + -
226A ALA* 3.7 23.3 - - + -
228A SER 3.0 14.1 + - - +
229A ASP 3.0 1.0 - - - -
230A HIS* 1.3 83.0 - - + +
232A SER* 1.3 56.0 + - - +
234A HIS* 4.0 7.6 - - - -
235A ASN* 2.8 40.0 + - - +
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Residues in contact with SER 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A LEU* 3.7 15.5 - - - +
158A SER* 2.7 47.9 + - - -
159A GLN* 3.3 15.1 + - - +
162A ALA* 3.6 5.6 - - - +
163A ASN* 5.1 1.2 - - - +
229A ASP 3.0 6.4 + - - -
231A ALA* 1.3 76.9 - - - +
233A TRP* 1.3 66.3 + - - +
235A ASN* 3.4 7.0 + - - +
236A ALA* 3.1 23.2 + - - +
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Residues in contact with TRP 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A VAL* 4.1 10.4 - - + +
146A MET* 3.5 30.1 - - + -
148A TYR* 2.8 28.5 + + - -
158A SER* 5.0 2.4 - - - -
161A LEU 4.2 1.3 - - - -
162A ALA* 3.7 34.3 - - + +
165A TYR* 3.9 27.6 - + + -
172A VAL* 3.9 26.2 - - + -
175A ALA* 3.6 25.1 - - + -
176A LEU 6.6 0.2 - - - -
177A GLN* 5.8 1.1 - - + -
229A ASP 3.5 17.5 - - - -
230A HIS* 3.1 8.8 + - - +
232A SER* 1.3 76.3 - - - +
234A HIS* 1.3 66.6 + - - +
236A ALA* 3.1 8.4 + - - +
237A GLY 3.2 0.5 + - - -
238A TYR* 3.0 52.7 + + + +
240A ALA* 4.2 5.8 - - + -
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Residues in contact with HIS 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A TYR* 3.3 51.9 - + - +
197A THR* 3.7 16.5 + - - -
198A ASP* 5.6 1.0 - - - +
230A HIS 2.9 10.6 + - - +
231A ALA* 3.6 5.4 - - - +
233A TRP* 1.3 77.5 - - - +
235A ASN* 1.3 70.9 + - - +
237A GLY* 2.9 21.1 + - - -
238A TYR 3.6 13.8 + - - +
240A ALA* 4.2 3.6 + - + +
299A NA 2.0 32.1 - - - -
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Residues in contact with ASN 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A LEU* 6.1 1.4 - - - +
159A GLN* 5.9 3.8 - - - +
166A LYS* 4.9 2.4 + - - -
196A TYR* 3.7 17.6 - - - -
231A ALA* 2.8 28.1 + - - +
232A SER* 3.9 5.9 - - - +
233A TRP 3.2 0.2 - - - -
234A HIS* 1.3 92.1 - - - +
236A ALA* 1.3 60.6 + - - +
237A GLY* 3.1 1.7 + - - -
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Residues in contact with ALA 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ALA* 4.0 16.8 - - + +
163A ASN* 4.1 14.1 - - - +
166A LYS* 3.2 36.0 + - + +
232A SER 3.1 17.8 + - - +
233A TRP 3.1 5.3 + - - +
235A ASN* 1.3 75.5 - - - +
237A GLY* 1.3 59.4 + - - +
238A TYR* 3.6 23.7 + - + -
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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