Contacts of the helix formed by residues 231 - 235 (chain A) in PDB entry 3BMW
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 ALA 231 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ASN* 4.4 9.4 - - + -
141A HIS* 4.8 0.2 - - + -
195A LEU* 4.2 11.2 - - + -
230A ASP* 1.3 85.0 - - - +
232A VAL* 1.3 59.9 + - - +
233A LYS* 3.2 3.6 - - - -
234A HIS* 2.9 38.0 + - + +
235A MET* 3.7 7.3 - - - +
258A GLU* 3.1 24.4 + - - -
694A ACI 4.5 0.2 - - + -
3C G6D 3.5 16.2 - - - +
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LEU* 3.4 36.1 - - + +
230A ASP 4.1 0.7 - - - +
231A ALA* 1.3 72.2 - - - +
233A LYS* 1.3 60.9 + - - +
234A HIS 3.1 6.3 + - - -
235A MET* 3.5 5.4 - - + +
240A GLN* 2.9 47.7 + - - +
257A GLY* 3.7 10.1 - - - -
258A GLU 3.0 28.7 + - - +
259A TRP* 3.9 16.9 - - + +
273A PHE* 3.7 25.7 - - + -
279A MET* 4.1 3.4 - - - -
281A LEU* 4.0 3.4 - - + -
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Residues in contact with LYS 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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184A PHE* 4.9 4.3 - - - +
187A TYR* 3.8 10.8 - - + +
190A GLY* 4.3 2.9 - - - +
191A ILE* 3.6 15.6 - - - +
231A ALA 5.0 0.9 - - - -
232A VAL* 1.3 80.3 - - - +
234A HIS* 1.3 81.3 + - + +
235A MET 3.5 2.0 - - - -
258A GLU 4.2 1.3 + - - +
259A TRP* 3.5 44.1 - - + +
260A PHE 3.4 31.0 + - - +
265A GLU* 4.5 9.5 + - - -
267A ASP* 5.2 3.5 + - - -
2C GLC 2.8 42.7 + - - +
3C G6D 3.6 6.5 - - - +
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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
----------------------------------------------------------
140A ASN* 3.5 17.5 - - - +
182A THR* 4.6 3.2 - - + +
184A PHE* 3.5 29.8 - + - -
190A GLY* 2.8 30.9 + - - +
191A ILE* 3.1 11.3 - - - +
195A LEU* 3.8 17.6 - - + +
231A ALA* 2.9 28.4 + - + +
233A LYS* 1.3 102.1 - - + +
235A MET* 1.3 56.4 + - - +
698A CA 2.3 31.9 - - - -
3C G6D 2.6 33.3 + - - -
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Residues in contact with MET 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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139A PRO* 3.7 22.9 - - + -
140A ASN* 3.4 40.2 - - + +
187A TYR* 4.6 2.8 + - - -
191A ILE* 3.8 13.0 - - - +
203A GLN* 3.7 18.6 - - - +
229A LEU* 4.4 4.0 - - + -
230A ASP 3.3 25.8 - - - +
231A ALA 3.7 9.4 - - - +
232A VAL* 3.5 6.8 + - - +
233A LYS 4.4 0.3 - - - -
234A HIS* 1.3 76.3 - - - +
236A PRO* 1.3 75.4 - - + +
237A PHE 3.4 1.6 + - - -
239A TRP* 4.0 11.7 - - + -
240A GLN* 3.1 39.4 + - + +
698A CA 4.5 0.4 - - - -
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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