Contacts of the strand formed by residues 228 - 233 (chain A) in PDB entry 4LXZ
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 228 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A GLU* 4.2 7.2 - - + +
193A TYR* 3.9 21.3 - - + -
200A THR* 3.5 16.2 - - - +
218A ASP 3.8 5.0 - - - +
219A ILE* 3.3 42.8 + - - +
220A GLY* 3.7 6.5 - - - +
226A TYR 3.5 1.8 - - - -
227A TYR* 1.3 79.6 + - - +
229A VAL* 1.3 64.0 + - - +
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Residues in contact with VAL 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLU* 4.9 0.9 + - - +
199A MET* 4.5 10.1 - - + -
200A THR 2.8 16.3 + - - +
201A VAL* 4.0 28.5 - - + -
202A SER 3.0 24.4 + - - -
219A ILE* 6.0 0.7 - - - -
226A TYR 4.7 2.7 - - - +
228A ALA* 1.3 80.8 - - - +
230A ASN* 1.4 67.7 + - - +
231A PHE* 5.9 0.4 - - + -
249A ILE* 4.9 6.5 - - + -
253A VAL* 5.1 1.6 - - + -
371A LEU* 3.9 33.7 - - + -
374A ASN* 6.2 4.3 - - + -
375A LEU* 4.3 25.4 - - + -
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Residues in contact with ASN 230 (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 HIS* 2.9 28.6 + - - -
189A GLU* 2.8 24.0 + - - +
202A SER* 3.5 4.6 - - - -
204A HIS* 3.3 3.4 - - + -
214A GLY* 3.4 19.7 - - - +
215A ASP 3.4 21.0 + - - +
216A LEU* 3.5 6.6 + - - +
218A ASP* 3.0 29.1 + - - +
219A ILE* 6.3 0.2 - - - +
228A ALA 4.5 0.2 + - - -
229A VAL* 1.4 81.0 - - - +
231A PHE* 1.3 59.5 + - - +
232A PRO* 3.3 9.0 - - - +
371A LEU* 3.4 22.3 - - - +
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Residues in contact with PHE 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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201A VAL* 6.5 0.2 - - + -
202A SER 2.8 11.0 + - - +
203A PHE* 3.6 26.8 - + + -
204A HIS* 3.2 24.7 + - - +
229A VAL* 5.2 0.9 - - + +
230A ASN* 1.3 72.3 - - - +
232A PRO* 1.4 71.6 - - - +
233A MET* 3.6 13.6 + - + +
245A ILE* 3.8 30.7 - - + -
249A ILE* 4.5 3.1 - - + -
363A TYR* 4.6 0.7 - + - -
364A MET* 3.6 48.9 - - + -
367A ILE* 3.6 25.4 - - + -
368A LYS* 4.0 12.3 - - + -
371A LEU* 3.6 21.8 - - + -
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Residues in contact with PRO 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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204A HIS* 3.6 8.9 - - - +
206A TYR* 3.4 26.7 - - + -
214A GLY 4.1 6.1 - - - +
216A LEU* 3.6 22.4 - - + +
230A ASN 3.3 12.3 - - - +
231A PHE* 1.4 89.3 - - - +
233A MET* 1.3 53.6 + - - +
363A TYR* 2.7 29.0 + - - +
367A ILE* 4.1 9.5 - - + +
335B TYR* 3.3 35.7 - - + +
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Residues in contact with MET 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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203A PHE* 3.9 14.4 - - + -
204A HIS 2.8 21.1 + - - +
205A LYS* 3.4 4.4 - - - +
206A TYR 2.9 28.5 + - - +
231A PHE* 3.8 28.3 - - + +
232A PRO* 1.3 78.4 - - - +
234A ARG* 1.3 66.0 + - - +
237A ILE* 3.7 26.0 - - + -
242A TYR* 3.8 20.6 - - + -
245A ILE* 3.9 17.0 - - + -
279A PHE* 3.7 32.3 - - + -
359A ASN* 3.6 10.5 - - - +
363A TYR* 4.1 1.1 - - - -
364A MET* 4.7 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