Contacts of the strand formed by residues 227 - 233 (chain A) in PDB entry 3SOQ
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 PRO 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A ASN* 3.1 22.7 + - - +
199A ALA* 3.9 23.3 - - + -
200A ASP 3.9 11.2 - - - +
201A ALA* 3.4 21.3 - - - +
224A LEU* 3.6 28.7 - - + +
225A PRO 3.8 0.2 - - - -
226A HIS* 1.3 90.0 - - - +
228A PHE* 1.3 60.2 + - - +
239A TRP* 4.0 20.2 - - + +
240A THR 3.4 8.7 - - - +
241A ASP* 3.3 6.5 - - - +
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Residues in contact with PHE 228 (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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54A ALA 4.6 2.2 - - - -
98A ASP 4.7 7.0 - - - -
141A ARG* 3.7 37.7 - - + -
185A ASN* 2.9 38.8 - - - +
186A GLY* 3.1 2.3 + - - -
199A ALA* 5.8 0.2 - - - -
226A HIS 3.5 0.2 + - - -
227A PRO* 1.3 74.7 - - - +
229A ALA* 1.3 61.2 + - + +
240A THR* 2.8 15.7 + - - +
242A TRP* 3.3 50.7 - + + +
269A MET* 3.4 45.8 - - + -
270A ASP* 3.6 11.2 - - + -
42Z ILE* 4.0 19.5 - - + -
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Residues in contact with ALA 229 (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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185A ASN 4.8 0.7 - - - +
186A GLY* 4.0 4.7 - - - -
227A PRO* 6.4 0.2 - - - -
228A PHE* 1.3 84.3 - - + +
230A LEU* 1.3 61.6 + - - +
239A TRP* 3.1 8.1 - - - +
240A THR* 3.0 27.0 + - - +
269A MET 3.6 6.3 - - - +
270A ASP* 3.3 43.3 - - - +
271A ILE* 3.6 8.1 - - + +
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Residues in contact with LEU 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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186A GLY* 4.0 7.2 - - - -
187A LEU 3.7 16.8 - - - +
188A THR* 3.5 21.1 + - + -
197A TYR* 3.7 42.6 - - + +
198A TRP* 3.8 17.5 - - - +
199A ALA* 4.1 4.9 - - + +
206A ILE* 4.2 13.9 - - + -
229A ALA* 1.3 77.4 - - - +
231A THR* 1.3 69.9 + - - +
237A LEU* 4.3 9.4 - - + -
238A TYR 3.4 17.3 - - - +
239A TRP* 3.8 22.9 - - + -
270A ASP* 5.6 0.3 - - - +
271A ILE* 4.1 6.3 - - - +
272A HIS* 5.9 1.0 + - - -
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Residues in contact with THR 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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23A LEU* 4.2 5.6 - - + -
188A THR* 3.9 8.3 - - - -
230A LEU* 1.3 80.6 - - - +
232A LEU* 1.3 71.3 + - - +
237A LEU* 3.6 4.7 - - - +
238A TYR* 2.7 50.8 + - + +
271A ILE* 3.6 24.0 - - + +
272A HIS* 3.6 12.2 + - - -
273A ALA* 3.0 32.3 + - - +
278A ARG* 4.1 9.0 + - - -
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Residues in contact with LEU 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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188A THR* 4.0 11.7 + - + -
189A LEU 4.3 1.3 - - - +
190A ASP* 3.7 41.3 - - + +
197A TYR* 3.8 14.6 - - + -
231A THR* 1.3 85.5 + - - +
233A PHE* 1.3 70.6 + - - +
234A GLU 3.8 18.8 - - - +
236A ILE 3.5 11.2 - - - +
237A LEU* 3.7 20.2 - - + -
238A TYR* 4.6 2.2 - - - -
252A LYS* 4.2 5.8 - - + -
273A ALA* 3.5 5.7 - - - +
278A ARG* 3.0 47.4 + - - +
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Residues in contact with PHE 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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20A ALA* 4.9 1.6 - - - -
21A PRO* 3.3 50.3 - - + -
232A LEU* 1.3 77.5 - - - +
234A GLU* 1.3 105.4 + - + +
235A ASP 3.1 0.2 + - - -
236A ILE* 3.0 26.2 + - - +
238A TYR* 4.2 4.2 + - + -
273A ALA* 3.9 4.7 - - + -
275A SER* 3.6 26.5 - - - -
277A GLN* 3.8 31.4 - - + -
278A ARG* 3.7 24.9 - - + +
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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