Contacts of the strand formed by residues 236 - 241 (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 ILE 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A LEU* 3.5 2.4 - - - +
233A PHE 3.0 31.9 + - - +
234A GLU* 3.4 1.9 - - + -
235A ASP* 1.3 91.4 - - + +
237A LEU* 1.3 73.2 + - - +
238A TYR* 3.3 41.3 - - + +
249A ALA* 3.9 9.6 - - + -
250A CYS 3.4 9.9 - - - +
251A ASN* 4.2 12.1 - - + +
252A LYS* 4.7 1.1 - - - -
259A ARG* 3.9 23.3 - - - +
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Residues in contact with LEU 237 (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* 4.6 0.7 - - + -
197A TYR* 3.6 45.5 - - + -
206A ILE* 4.0 13.7 - - + -
219A VAL* 3.8 22.2 - - + -
230A LEU* 4.3 8.7 - - + -
231A THR 3.6 10.5 - - - +
232A LEU* 3.7 26.5 - - + -
235A ASP 4.2 0.4 + - - -
236A ILE* 1.3 76.4 - - - +
238A TYR* 1.3 60.7 + - - +
239A TRP* 4.0 11.6 - - + -
249A ALA* 3.1 24.8 - - - -
250A CYS* 2.9 18.6 + - - +
252A LYS* 3.8 12.6 - - + -
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Residues in contact with TYR 238 (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* 4.1 9.0 - - - +
21A PRO* 3.4 31.5 - - + +
23A LEU* 3.8 28.7 - - + -
36A ALA* 4.0 16.1 - - + +
230A LEU* 3.4 1.7 - - - +
231A THR* 2.7 55.1 + - + +
232A LEU 4.7 0.4 - - - -
233A PHE* 4.2 13.5 + - + -
236A ILE* 3.3 47.7 - - + +
237A LEU* 1.3 71.2 - - - +
239A TRP* 1.3 64.7 + - - +
247A ILE* 4.6 2.9 - - + -
248A LEU 3.3 7.6 - - - +
249A ALA* 3.7 18.8 - - + -
259A ARG* 5.3 1.7 + - - -
261A ILE* 4.4 9.6 - - + -
271A ILE* 4.7 1.8 - - + -
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Residues in contact with TRP 239 (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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206A ILE* 3.6 25.1 - - + -
220A VAL* 4.3 2.9 - - + -
224A LEU* 3.6 28.0 - - + +
227A PRO* 4.0 18.3 - - + +
229A ALA 3.1 17.3 - - - +
230A LEU* 3.8 14.4 - - + -
237A LEU* 4.0 6.3 - - + -
238A TYR* 1.3 81.2 - - - +
240A THR* 1.3 74.3 + - - +
241A ASP* 4.7 2.9 + - + +
247A ILE* 3.3 6.2 - - - +
248A LEU* 2.8 59.5 + - + +
249A ALA 3.9 4.5 - - - -
250A CYS* 3.5 40.4 - - + -
258A LEU* 3.5 33.9 - - + -
271A ILE* 4.6 3.1 - - - -
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Residues in contact with THR 240 (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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25A TYR* 4.7 5.4 - - + -
227A PRO* 3.4 4.9 - - - +
228A PHE* 2.8 29.2 + - - +
229A ALA 3.0 18.4 + - - -
239A TRP* 1.3 79.6 - - - +
241A ASP* 1.3 61.6 + - - +
246A SER 3.6 3.6 - - - -
247A ILE* 4.0 16.2 - - + -
268A PRO* 3.8 26.7 - - + -
269A MET 2.7 29.5 + - - +
271A ILE* 4.0 18.8 - - + +
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Residues in contact with ASP 241 (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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224A LEU* 4.7 1.4 - - - +
225A PRO* 3.4 13.6 - - - +
226A HIS 2.8 33.8 + - - -
227A PRO* 3.3 5.6 - - + +
239A TRP* 4.7 2.9 + - + -
240A THR* 1.3 76.0 - - - +
242A TRP* 1.3 61.1 + - - +
243A SER* 2.7 31.4 + - - -
244A THR* 2.8 34.3 + - - +
245A HIS* 3.0 28.9 + - - -
246A SER 3.1 8.5 + - - -
248A LEU* 3.7 13.5 - - + +
268A PRO* 3.7 4.1 - - - +
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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