Contacts of the strand formed by residues 241 - 245 (chain A) in PDB entry 1O9S
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 VAL 241 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A PRO* 4.2 13.1 - - + +
211A TYR* 2.6 40.5 + - + +
215A ARG* 3.7 2.8 - - - -
239A ASN 3.9 1.4 + - - -
240A THR* 1.3 79.3 - - - +
242A MET* 1.3 60.7 + - - +
243A SER 4.3 1.8 - - - +
244A PHE* 3.9 28.9 - - + -
308A PHE* 4.2 13.5 - - + -
318A CYS* 4.0 24.2 - - + -
319A ILE 3.6 4.5 - - - -
320A ARG* 3.4 35.9 - - - +
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Residues in contact with MET 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A TYR* 4.7 4.0 - - - -
212A GLU* 3.8 17.7 - - - +
215A ARG* 3.6 38.5 - - + +
216A VAL* 3.6 12.6 - - + +
232A SER* 3.9 20.2 - - - -
234A VAL* 4.7 1.3 - - + +
236A VAL* 3.9 40.2 - - + -
240A THR* 3.5 15.5 - - - +
241A VAL* 1.3 81.6 - - - +
243A SER* 1.3 59.5 + - - +
303A CYS* 5.2 0.7 - - - -
319A ILE* 2.8 17.2 + - + +
321A THR* 3.6 13.5 - - + +
331A LEU* 3.9 27.4 - - + -
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Residues in contact with SER 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A GLU* 2.5 28.0 + - - +
216A VAL* 4.4 1.5 - - - +
230A LEU* 3.7 22.2 - - - +
241A VAL* 4.0 1.5 - - - +
242A MET* 1.3 81.2 - - - +
244A PHE* 1.3 66.0 + - - +
291A LEU* 3.4 5.4 - - - +
292A GLY* 3.1 16.5 + - - -
318A CYS* 3.2 8.5 - - - +
319A ILE* 2.8 38.5 + - - -
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Residues in contact with PHE 244 (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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148A TYR* 3.8 16.8 - + - -
209A ASP* 3.3 40.4 - - + -
211A TYR* 3.8 27.1 - + - -
212A GLU* 2.9 15.7 + - + -
241A VAL* 3.9 13.0 - - + -
243A SER* 1.3 78.4 - - - +
245A TYR* 1.3 57.6 + - - +
246A ASN 3.6 0.7 - - - -
290A SER* 3.3 21.3 - - - -
292A GLY* 2.8 26.1 + - - -
308A PHE* 3.4 35.9 - + - -
310A HIS* 3.8 15.0 - + - -
313A PHE* 4.4 3.8 - + + -
316A ILE* 3.9 13.5 - - + -
317A LYS 3.9 1.6 - - - -
318A CYS* 4.1 5.6 - - + -
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Residues in contact with TYR 245 (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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244A PHE* 1.3 71.3 - - - +
246A ASN* 1.3 63.9 + - - +
265A ASN* 2.7 33.2 + - - +
267A LEU* 3.6 27.3 - - + +
275A ILE* 3.8 24.6 - - + +
277A VAL* 4.4 5.4 - - + -
292A GLY* 3.6 21.3 - - - +
293A HIS* 3.6 27.3 - - + +
305A TYR* 3.7 28.3 - + + -
316A ILE* 3.6 16.6 - - - +
317A LYS* 2.8 27.3 + - + +
318A CYS* 4.3 3.8 - - - +
319A ILE* 4.8 0.4 - - + -
4K MLZ 2.9 28.0 + - - +
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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