Contacts of the strand formed by residues 241 - 245 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ASP 4.2 0.4 - - - +
149B PRO* 4.1 20.9 - - + +
211B TYR* 2.8 38.4 + - + +
215B ARG* 3.9 1.2 - - - -
239B ASN 3.8 1.0 + - - -
240B THR* 1.3 79.5 - - - +
242B MET* 1.3 61.4 + - - +
243B SER 4.4 2.0 - - - +
244B PHE* 3.9 28.3 - - + -
308B PHE* 4.1 10.3 - - + -
318B CYS* 4.1 21.1 - - + -
319B ILE 3.5 4.9 - - - +
320B ARG* 3.5 36.1 - - - +
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Residues in contact with MET 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B TYR* 4.5 8.5 - - - -
212B GLU* 3.8 11.3 - - - +
215B ARG* 3.6 41.3 - - + +
216B VAL* 3.5 12.1 - - + +
232B SER* 3.7 22.2 - - - -
234B VAL* 4.8 0.9 - - + +
236B VAL* 3.8 39.7 - - + -
240B THR* 3.4 17.3 - - - +
241B VAL* 1.3 79.9 - - - +
243B SER* 1.3 63.5 + - - +
303B CYS* 5.1 1.3 - - - -
319B ILE* 2.8 11.7 + - + +
321B THR* 3.6 13.9 - - + +
331B LEU* 4.0 26.2 - - + -
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Residues in contact with SER 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLU* 2.6 26.7 + - - -
216B VAL* 4.4 3.1 - - - -
230B LEU* 3.7 23.5 - - - +
241B VAL* 4.4 1.3 - - - +
242B MET* 1.3 82.6 - - - +
244B PHE* 1.3 63.3 + - - +
291B LEU* 3.3 4.7 - - - +
292B GLY* 3.0 18.7 + - - -
318B CYS* 3.2 8.1 - - - +
319B ILE* 2.7 40.5 + - - -
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Residues in contact with PHE 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TYR* 3.9 11.4 - + - -
209B ASP* 3.4 35.7 - - + -
211B TYR* 3.7 29.4 - + - -
212B GLU* 2.8 21.9 + - + +
241B VAL* 3.9 11.7 - - + -
243B SER* 1.3 79.3 + - - +
245B TYR* 1.3 61.1 + - - +
246B ASN 3.6 0.4 - - - -
290B SER* 3.3 21.0 - - - -
292B GLY* 2.8 21.5 + - - -
308B PHE* 3.3 36.8 - + - -
310B HIS* 3.8 21.1 - + - -
313B PHE* 4.4 3.4 - + + -
316B ILE* 3.8 14.1 - - + -
317B LYS 3.9 1.8 - - - -
318B CYS* 4.1 5.6 - - + -
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Residues in contact with TYR 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B PHE* 1.3 71.6 - - - +
246B ASN* 1.3 61.9 + - - +
265B ASN* 2.8 32.0 + - - -
267B LEU* 3.6 34.5 - - + +
275B ILE* 3.8 22.8 - - + +
277B VAL* 4.3 5.2 - - + -
290B SER* 4.7 0.2 - - - -
292B GLY* 3.6 19.7 - - - +
293B HIS* 3.6 30.8 - - + +
305B TYR* 3.7 23.3 - + + -
316B ILE* 3.7 12.4 - - - +
317B LYS* 2.8 30.8 + - + +
318B CYS* 4.2 3.8 - - - +
319B ILE* 4.9 0.2 - - + -
4L MLZ 3.2 25.9 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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