Contacts of the strand formed by residues 249 - 255 (chain D) in PDB entry 2O1S
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 ASN 249 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244D GLU* 4.1 6.0 - - - +
247D GLY 4.1 0.4 + - - -
248D PHE* 1.3 70.9 - - - +
250D TYR* 1.3 61.1 + - - +
251D ILE* 4.1 20.1 - - - +
269D MSE 4.5 0.5 - - - +
272D LEU* 4.3 9.7 - - - +
275D PRO 3.0 7.0 + - - +
276D GLN* 2.8 38.0 + - - +
277D PHE 2.9 26.5 + - - +
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Residues in contact with TYR 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D THR* 3.7 29.7 + - + -
243D PHE* 4.2 10.9 - + + -
244D GLU* 3.2 34.6 + - + +
248D PHE 3.5 1.0 + - - +
249D ASN* 1.3 75.8 + - - +
251D ILE* 1.3 74.7 + - - +
252D GLY 3.5 21.3 - - - -
253D PRO* 3.9 9.5 - - + +
277D PHE* 3.5 30.3 - + + -
279D HIS* 2.6 48.3 + - + +
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Residues in contact with ILE 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D ASN* 4.1 15.3 - - - +
250D TYR* 1.3 88.4 - - - +
252D GLY* 1.3 63.5 + - - +
254D VAL* 4.7 5.6 - - + -
265D THR* 4.6 7.6 - - + -
269D MSE 3.4 37.9 - - + -
272D LEU* 6.0 1.3 - - + -
277D PHE 3.0 6.1 + - - -
278D LEU* 3.5 15.3 - - + +
279D HIS* 2.9 28.2 + - - +
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Residues in contact with GLY 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D TYR* 3.5 17.7 - - - -
251D ILE* 1.3 80.0 - - - +
253D PRO* 1.3 79.6 - - - +
254D VAL* 3.8 8.3 - - - -
279D HIS* 4.3 0.4 - - - -
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Residues in contact with PRO 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D TYR* 3.9 10.1 - - + +
252D GLY* 1.3 86.3 - - - +
254D VAL* 1.3 60.7 + - - +
279D HIS* 3.1 22.2 - - + +
281D MSE 3.6 34.8 - - + -
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Residues in contact with VAL 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D ILE* 4.7 6.3 - - + -
252D GLY* 4.0 13.0 - - - +
253D PRO* 1.3 80.0 - - - +
255D ASP* 1.3 75.4 + - + +
256D GLY 2.9 2.6 + - - -
261D GLY 5.5 5.2 - - - +
262D LEU* 4.1 7.9 - - + -
265D THR* 5.1 13.9 - - - +
278D LEU* 4.2 11.7 - - + -
279D HIS 2.7 9.1 + - - +
280D ILE* 3.6 21.1 - - + -
281D MSE 2.9 30.2 + - - +
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Residues in contact with ASP 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254D VAL* 1.3 84.1 - - + +
256D GLY* 1.3 59.3 + - - +
257D HIS* 3.1 28.6 + - - +
258D ASP* 3.1 34.0 + - + +
262D LEU* 3.7 7.6 + - - +
281D MSE 4.4 5.6 - - - +
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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