Contacts of the strand formed by residues 258 - 262 (chain C) in PDB entry 3O4O
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 MET 258 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A ARG* 3.2 35.4 - - + +
46A PHE* 3.2 42.0 - - + -
48A GLN* 5.0 16.6 - - - +
56A ILE* 6.2 3.4 - - + -
256C THR 3.8 4.5 - - - +
257C THR* 1.3 80.3 - - - +
259C LEU* 1.3 75.0 + - - +
260C TRP* 3.6 5.4 + - + +
282C ARG* 4.9 17.7 - - - +
294C GLU* 5.7 0.7 - - - +
314C VAL 3.6 0.2 - - - +
315C VAL* 3.3 6.1 - - - +
316C HIS* 2.9 48.8 + - + +
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Residues in contact with LEU 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C CYS 4.0 6.5 - - - +
247C VAL* 3.5 39.7 - - + -
257C THR* 5.0 2.6 - - + +
258C MET* 1.3 80.3 - - - +
260C TRP* 1.3 62.3 + - - +
261C TRP* 3.8 3.6 + - + -
279C GLU* 5.4 2.8 - - - +
282C ARG* 4.5 20.7 + - - +
294C GLU* 4.8 19.7 + - + +
295C VAL 5.1 0.4 - - - -
296C PRO* 3.4 38.8 - - + +
313C CYS* 3.4 30.7 - - - -
314C VAL 3.6 4.3 - - - +
315C VAL* 4.3 9.0 - - + -
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Residues in contact with TRP 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLN* 3.0 47.6 - - - +
51A GLU* 3.3 39.0 - - + -
93A LYS* 6.2 2.2 - - + -
94A LYS* 4.4 3.9 - - - +
258C MET* 3.6 6.8 + - + +
259C LEU* 1.3 75.1 - - - +
261C TRP* 1.3 70.9 + - - +
262C THR* 3.6 31.0 - - + -
264C ASN 5.8 1.6 - - - -
267C HIS* 3.1 53.5 + + - -
279C GLU* 4.9 7.2 - - - -
314C VAL* 2.7 71.5 + - + +
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Residues in contact with TRP 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C ILE* 3.4 44.9 - - + -
244C PRO 3.8 8.5 - - - -
245C CYS* 3.5 29.4 - - + -
259C LEU* 3.8 3.9 + - + +
260C TRP* 1.3 79.8 + - - +
262C THR* 1.3 78.8 + - - +
267C HIS 3.6 4.0 - - - +
268C ILE* 3.1 31.8 - - + +
279C GLU* 4.5 15.0 + - + +
296C PRO* 3.5 27.4 - - + -
298C ILE* 3.6 24.9 - - + +
311C PHE* 4.5 14.3 - + + +
312C LYS 3.4 22.8 + - - +
313C CYS* 4.3 13.7 - - + -
314C VAL 4.5 0.7 - - - +
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Residues in contact with THR 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C TRP* 3.6 37.9 - - + -
261C TRP* 1.3 79.6 - - - +
263C ALA* 1.3 66.8 + - - +
264C ASN* 3.5 22.4 + - - +
265C ASP 4.0 1.0 - - - -
267C HIS* 2.8 31.0 + - - -
268C ILE* 4.3 1.1 - - - -
312C LYS* 2.4 37.6 + - + +
314C VAL* 4.1 13.0 - - + -
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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