Contacts of the strand formed by residues 334 - 339 (chain C) in PDB entry 1L6O
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 334 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C THR* 3.6 0.9 - - - -
257C LEU* 2.9 38.2 + - + +
259C MSE 3.5 31.6 - - + -
265C LEU* 3.7 24.0 - - + -
307C VAL* 4.4 11.2 - - + -
308C ASN* 3.6 5.4 - - - +
327C ILE* 4.6 11.7 - - + +
328C VAL* 4.0 28.3 - - + +
330C LYS 4.9 2.0 - - - +
332C GLY 3.6 8.1 - - - +
333C PRO* 1.3 81.9 - - - +
335C VAL* 1.3 64.3 + - - +
336C LEU* 4.2 22.9 - - + -
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Residues in contact with VAL 335 (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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254C THR* 3.9 26.9 - - + -
255C VAL 3.5 4.9 - - - +
256C THR* 3.7 21.3 - - - +
306C GLN 4.0 0.2 - - - +
307C VAL* 3.4 9.9 - - - +
308C ASN* 2.7 46.5 + - - +
309C ASP 6.0 0.4 - - - +
333C PRO* 5.6 2.0 - - + -
334C ILE* 1.3 75.6 - - - +
336C LEU* 1.3 66.2 + - - +
337C THR* 4.9 4.7 - - - +
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Residues in contact with LEU 336 (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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253C ILE 3.9 0.5 - - - +
254C THR* 3.2 2.7 - - - -
255C VAL* 2.8 40.5 + - + +
257C LEU* 4.3 19.5 - - + -
265C LEU* 4.7 7.0 - - + -
267C ILE* 4.7 17.3 - - + -
283C ILE* 5.3 1.1 - - + -
292C VAL* 5.0 1.8 - - + -
298C ILE* 3.9 25.8 - - + -
304C LEU* 4.1 21.5 - - + -
306C GLN 3.8 1.1 - - - -
307C VAL* 4.1 26.5 - - + -
324C LEU* 4.6 8.5 - - + -
334C ILE* 4.2 9.9 - - + -
335C VAL* 1.3 83.6 - - - +
337C THR* 1.3 65.3 + - - +
338C VAL* 4.0 2.1 + - + +
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Residues in contact with THR 337 (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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252C ILE* 4.2 17.3 - - + -
253C ILE 3.4 9.6 - - - +
254C THR* 3.7 17.2 + - - +
304C LEU* 4.0 4.7 - - - +
305C LEU* 3.1 33.8 + - + -
306C GLN* 3.0 38.9 + - + +
335C VAL* 4.9 4.5 - - - +
336C LEU* 1.3 76.9 - - - +
338C VAL* 1.2 66.1 + - - +
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Residues in contact with VAL 338 (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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252C ILE* 3.6 2.9 - - - -
253C ILE* 2.8 44.6 + - + +
255C VAL* 5.7 1.3 - - + -
283C ILE* 5.4 2.5 - - + -
298C ILE* 4.7 24.2 - - + -
302C ASP* 3.6 22.0 - - + +
303C MSE 2.6 36.6 - - - +
304C LEU* 4.3 6.5 - - + -
305C LEU* 4.0 7.2 - - - +
336C LEU* 5.2 2.5 - - + +
337C THR* 1.2 81.2 - - - +
339C ALA* 1.3 67.0 + - - +
340C LYS* 3.9 4.9 + - - +
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Residues in contact with ALA 339 (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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251C MSE 3.8 5.2 - - - +
252C ILE* 4.3 7.9 - - + -
302C ASP* 3.3 3.6 - - - -
303C MSE 2.7 49.4 + - + +
305C LEU* 3.9 17.3 - - + +
338C VAL* 1.3 84.2 - - - +
340C LYS* 1.3 66.6 + - - +
341C LEU* 3.4 0.9 + - - -
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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
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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