Contacts of the strand formed by residues 350 - 354 (chain C) in PDB entry 1OYX
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 LYS 350 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348C GLY 4.4 3.2 + - - +
349C MSE 1.3 76.3 - - - +
351C LEU* 1.3 65.7 + - - +
365C ALA 3.3 7.9 - - - +
366C SER* 2.7 31.7 + - - +
380C ASP* 2.8 20.9 + - - +
400C VAL* 3.7 5.6 + - + +
424C TRP* 3.7 17.7 - - + -
427C TYR* 3.8 14.0 + - + -
428C LEU* 3.6 25.8 - - + -
431C THR* 3.8 25.8 + - - +
433C ALA* 3.9 12.8 - - + -
434C SER 2.9 7.6 + - - +
435C ALA* 3.5 3.5 - - - -
436C VAL* 2.9 23.9 + - - +
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Residues in contact with LEU 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C PHE* 4.7 5.6 - - + -
350C LYS* 1.3 80.9 - - - +
352C GLU* 1.3 68.3 + - - +
353C ALA* 4.8 1.3 - - + -
365C ALA* 2.9 43.3 + - + +
366C SER 3.9 22.9 - - - +
367C VAL* 3.9 15.7 - - + -
377C VAL* 4.5 10.3 - - + -
397C ILE* 3.7 40.6 - - + -
398C HIS 3.5 8.1 - - - +
400C VAL* 4.0 9.6 - - - +
424C TRP* 3.5 8.6 - - - -
436C VAL* 4.5 2.0 - - + -
441C PHE* 3.9 17.7 - - + -
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Residues in contact with GLU 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C LEU* 1.3 77.1 - - - +
353C ALA* 1.3 61.6 + - - +
362C VAL* 4.0 13.7 - - + -
363C CYS 3.4 3.6 - - - +
397C ILE* 3.4 2.6 - - - -
398C HIS* 2.8 42.4 + - + +
399C PRO 3.4 13.0 - - - +
400C VAL* 4.2 0.4 - - - -
401C GLY* 2.8 23.6 + - - -
402C TRP* 3.4 7.3 + - - +
403C CYS* 2.7 41.0 + - - +
404C GLN 5.0 0.3 + - - -
410C LEU* 4.2 14.2 - - + +
424C TRP* 2.8 29.0 + - + +
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Residues in contact with ALA 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C LEU* 4.2 1.1 - - + -
352C GLU* 1.3 75.6 - - - +
354C VAL* 1.3 63.3 + - - +
355C ASP 3.5 1.4 + - - -
362C VAL* 4.1 3.6 - - - -
363C CYS 2.8 38.4 + - - +
365C ALA* 3.7 11.4 - - + -
377C VAL* 3.6 30.5 - - + -
379C PHE* 3.5 12.1 - - + -
388C TYR* 3.7 9.4 - - - +
396C TYR 3.5 4.5 - - - +
397C ILE* 4.4 4.5 - - + -
398C HIS* 5.6 0.2 - - - -
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Residues in contact with VAL 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C ALA* 1.3 71.6 - - - +
355C ASP* 1.3 75.5 + - - +
356C ARG* 3.2 9.1 + - - +
359C PRO* 3.8 27.6 - - + +
361C LEU 3.5 5.6 - - - +
362C VAL* 4.2 17.9 - - + +
379C PHE* 3.4 1.4 - - - -
388C TYR* 2.7 27.4 + - - -
395C PRO 5.0 1.1 - - - +
396C TYR* 2.9 48.7 + - + +
398C HIS* 4.7 10.8 - - + +
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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