Contacts of the strand formed by residues 264 - 268 (chain C) in PDB entry 3TKY
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 ALA 264 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C LEU* 3.7 34.5 - - + -
206C THR 3.3 2.7 + - - +
207C ILE* 3.5 5.2 - - + +
208C VAL* 2.8 26.7 + - - +
262C GLY 3.1 1.9 - - - -
263C ASP* 1.3 82.6 - - - +
265C ILE* 1.3 67.5 + - - +
290C LEU* 3.5 1.6 - - - -
295C LYS* 3.4 15.9 - - + +
297C ILE* 4.4 13.9 - - + -
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Residues in contact with ILE 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C VAL* 3.2 25.6 - - + +
210C VAL* 3.5 29.6 - - + -
259C VAL* 4.1 11.9 - - + -
260C PRO 4.3 5.4 - - - +
262C GLY 5.4 1.1 - - - +
264C ALA* 1.3 75.6 - - - +
266C PHE* 1.3 60.2 + - - +
267C ILE* 4.5 1.8 - - + -
286C CYS* 3.6 48.2 - - + +
289C ALA* 4.3 4.3 - - + +
290C LEU* 3.7 17.4 - - + +
295C LYS 3.2 8.3 + - - +
296C VAL* 3.3 11.5 - - + +
297C ILE* 2.7 36.1 + - - +
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Residues in contact with PHE 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C MET* 3.7 26.9 - - + -
194C ILE* 5.7 0.9 - - + -
201C PHE* 3.6 31.4 - + + -
207C ILE* 6.1 3.1 - - + -
208C VAL 2.8 13.6 + - - +
209C ASP* 3.1 27.2 - - + +
210C VAL 3.0 25.1 + - - -
217C VAL* 3.7 20.4 - - + -
221C ILE* 4.9 3.6 - - + -
265C ILE* 1.3 73.3 - - - +
267C ILE* 1.3 62.7 + - - +
268C LYS* 3.5 22.4 - - + -
297C ILE* 3.3 36.3 - - + -
299C ALA* 4.0 20.4 - - + -
361C VAL* 5.2 4.9 - - + -
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Residues in contact with ILE 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C VAL* 3.4 38.6 - - + +
265C ILE* 4.5 4.5 - - + -
266C PHE* 1.3 76.1 - - - +
268C LYS* 1.3 60.4 + - - +
269C TRP 4.1 0.6 + - - -
270C ILE* 3.8 19.2 + - + -
271C CYS* 3.2 33.9 - - - +
282C LEU* 4.1 18.8 - - + -
283C LEU* 4.1 4.5 - - + -
296C VAL* 3.9 14.6 - - + -
297C ILE 2.9 4.0 + - - -
298C VAL* 3.9 28.0 - - + +
299C ALA 2.8 25.1 + - - +
300C GLU* 5.4 0.3 - - - +
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Residues in contact with LYS 268 (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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186C ASN* 4.4 6.9 - - - +
187C SER* 2.9 42.4 + - - +
190C THR* 4.4 19.7 - - - -
191C MET* 4.7 7.0 - - + -
194C ILE* 5.9 0.2 - - - -
209C ASP* 4.7 1.0 + - - -
217C VAL* 4.7 4.3 - - + -
266C PHE* 3.5 29.6 - - + -
267C ILE* 1.3 72.1 - - - +
269C TRP* 1.3 97.0 + - + +
270C ILE* 3.2 5.8 + - - +
299C ALA* 3.4 18.6 - - + +
359C THR* 4.8 11.0 + - + -
370C SAH 2.9 38.4 + - - +
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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
------------------------------------------------------------
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