Contacts of the strand formed by residues 304 - 308 (chain C) in PDB entry 5PAO
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 304 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C VAL* 3.4 8.0 - - - +
250C SER 2.8 32.0 + - - +
251C ALA 4.1 1.8 - - - -
252C ALA* 4.0 9.9 - - - +
255C PHE* 3.8 29.6 - - + -
288C VAL* 4.4 1.6 - - + -
289C ILE 3.3 10.5 - - - +
290C ILE* 4.1 7.2 - - + -
303C ILE* 1.3 80.5 - - - +
305C LEU* 1.3 61.8 + - - +
306C LEU* 3.8 8.1 - - + -
446C TRP* 5.2 0.7 - - - -
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Residues in contact with LEU 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C ILE* 4.5 4.9 - - + -
247C TRP* 3.5 45.5 - - + -
248C VAL 3.6 11.7 - - - +
249C VAL* 4.3 10.1 - - + -
287C GLN 3.8 0.2 - - - +
289C ILE* 2.8 49.8 + - + +
304C ALA* 1.3 72.5 - - - +
306C LEU* 1.3 58.7 + - - +
446C TRP* 4.6 4.6 - - + -
447C LEU* 3.8 31.4 - - + +
450C LEU* 3.7 31.9 - - + -
451C MET* 4.0 12.6 - - + -
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Residues in contact with LEU 306 (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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230C LEU* 3.9 31.4 - - + -
246C ILE 3.6 0.7 - - - +
247C TRP* 3.4 9.7 - - - -
248C VAL* 2.7 53.7 + - + +
250C SER* 4.3 4.0 - - - -
255C PHE* 3.9 23.6 - - + -
264C LEU* 4.7 0.2 - - + -
266C ALA* 5.7 0.4 - - + -
285C VAL* 4.0 29.2 - - + -
287C GLN 3.2 6.3 - - - +
288C VAL* 4.2 8.3 - - + -
304C ALA* 3.8 26.5 - - + +
305C LEU* 1.3 79.2 - - - +
307C ARG* 1.3 60.2 + - - +
308C LEU* 4.0 1.8 - - + -
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Residues in contact with ARG 307 (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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246C ILE* 3.4 30.7 - - + +
247C TRP* 3.5 42.8 - - + -
285C VAL* 3.7 3.1 - - - -
286C ALA* 2.8 32.1 + - + -
287C GLN* 2.9 28.1 + - + +
305C LEU 4.2 0.2 + - - -
306C LEU* 1.3 71.5 - - - +
308C LEU* 1.3 72.0 + - - +
451C MET 5.2 1.4 + - - -
453C SER 3.8 10.5 + - - -
454C GLU* 5.7 0.4 + - - -
455C PRO* 3.6 46.5 - - - +
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Residues in contact with LEU 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C LEU* 4.6 4.3 - - + -
245C THR 4.1 12.3 - - - +
246C ILE* 2.8 31.2 + - - +
248C VAL* 4.1 24.7 - - + -
266C ALA* 3.7 25.8 - - + -
268C LEU* 4.7 4.5 - - + -
283C ARG* 4.1 10.5 - - + -
284C ARG 3.5 9.9 - - - +
285C VAL* 4.5 8.1 - - + -
286C ALA* 4.2 1.8 - - - +
306C LEU* 5.0 2.2 - - + +
307C ARG* 1.3 90.5 + - - +
309C HIS* 1.3 66.1 + - - +
310C GLN* 3.3 13.3 + - - +
312C VAL* 3.9 27.6 - - + -
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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