Contacts of the strand formed by residues 407 - 412 (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 PRO 407 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C TRP* 4.4 16.2 - - + +
227C GLN* 3.4 19.3 - - - +
240C GLY 3.7 8.3 - - - +
241C THR* 3.1 30.7 - - + +
321C LEU* 4.3 13.5 - - + -
340C LEU 3.4 1.1 - - - +
341C VAL* 3.3 24.0 - - - +
342C SER* 3.4 19.0 + - - +
406C GLY* 1.3 86.6 - - - +
408C HIS* 1.3 60.9 + - - +
409C ALA* 3.9 3.8 - - + +
418C LEU* 4.2 1.1 - - + -
420C GLY 4.0 3.6 - - - +
422C VAL* 4.5 2.0 - - - +
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Residues in contact with HIS 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C SER* 3.2 32.2 - - - -
340C LEU 3.3 4.9 - - - -
341C VAL* 3.7 22.9 - - + -
362C VAL* 4.1 9.7 + - + +
364C ARG* 4.9 11.5 - - + +
388C PHE* 3.5 36.9 - + - -
390C ALA* 4.2 8.2 - - + +
406C GLY 3.8 0.2 + - - -
407C PRO* 1.3 71.0 - - - +
409C ALA* 1.3 58.1 - - - +
410C THR* 3.9 0.4 - - - -
418C LEU* 3.9 2.8 - - - +
419C THR* 2.8 52.1 + - - -
420C GLY* 2.9 26.7 + - - +
437C TYR* 4.1 12.1 - + + -
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Residues in contact with ALA 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C TRP* 4.4 10.1 - - + +
321C LEU* 3.9 26.7 - - + -
339C SER* 3.2 3.7 - - - -
340C LEU* 2.8 40.7 + - + +
407C PRO* 4.7 4.7 - - + -
408C HIS* 1.3 72.7 - - - +
410C THR* 1.3 61.9 + - - +
416C TRP* 3.5 21.6 - - + -
417C TYR 3.3 5.4 - - - +
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Residues in contact with THR 410 (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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333C LEU* 4.0 19.6 + - + +
336C VAL* 3.6 35.4 - - + +
339C SER* 2.6 24.1 + - - +
408C HIS* 3.9 0.7 - - - -
409C ALA* 1.3 71.2 - - - +
411C HIS* 1.3 66.6 + - - +
416C TRP* 3.4 4.6 - - - -
417C TYR* 2.9 36.5 + - - -
419C THR* 2.6 35.5 + - - +
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Residues in contact with HIS 411 (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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336C VAL* 3.8 21.5 - - + +
338C PHE 5.1 2.4 + - - +
410C THR* 1.3 75.3 - - - +
412C TYR* 1.3 63.7 + - - +
413C ARG* 4.1 4.2 + - - -
414C GLY* 3.3 34.0 + - - -
415C THR 3.5 14.4 - - - -
416C TRP* 3.5 51.7 - + + -
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Residues in contact with TYR 412 (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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154A GLU* 4.3 3.5 + - - +
155A ASN* 3.5 21.7 - - - +
159A GLU* 3.6 21.4 - - - +
328C PHE* 3.7 14.8 - + - -
332C THR* 3.5 23.1 - - + +
333C LEU* 3.7 19.5 - - + -
336C VAL* 4.4 14.6 - - + -
410C THR 3.8 0.6 + - - -
411C HIS* 1.3 75.1 - - - +
413C ARG* 1.3 118.8 + - + +
414C GLY 3.1 2.4 + - - -
415C THR* 2.9 21.6 + - - +
417C TYR* 4.0 9.2 + - + -
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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