Contacts of the helix formed by residues 565 - 571 (chain C) in PDB entry 4P3N
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 PHE 565 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469C MET* 4.4 0.4 - - + -
506C LEU 5.2 1.6 - - - -
507C GLY* 5.3 11.7 - - - -
511C VAL* 3.7 32.5 - - + -
512C TRP* 4.0 32.5 - + - -
515C ALA* 3.6 29.4 - - + -
540C TYR 2.9 16.2 + - - +
542C PRO* 3.8 25.4 - - + -
563C LEU* 4.3 3.6 - - + -
564C ASP* 1.3 74.5 - - - +
566C GLN* 1.3 65.1 + - + +
568C PRO* 3.5 12.7 - - - +
569C ILE* 3.5 20.7 - - + +
586C PRO 5.9 0.2 - - - -
587C VAL* 3.7 33.9 - - + +
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Residues in contact with GLN 566 (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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506C LEU* 3.2 45.6 - - + +
507C GLY* 4.0 5.5 + - - -
539C PHE* 4.8 7.2 - - + -
540C TYR* 3.7 22.4 + - + -
564C ASP* 2.8 9.8 + - - +
565C PHE* 1.3 78.9 - - + +
567C LEU* 1.3 59.7 + - + +
569C ILE* 3.0 27.3 + - - +
570C ARG* 2.9 48.0 + - + +
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Residues in contact with LEU 567 (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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386C SER* 4.1 23.1 - - - +
388C HIS* 6.4 0.7 - - + -
413C CYS* 4.0 15.5 - - + -
414C PRO* 5.3 2.0 - - + -
417C CYS* 3.7 20.2 - - - -
564C ASP* 3.0 26.2 + - - +
566C GLN* 1.3 78.6 - - + +
568C PRO* 1.4 66.9 - - + +
570C ARG* 3.4 4.6 + - + -
571C PHE* 3.1 49.5 + - + +
573C LEU* 4.6 0.2 - - - +
588C ILE* 3.6 13.9 - - + -
590C HIS* 3.5 23.3 - - + +
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Residues in contact with PRO 568 (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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564C ASP 3.6 12.6 - - - +
565C PHE* 3.5 20.6 - - - +
567C LEU* 1.4 93.5 - - + +
569C ILE* 1.3 56.4 + - - +
572C ASN* 3.1 6.1 + - - -
573C LEU* 2.9 44.4 + - + -
585C ARG* 3.6 19.1 + - + -
586C PRO* 3.4 28.3 - - + +
588C ILE* 3.8 20.2 - - + +
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Residues in contact with ILE 569 (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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507C GLY* 5.4 9.2 - - - -
565C PHE* 3.5 15.5 - - + +
566C GLN* 3.0 31.0 + - - +
568C PRO* 1.3 75.2 - - - +
570C ARG* 1.3 69.8 + - + +
572C ASN* 3.0 15.1 + - - +
585C ARG* 3.7 30.9 + - - +
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Residues in contact with ARG 570 (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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384C MET 3.6 17.8 + - - -
385C THR* 3.2 39.9 + - - +
386C SER 5.0 7.1 + - - +
387C GLY* 4.7 8.5 - - - -
390C GLN* 4.3 14.5 - - - +
391C HIS* 6.1 2.0 + - - -
566C GLN* 2.9 36.4 + - + +
567C LEU* 3.9 7.4 - - + +
569C ILE* 1.3 79.7 - - + +
571C PHE* 1.3 66.2 + - + +
572C ASN* 3.7 1.0 + - - +
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Residues in contact with PHE 571 (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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382C LEU* 3.6 33.7 - - + -
385C THR* 3.7 25.4 - - + -
386C SER* 3.8 26.7 - - - -
414C PRO* 3.8 20.9 - - + -
417C CYS* 3.8 17.3 - - + -
418C LEU* 4.0 20.4 - - + -
421C ASP* 4.2 11.9 - - + +
567C LEU* 3.1 30.6 + - + +
570C ARG* 1.3 75.8 - - + +
572C ASN* 1.3 71.1 + - - +
573C LEU* 3.2 22.9 + - + +
338D LEU* 5.7 0.4 - - + -
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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
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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