Contacts of the helix formed by residues 606 - 615 (chain C) in PDB entry 4PE5
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 606 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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574C ALA* 4.0 29.8 - - + +
577C LEU* 4.6 11.9 - - + -
578C TYR* 4.9 9.9 - - + +
605C SER* 1.3 78.4 - - - +
607C MET* 1.3 60.6 + - - +
609C PHE* 3.3 7.9 + - - +
610C SER* 2.9 31.1 + - - -
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Residues in contact with MET 607 (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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574C ALA* 5.1 5.3 - - + +
605C SER 3.3 5.9 - - - +
606C ALA* 1.3 79.4 - - - +
608C TRP* 1.3 57.2 + - - +
610C SER* 3.9 4.1 - - - -
611C TRP* 2.9 34.0 + - - +
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Residues in contact with TRP 608 (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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630B ILE* 5.8 9.2 - - + -
605C SER* 3.7 14.7 + - - +
606C ALA 3.3 0.2 - - - -
607C MET* 1.3 78.4 - - - +
609C PHE* 1.3 57.3 + - - +
611C TRP* 4.9 2.7 - - - -
612C GLY* 2.9 26.4 + - - +
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Residues in contact with PHE 609 (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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605C SER 3.4 12.7 + - - +
606C ALA* 3.3 11.6 + - - +
607C MET 3.2 0.4 - - - -
608C TRP* 1.3 78.2 - - - +
610C SER* 1.3 59.5 + - - +
612C GLY* 4.9 0.2 - - - -
613C VAL* 2.9 31.4 + - - +
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Residues in contact with SER 610 (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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570C VAL* 4.5 26.2 - - - -
573C VAL* 6.1 1.6 - - - -
574C ALA* 4.7 9.0 - - - -
606C ALA 2.9 17.4 + - - -
607C MET* 4.0 3.6 - - - -
609C PHE* 1.3 76.6 - - - +
611C TRP* 1.3 58.1 + - - +
613C VAL* 3.3 4.3 + - - +
614C LEU* 2.9 32.0 + - - +
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Residues in contact with TRP 611 (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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633B SER* 4.8 17.1 - - - -
607C MET 2.9 18.4 + - - +
608C TRP* 4.7 2.9 - - - +
610C SER* 1.3 76.7 - - - +
612C GLY* 1.3 57.4 + - - +
614C LEU* 4.1 6.5 - - - -
615C LEU* 3.3 28.6 + - - +
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Residues in contact with GLY 612 (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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633B SER* 6.0 2.5 - - - -
608C TRP 2.9 22.3 + - - -
609C PHE* 3.8 0.9 - - - -
611C TRP* 1.3 78.4 - - - +
613C VAL* 1.3 58.0 + - - +
615C LEU* 5.3 0.4 - - - -
616C ASN 3.1 33.2 + - - -
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Residues in contact with VAL 613 (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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609C PHE 2.9 18.6 + - - +
610C SER* 3.9 4.5 - - - +
612C GLY* 1.3 76.8 - - - +
614C LEU* 1.3 64.0 + - - +
616C ASN* 3.4 9.7 + - - +
636C TRP* 5.5 6.1 - - + +
637C ALA* 5.2 18.5 - - + +
640C ALA* 3.8 13.9 - - + +
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Residues in contact with LEU 614 (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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570C VAL* 6.0 5.2 - - + -
610C SER 2.9 18.9 + - - +
611C TRP* 4.4 4.9 - - - +
613C VAL* 1.3 79.1 - - - +
615C LEU* 1.3 57.9 + - + +
616C ASN* 3.2 3.0 + - - +
640C ALA* 4.3 15.9 - - + +
644C VAL* 6.1 1.0 - - - +
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Residues in contact with LEU 615 (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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633B SER* 3.9 12.3 - - - +
636B ALA* 3.6 21.0 - - + +
637B PHE* 3.8 33.2 - - + +
640B VAL* 4.9 6.4 - - - +
611C TRP 3.3 18.6 + - - +
612C GLY* 3.9 1.3 - - - -
614C LEU* 1.3 76.8 - - + +
616C ASN* 1.3 71.7 + - - +
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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