Contacts of the helix formed by residues 609 - 619 (chain C) in PDB entry 3P23
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 609 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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607C SER 3.9 0.8 + - - +
608C PHE* 1.3 80.5 - - - +
610C ASP* 1.3 64.3 + - - +
611C ARG 3.3 2.5 - - - -
612C GLU* 3.2 36.2 + - + +
613C VAL* 3.4 15.2 + - - +
687C ARG* 5.8 1.3 - - - +
713C GLY* 3.9 17.7 - - - -
714C LEU 4.4 2.5 - - - +
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Residues in contact with ASP 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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608C PHE* 3.3 34.7 + - - +
609C ALA* 1.3 72.7 - - - +
611C ARG* 1.3 65.8 + - + +
612C GLU 3.0 1.4 + - - -
613C VAL* 3.1 5.9 + - - +
614C GLN* 3.0 29.2 + - + +
631C THR* 3.8 16.0 - - - +
633C LYS* 5.2 6.4 + - - -
638C GLN* 5.8 0.9 + - - -
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Residues in contact with ARG 611 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609C ALA* 3.3 1.0 - - + -
610C ASP* 1.3 80.8 - - + +
612C GLU* 1.3 60.9 + - + +
614C GLN* 3.2 27.3 - - - +
615C LEU* 3.0 29.2 - - + +
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Residues in contact with GLU 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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609C ALA* 3.2 27.4 + - + +
610C ASP 3.0 1.0 + - - -
611C ARG* 1.3 79.8 - - + +
613C VAL* 1.3 62.8 + - + +
614C GLN 3.0 4.9 - - - -
615C LEU* 3.1 21.4 + - + +
616C LEU* 3.4 11.0 + - - +
683C ASN 4.9 2.6 - - - +
684C ILE* 3.8 50.8 - - + +
685C VAL 5.0 3.5 + - - +
687C ARG* 4.8 7.1 + - - -
712C PHE* 5.2 3.0 - - + -
713C GLY* 4.1 13.2 + - - -
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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
----------------------------------------------------------
608C PHE* 3.4 24.9 - - + -
609C ALA 3.5 10.3 - - - +
610C ASP* 3.1 5.8 + - - +
612C GLU* 1.3 73.2 - - + +
614C GLN* 1.3 64.0 + - - +
616C LEU* 3.8 17.4 + - + +
617C ARG* 3.6 27.5 - - + +
628C TYR* 3.3 59.0 - - + +
712C PHE* 4.9 5.2 - - + +
713C GLY* 6.2 0.9 - - - -
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Residues in contact with GLN 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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610C ASP* 3.0 19.1 + - - +
611C ARG* 3.2 33.1 - - - +
613C VAL* 1.3 76.8 - - - +
615C LEU* 1.3 61.5 + - + +
617C ARG* 2.7 42.6 + - - +
618C GLU* 3.3 14.3 + - + +
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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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611C ARG* 3.0 25.4 - - + +
612C GLU* 3.1 12.5 + - + +
614C GLN* 1.3 86.9 - - + +
616C LEU* 1.3 57.0 + - - +
617C ARG 3.0 5.0 + - - -
618C GLU* 3.3 23.8 + - - +
619C SER* 3.1 27.5 + - - -
682C LEU* 3.8 38.4 - - + +
683C ASN 5.8 0.2 - - - +
684C ILE* 4.6 11.2 - - + -
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Residues in contact with LEU 616 (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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612C GLU 3.4 12.4 + - - +
613C VAL* 4.1 14.8 - - + +
614C GLN 3.0 1.4 + - - -
615C LEU* 1.3 74.4 - - - +
617C ARG* 1.3 61.3 + - - +
619C SER* 4.3 3.8 - - - -
620C ASP 3.9 13.2 - - - +
621C GLU* 5.2 2.9 - - - +
625C VAL* 4.3 11.0 - - + -
626C ILE 5.3 0.7 - - - +
678C HIS* 3.7 24.8 + - + +
679C LEU* 4.0 18.2 - - + -
682C LEU* 3.6 20.9 - - + -
684C ILE* 4.3 5.8 - - + -
712C PHE* 3.3 41.1 - - + -
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Residues in contact with ARG 617 (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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614A GLN* 4.9 0.2 + - - -
617A ARG* 3.1 46.2 - - + +
618A GLU* 3.0 32.1 + - - +
619A SER* 4.5 0.8 - - - +
620A ASP* 3.8 24.6 + - - +
613C VAL* 3.6 25.1 + - + +
614C GLN* 2.7 15.1 + - - +
616C LEU* 1.3 81.5 - - - +
618C GLU* 1.3 61.8 + - + +
619C SER 2.8 13.4 - - - +
620C ASP 4.9 0.2 - - - -
628C TYR* 3.5 15.4 + - - +
629C PHE 3.1 26.7 + - - -
630C CYS* 5.0 1.6 - - - +
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Residues in contact with GLU 618 (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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614A GLN* 3.3 33.2 + - - +
617A ARG* 4.8 1.9 + - - -
618A GLU* 5.0 18.8 - - + +
614C GLN* 3.3 14.8 + - + +
615C LEU* 3.7 27.1 - - - +
617C ARG* 1.3 78.4 - - - +
619C SER* 1.3 63.3 + - - +
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Residues in contact with SER 619 (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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617A ARG* 4.3 0.9 - - - -
615C LEU 3.1 12.8 + - - -
616C LEU* 4.0 2.8 - - - +
617C ARG 2.8 18.4 - - - +
618C GLU* 1.3 79.7 - - - +
620C ASP* 1.3 83.5 + - - +
678C HIS* 4.0 15.2 - - - -
682C LEU* 3.8 29.6 - - - +
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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