Contacts of the helix formed by residues 729 - 741 (chain C) in PDB entry 3A8P
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 SER 729 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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711C LEU* 3.7 15.6 - - - +
722C LEU* 4.8 0.3 - - - +
727C VAL* 3.7 15.2 - - - +
728C LEU* 1.3 77.0 - - - +
730C VAL* 1.3 67.2 + - - +
731C SER* 3.5 10.2 + - - -
732C SER* 3.1 16.9 + - - -
733C PHE* 2.9 24.3 + - - +
708D LYS* 6.3 0.9 - - - -
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Residues in contact with VAL 730 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572C ILE* 4.4 11.4 - - + -
574C GLN* 3.9 20.2 - - + +
687C MET* 4.1 1.0 - - - +
690C PHE* 3.6 25.6 - - + -
707C PRO* 3.4 46.4 - - + +
710C LEU* 3.8 19.3 - - + -
711C LEU* 3.8 13.0 - - + +
729C SER* 1.3 75.1 - - - +
731C SER* 1.3 58.5 - - - +
733C PHE* 3.4 3.6 + - - +
734C HIS* 2.9 27.4 + - - +
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Residues in contact with SER 731 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572C ILE* 5.6 0.3 + - - +
574C GLN* 4.2 15.1 - - - +
587C CYS* 3.3 41.0 + - - +
589C SER* 3.6 22.4 + - - -
595C VAL* 3.8 11.3 - - - +
727C VAL* 6.2 0.7 - - - -
729C SER* 3.2 8.9 + - - -
730C VAL* 1.3 79.9 - - - +
732C SER* 1.3 61.6 + - - +
734C HIS* 3.3 4.7 + - - +
735C ALA* 3.1 19.6 + - - +
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Residues in contact with SER 732 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517C VAL* 5.3 2.5 - - - -
525C LEU* 4.1 0.9 - - - +
595C VAL* 4.5 6.9 - - - +
722C LEU* 3.6 14.5 - - - +
725C LEU* 4.4 8.3 - - - -
727C VAL* 2.6 44.9 + - - +
728C LEU* 3.6 0.9 - - - -
729C SER* 3.1 21.1 + - - -
731C SER* 1.3 76.1 - - - +
733C PHE* 1.3 60.1 + - - +
735C ALA* 3.3 8.4 + - - +
736C LEU* 2.9 28.2 + - - +
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Residues in contact with PHE 733 (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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683C GLU* 3.7 52.0 - - + -
687C MET* 3.4 14.4 - - + -
710C LEU* 3.8 37.2 - - + -
711C LEU* 4.2 8.3 - - + -
713C ALA* 4.2 2.5 - - + -
714C THR* 3.3 34.1 - - + -
718C SER* 4.6 2.2 - - - -
722C LEU* 3.8 20.4 - - + -
729C SER 2.9 20.6 + - - +
730C VAL 3.5 3.8 - - - +
732C SER* 1.3 78.3 + - - +
734C HIS* 1.3 61.4 + - - +
736C LEU* 3.2 8.2 + - + +
737C VAL* 3.1 26.7 + - + +
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Residues in contact with HIS 734 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570C ASP 3.9 15.8 + - - -
572C ILE* 3.6 23.0 - - + +
589C SER* 2.9 33.0 + - - +
590C ASN 3.2 17.0 - - - -
591C SER* 4.6 0.6 - - - -
687C MET* 3.3 35.5 - - + +
691C ARG* 4.8 5.4 + - - -
730C VAL 2.9 15.2 + - - +
731C SER 3.4 9.2 - - - +
732C SER 3.2 0.2 - - - -
733C PHE* 1.3 73.6 - - - +
735C ALA* 1.3 59.3 + - - +
737C VAL* 3.2 3.4 + - + +
738C CYS* 3.0 41.9 + - - -
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Residues in contact with ALA 735 (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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517C VAL* 4.8 1.1 - - + -
525C LEU* 3.9 13.2 - - + +
589C SER* 4.9 1.3 - - - -
590C ASN 5.4 1.1 - - - -
593C GLY* 3.6 35.9 - - - +
594C ASP 4.8 0.7 - - - +
595C VAL* 3.7 24.5 - - + -
731C SER 3.1 5.3 + - - -
732C SER* 3.6 8.7 - - - +
734C HIS* 1.3 76.4 - - - +
736C LEU* 1.3 62.9 + - - +
738C CYS* 3.4 3.7 + - - +
739C SER* 3.0 23.7 + - - -
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Residues in contact with LEU 736 (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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525C LEU* 3.7 18.1 - - + +
718C SER* 3.7 33.9 - - - +
721C ALA* 4.6 13.5 - - + -
722C LEU* 4.0 14.6 - - + -
732C SER 2.9 13.2 + - - +
733C PHE* 3.4 13.2 - - + +
734C HIS 3.2 0.2 - - - -
735C ALA* 1.3 78.5 - - - +
737C VAL* 1.3 61.1 + - - +
739C SER* 2.6 29.7 + - - +
740C ARG* 3.6 35.9 - - - +
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Residues in contact with VAL 737 (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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683C GLU* 4.2 15.7 - - + +
684C LYS* 3.8 40.8 - - + +
687C MET* 4.2 16.8 - - + -
733C PHE* 3.1 33.1 + - + +
734C HIS* 3.7 7.0 - - + +
736C LEU* 1.3 76.1 - - - +
738C CYS* 1.3 64.5 - - - +
740C ARG* 3.3 33.4 + - - +
741C ASP* 3.4 13.1 + - + +
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Residues in contact with CYS 738 (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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519C LEU* 5.4 0.9 - - - +
590C ASN 3.5 4.7 - - - -
591C SER* 3.3 37.0 - - - +
592C CYS* 4.1 2.2 - - - -
593C GLY* 3.6 16.4 - - - +
734C HIS* 3.0 50.7 + - - +
735C ALA 3.7 1.6 - - - +
737C VAL* 1.3 78.9 - - - +
739C SER* 1.3 62.1 + - - +
740C ARG 3.1 1.4 + - - -
741C ASP* 3.6 19.5 + - - +
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Residues in contact with SER 739 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519C LEU* 3.5 36.8 - - - -
523C ARG* 2.8 50.4 + - - +
525C LEU* 4.4 4.6 - - - +
593C GLY* 5.0 0.2 - - - -
735C ALA 3.0 15.0 + - - -
736C LEU* 2.6 29.5 + - - +
738C CYS* 1.3 77.0 - - - +
740C ARG* 1.3 55.4 + - - +
741C ASP 5.1 0.4 - - - -
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Residues in contact with ARG 740 (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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523C ARG* 3.3 36.3 + - - +
680C GLN* 3.8 49.8 + - - +
683C GLU* 2.7 25.0 + - - +
718C SER* 2.8 28.9 + - - +
733C PHE* 5.5 0.2 - - - -
736C LEU* 3.6 37.6 + - + +
737C VAL* 3.3 18.2 + - - +
738C CYS 3.1 0.8 - - - -
739C SER* 1.3 82.9 - - - +
741C ASP* 1.3 69.0 + - - +
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Residues in contact with ASP 741 (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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684C LYS* 4.8 20.9 - - + +
737C VAL 3.4 11.8 + - - +
738C CYS* 3.6 13.4 + - - +
739C SER 5.1 0.2 - - - -
740C ARG* 1.3 85.7 - - - +
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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