Contacts of the helix formed by residues 713 - 720 (chain C) in PDB entry 1DQ8
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 713 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575C LEU 4.1 4.3 - - - +
576C GLY* 3.5 29.4 - - - +
711C VAL* 3.6 4.0 - - + +
712C ILE* 1.3 90.8 - - + +
714C ALA* 1.3 66.2 + - - +
715C LYS* 4.3 5.2 - - + +
716C VAL* 2.9 34.7 + - + +
717C VAL* 2.9 10.6 + - - +
790C ASP* 3.5 11.9 - - - +
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Residues in contact with ALA 714 (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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712C ILE 3.5 1.0 + - - -
713C PRO* 1.3 72.4 - - - +
715C LYS* 1.3 61.7 + - - +
717C VAL* 3.2 9.1 + - - +
718C ARG* 3.1 31.1 + - - +
725C THR* 4.5 0.9 - - - +
789C GLU* 3.1 41.1 - - + +
790C ASP* 3.0 14.6 + - - +
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Residues in contact with LYS 715 (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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713C PRO* 3.1 4.6 - - + +
714C ALA* 1.3 78.8 - - - +
716C VAL* 1.3 62.8 + - + +
718C ARG* 3.4 7.7 + - - +
719C GLU* 2.9 63.7 + - + +
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Residues in contact with VAL 716 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572C ALA* 3.6 27.6 - - + +
575C LEU* 3.8 27.6 - - + +
712C ILE* 3.6 21.1 - - + -
713C PRO* 2.9 28.5 + - + +
715C LYS* 1.3 76.5 - - + +
717C VAL* 1.3 66.7 + - - +
719C GLU* 4.5 1.6 - - - +
720C VAL* 2.9 38.4 + - + +
721C LEU* 3.4 1.3 + - - +
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Residues in contact with VAL 717 (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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712C ILE* 3.6 23.6 - - + +
713C PRO 2.9 20.1 + - - +
714C ALA 3.5 7.2 - - - +
716C VAL* 1.3 77.1 - - - +
718C ARG* 1.3 56.2 + - - +
721C LEU* 3.0 34.7 + - + +
722C LYS 3.0 9.2 + - - -
723C THR* 3.4 17.0 + - + +
724C THR* 3.6 31.2 - - - +
725C THR* 3.7 17.3 - - - +
728C MET* 4.4 6.1 - - + -
791C LEU* 4.0 11.9 - - + -
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Residues in contact with ARG 718 (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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714C ALA* 3.1 20.3 + - - +
715C LYS* 3.7 9.6 - - - +
717C VAL* 1.3 78.1 - - - +
719C GLU* 1.3 62.4 + - + +
722C LYS* 3.0 27.8 + - - +
723C THR 3.3 18.6 - - - +
724C THR* 4.4 19.3 - - + +
789C GLU* 5.2 10.3 + - - -
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Residues in contact with GLU 719 (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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715C LYS* 2.9 56.8 + - + +
716C VAL* 4.7 1.1 - - - +
718C ARG* 1.3 77.6 - - + +
720C VAL* 1.3 58.7 + - + +
722C LYS* 2.7 30.8 + - - -
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Residues in contact with VAL 720 (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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102C COA 3.2 20.0 + - + +
568C ARG* 3.4 36.6 + - + +
571C ARG* 4.4 11.4 - - + -
572C ALA* 4.0 15.0 - - + +
575C LEU* 3.8 29.2 - - + -
716C VAL* 2.9 26.4 + - + +
719C GLU* 1.3 77.7 - - + +
721C LEU* 1.3 60.9 + - + +
722C LYS* 3.1 16.8 + - - +
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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