Contacts of the helix formed by residues 727 - 738 (chain u) in PDB entry 6FF7
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 VAL 727 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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691u GLU* 5.7 3.1 - - + -
709u ILE* 5.6 10.3 - - + -
724u PHE* 3.1 21.4 + - + +
726u SER* 1.3 79.6 - - - +
728u LEU* 1.3 64.7 + - - +
729u LYS 3.3 3.1 + - - -
730u PRO* 3.7 6.4 - - - +
731u LEU* 3.4 19.9 + - - +
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Residues in contact with LEU 728 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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980q GLN* 4.2 24.2 - - + -
724u PHE 3.7 8.2 + - - +
725u ASP* 4.2 6.8 + - - +
726u SER 3.8 0.4 - - - -
727u VAL* 1.3 78.9 - - - +
729u LYS* 1.3 57.0 + - - +
731u LEU* 3.4 7.3 + - - +
732u TRP* 2.9 30.1 + - - +
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Residues in contact with LYS 729 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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978q PHE* 3.5 34.3 + - + +
979q GLU* 4.8 5.4 - - + -
980q GLN 5.3 1.3 - - - +
725u ASP 5.0 1.8 + - - -
726u SER 5.1 3.5 - - - +
727u VAL 3.3 1.0 - - - +
728u LEU* 1.3 76.2 - - - +
730u PRO* 1.4 62.0 - - - +
732u TRP* 3.3 4.0 + - - +
733u LYS* 2.9 27.6 + - - +
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Residues in contact with PRO 730 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694u LEU* 4.3 28.2 - - + +
695u VAL* 6.4 0.9 - - + -
726u SER 5.5 3.5 - - - +
727u VAL* 3.7 7.8 - - - +
729u LYS* 1.4 75.8 - - - +
731u LEU* 1.3 58.0 + - - +
733u LYS* 3.7 7.9 - - + +
734u GLY* 2.9 25.3 + - - -
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Residues in contact with LEU 731 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727u VAL 3.4 13.5 + - - +
728u LEU* 3.6 11.4 - - - +
729u LYS 3.3 0.8 - - - -
730u PRO* 1.3 78.3 - - - +
732u TRP* 1.3 56.6 + - - +
734u GLY* 3.3 1.8 + - - -
735u ILE* 2.9 30.0 + - - +
746u PHE* 4.5 22.0 - - + +
749u ALA* 5.7 5.4 - - + -
750u ILE* 5.4 9.4 - - + +
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Residues in contact with TRP 732 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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978q PHE* 5.2 6.3 - - - +
728u LEU 2.9 17.6 + - - +
729u LYS* 3.3 7.6 + - - +
731u LEU* 1.3 74.6 - - - +
733u LYS* 1.3 59.6 + - - +
735u ILE* 3.4 4.6 + - - +
736u ARG* 3.0 29.5 + - - +
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Residues in contact with LYS 733 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729u LYS 2.9 16.7 + - - +
730u PRO* 3.7 8.3 - - + +
732u TRP* 1.3 76.7 - - - +
734u GLY* 1.3 57.6 + - - +
736u ARG* 3.3 6.2 + - - +
737u GLN* 2.9 32.2 + - - +
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Residues in contact with GLY 734 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730u PRO 2.9 17.8 + - - -
731u LEU* 3.3 2.4 + - - -
732u TRP 3.2 0.2 - - - -
733u LYS* 1.3 75.7 - - - +
735u ILE* 1.3 58.3 + - - +
738u HIS* 3.0 43.5 + - - +
743u LEU* 5.2 2.1 - - - -
746u PHE* 5.0 8.7 - - - -
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Residues in contact with ILE 735 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731u LEU 2.9 17.2 + - - +
732u TRP* 3.8 4.3 - - - +
733u LYS 3.4 0.2 - - - -
734u GLY* 1.3 75.8 - - - +
736u ARG* 1.3 60.3 + - - +
738u HIS 4.5 6.5 - - - +
743u LEU* 5.7 6.7 - - + +
746u PHE* 4.9 11.6 - - + +
747u LEU* 6.0 2.0 - - + +
772u ILE* 5.7 9.8 - - + +
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Residues in contact with ARG 736 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732u TRP 3.0 17.7 + - - +
733u LYS* 3.3 6.5 + - - +
734u GLY 3.2 0.2 - - - -
735u ILE* 1.3 81.3 - - - +
737u GLN* 1.3 61.3 + - + +
738u HIS 4.9 0.8 - - - +
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Residues in contact with GLN 737 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733u LYS 2.9 15.3 + - - +
734u GLY* 5.5 0.2 - - - -
736u ARG* 1.3 78.3 - - + +
738u HIS* 1.3 62.5 + - + +
739u ARG* 4.2 0.7 + - - +
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Residues in contact with HIS 738 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734u GLY* 3.0 29.8 + - - +
735u ILE* 4.5 5.9 - - - +
736u ARG 4.9 0.3 - - - -
737u GLN* 1.3 78.6 - - + +
739u ARG* 1.3 62.8 + - - +
742u GLY* 5.6 4.3 - - - -
743u LEU* 3.8 17.2 - - - +
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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