Contacts of the helix formed by residues 730 - 739 (chain A) in PDB entry 6DBT
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 ASP 730 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619A CYS 5.1 0.7 - - - +
620A ASP* 4.6 11.7 - - - +
684A GLU* 3.9 9.2 - - - +
729A TYR* 1.3 73.6 - - - +
731A GLU* 1.3 70.0 + - - +
732A LYS* 4.4 7.2 - - - +
733A MET* 3.3 27.8 + - - +
734A VAL* 2.8 28.4 + - - +
814A ASP* 5.4 7.9 - - - -
817A HIS* 5.4 9.2 - - + -
980A SER* 5.0 2.2 + - - -
1103A CA 3.3 23.6 - - - -
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Residues in contact with GLU 731 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730A ASP* 1.3 83.1 - - - +
732A LYS* 1.3 58.7 + - - +
734A VAL* 3.2 10.1 + - - +
735A ARG* 2.9 37.3 + - + +
814A ASP* 5.0 9.3 - - + +
817A HIS* 4.0 11.8 + - - -
957A TYR* 3.1 34.9 + - + -
960A LYS* 4.1 23.3 - - - +
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Residues in contact with LYS 732 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684A GLU* 4.0 32.5 + - + +
685A SER* 4.7 13.5 + - - +
730A ASP* 3.3 8.8 - - - +
731A GLU* 1.3 79.4 + - - +
733A MET* 1.3 61.5 + - + +
735A ARG* 3.1 11.0 + - - +
736A GLU* 2.9 44.7 + - + +
742A ALA* 4.7 12.1 - - + +
743A SER* 5.6 10.1 - - - -
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Residues in contact with MET 733 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619A CYS* 3.3 42.8 - - - +
620A ASP* 4.9 0.4 - - - -
621A GLY 5.1 4.0 - - - +
640A VAL* 5.9 2.5 - - + -
684A GLU* 3.6 41.3 + - + +
690A LEU* 4.7 6.5 - - + -
729A TYR* 3.7 20.4 - - + -
730A ASP* 3.3 20.9 + - - +
731A GLU 3.4 0.4 - - - -
732A LYS* 1.3 77.4 - - - +
734A VAL* 1.3 60.8 + - - +
736A GLU* 4.2 10.8 - - - +
737A MET* 2.8 50.6 + - + +
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Residues in contact with VAL 734 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727A THR 5.5 1.3 - - - +
729A TYR* 3.8 25.4 - - + +
730A ASP 2.8 22.0 + - - +
731A GLU* 3.3 10.8 - - - +
733A MET* 1.3 75.6 - - - +
735A ARG* 1.3 66.3 + - - +
737A MET* 3.9 3.5 - - - +
738A GLU* 2.9 31.5 + - + +
750A THR* 4.1 26.9 - - + -
809A THR* 4.2 24.9 - - + +
811A PRO* 5.9 6.1 - - + -
812A THR 5.8 4.5 - - - +
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Residues in contact with ARG 735 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731A GLU* 2.9 23.6 + - + +
732A LYS* 3.4 7.9 - - - +
734A VAL* 1.3 80.5 - - - +
736A GLU* 1.3 52.3 + - - +
738A GLU* 3.3 2.4 + - - -
739A GLY* 2.6 31.4 + - - -
740A LEU* 3.1 35.0 + - - +
741A GLU* 3.3 26.0 + - - +
742A ALA* 3.9 14.1 - - + -
743A SER* 3.7 11.6 + - - +
745A SER* 3.1 23.2 + - - -
747A TYR 4.0 4.6 + - - -
748A ILE 2.6 32.9 + - - -
749A CYS 4.5 0.2 - - - -
750A THR* 3.3 28.2 + - - +
956A ASN* 3.8 9.5 - - - +
960A LYS* 5.1 1.2 - - - +
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Residues in contact with GLU 736 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684A GLU* 3.6 11.3 - - - +
685A SER* 3.4 31.7 - - - +
687A HIS* 3.4 36.5 + - + +
690A LEU* 5.0 6.2 - - - +
732A LYS* 2.9 33.7 + - + +
733A MET* 3.1 13.9 + - + +
735A ARG* 1.3 74.4 - - + +
737A MET* 1.3 70.4 + - + +
739A GLY* 3.0 14.4 + - - -
740A LEU 5.0 1.8 - - - +
742A ALA* 5.3 6.3 - - + -
805A PRO* 5.7 0.2 - - - +
806A PHE* 5.5 0.2 - - - -
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Residues in contact with MET 737 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619A CYS* 5.0 3.4 - - - -
687A HIS* 5.8 2.2 - - + +
690A LEU* 3.7 33.4 - - + -
694A LEU* 4.9 11.0 - - + -
729A TYR* 4.7 6.1 - - + -
733A MET* 2.8 46.0 + - + +
734A VAL* 4.2 2.9 - - - +
736A GLU* 1.3 76.4 - - + +
738A GLU* 1.3 58.5 + - - +
805A PRO* 3.7 2.6 - - - +
806A PHE* 3.5 47.9 + - + -
807A MET* 3.6 51.4 + - + +
809A THR* 5.3 4.5 - - + -
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Residues in contact with GLU 738 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734A VAL* 2.9 24.5 + - + +
735A ARG* 3.7 5.8 - - - +
737A MET* 1.3 78.7 - - - +
739A GLY* 1.3 54.4 + - - +
740A LEU* 3.3 26.1 + - + +
750A THR* 6.2 3.6 - - + -
772A HIS* 4.2 13.4 + - - +
775A ASN* 3.6 29.5 + - - +
801A VAL* 5.4 0.5 - - - +
803A ALA 3.9 1.2 - - - +
805A PRO* 3.0 35.6 - - - +
807A MET 4.2 5.4 - - - +
809A THR* 3.3 27.0 - - + +
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Residues in contact with GLY 739 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687A HIS* 5.9 0.2 - - - -
735A ARG 2.6 11.9 + - - -
736A GLU* 3.0 11.8 + - - -
737A MET 3.4 0.2 - - - -
738A GLU* 1.3 73.3 - - - +
740A LEU* 1.3 67.4 + - - +
802A SER* 4.3 4.7 + - - -
803A ALA* 3.1 45.3 + - - +
804A LYS 5.3 0.4 - - - -
805A PRO* 5.0 2.0 - - - -
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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