Contacts of the helix formed by residues 719 - 731 (chain A) in PDB entry 4BIC
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 719 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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720A GLN* 1.4 56.5 + - - +
721A PRO* 3.4 17.2 - - - +
722A LEU* 3.6 35.8 - - - +
723A HIS* 3.3 28.6 + - - +
750A ILE* 6.3 3.7 - - - +
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Residues in contact with GLN 720 (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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719A SER* 1.4 69.0 - - - +
721A PRO* 1.4 72.2 - - + +
723A HIS* 3.7 4.4 + - - +
724A GLU* 3.2 23.8 + - + +
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Residues in contact with PRO 721 (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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719A SER* 3.4 14.8 - - - +
720A GLN* 1.4 93.9 - - + +
722A LEU* 1.4 60.9 + - + +
724A GLU* 3.3 7.0 + - + +
725A GLU* 3.0 46.6 + - - +
827A LYS* 6.0 6.1 - - - -
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Residues in contact with LEU 722 (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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691A TYR* 4.9 15.0 - - + -
711A ILE* 3.8 35.9 - - + -
712A PRO 5.4 1.1 - - - +
719A SER* 3.6 30.7 - - - +
720A GLN 3.4 0.6 - - - -
721A PRO* 1.4 85.4 - - + +
723A HIS* 1.4 59.2 + - - +
725A GLU* 3.6 19.7 + - - +
726A ILE* 3.3 31.7 + - + +
750A ILE* 5.6 8.3 - - + -
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Residues in contact with HIS 723 (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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719A SER 3.3 16.9 + - - +
720A GLN* 4.1 5.4 - - - +
722A LEU* 1.4 75.9 - - - +
724A GLU* 1.4 57.9 + - - +
725A GLU 3.4 0.2 - - - -
726A ILE* 3.6 12.4 + - + +
727A ALA* 3.1 26.7 + - + +
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Residues in contact with GLU 724 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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720A GLN* 3.2 19.6 + - + +
721A PRO* 3.3 10.5 + - + +
723A HIS* 1.4 75.2 - - - +
725A GLU* 1.4 54.7 + - + +
727A ALA* 3.3 8.3 + - - +
728A LEU* 2.9 33.9 + - - +
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Residues in contact with GLU 725 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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721A PRO* 3.0 32.0 + - - +
722A LEU* 3.7 23.4 - - - +
723A HIS 3.4 0.4 - - - -
724A GLU* 1.4 73.1 - - + +
726A ILE* 1.4 61.5 + - + +
728A LEU* 3.8 9.0 - - + +
729A HIS* 3.1 30.7 + - - +
802A ARG* 5.6 1.9 + - - -
823A PHE* 3.3 26.2 - - - +
824A GLY* 3.0 31.6 - - - +
826A SER* 3.9 14.0 - - - +
827A LYS* 5.8 3.5 - - - +
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Residues in contact with ILE 726 (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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711A ILE* 5.6 2.2 - - + -
722A LEU* 3.3 22.2 + - + +
723A HIS* 3.8 11.9 - - + +
724A GLU 3.3 0.2 - - - -
725A GLU* 1.4 74.3 - - + +
727A ALA* 1.3 59.9 + - - +
729A HIS* 3.9 3.7 - - - +
730A LYS* 2.9 31.8 + - + +
740A TYR* 3.8 15.3 - - + +
743A SER* 3.4 25.1 - - - +
750A ILE* 3.8 30.5 - - + -
752A ILE* 4.2 24.9 - - + -
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Residues in contact with ALA 727 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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723A HIS* 3.1 18.5 + - + +
724A GLU* 3.4 9.6 - - - +
726A ILE* 1.3 77.6 - - - +
728A LEU* 1.4 61.6 + - - +
730A LYS* 3.5 15.1 - - - +
731A HIS* 4.0 8.8 + - - +
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Residues in contact with LEU 728 (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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724A GLU 2.9 17.0 + - - +
725A GLU* 3.8 10.5 - - + +
727A ALA* 1.4 72.7 - - - +
729A HIS* 1.4 66.0 + - - +
730A LYS 3.2 1.4 + - - -
731A HIS* 3.2 14.4 + - - +
732A LEU* 3.4 19.9 + - + +
799A ILE* 3.8 36.3 - - + -
823A PHE* 5.6 1.6 - - + -
826A SER* 3.6 32.1 - - - +
827A LYS* 4.5 5.8 - - - +
828A ARG* 3.6 40.5 + - + +
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Residues in contact with HIS 729 (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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725A GLU 3.1 16.7 + - - +
726A ILE* 4.2 4.0 - - - +
728A LEU* 1.4 77.8 - - - +
730A LYS* 1.3 61.5 + - - +
731A HIS 3.3 0.2 - - - -
732A LEU* 3.3 31.9 + - + +
737A ILE* 4.5 1.3 - - + -
738A VAL* 2.8 29.4 + - + -
740A TYR* 3.6 39.7 + - + +
752A ILE* 4.8 4.9 - - - +
754A MET* 4.3 21.1 - - + -
823A PHE* 3.6 38.9 + + + +
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Residues in contact with LYS 730 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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726A ILE* 2.9 20.6 + - + +
727A ALA* 3.5 12.3 - - - +
728A LEU 3.1 0.4 - - - -
729A HIS* 1.3 76.8 - - - +
731A HIS* 1.4 68.9 + - + +
732A LEU 3.8 3.1 + - - +
739A GLN* 5.5 1.4 + - - -
740A TYR* 3.6 33.2 - - + +
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Residues in contact with HIS 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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727A ALA 4.0 5.8 + - - +
728A LEU 3.2 10.0 + - - +
730A LYS* 1.4 87.3 - - + +
732A LEU* 1.3 62.7 + - + +
733A LYS* 3.7 4.0 + - - +
793A TYR* 3.9 4.9 + - - -
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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