Contacts of the helix formed by residues 719 - 731 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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714B ARG 6.1 7.2 - - - -
720B GLN* 1.3 63.0 + - - +
721B PRO* 3.8 11.5 - - - +
722B LEU* 3.6 21.0 - - - +
723B HIS* 3.2 31.4 + - - -
750B ILE* 5.9 1.9 - - - +
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Residues in contact with GLN 720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719B SER* 1.3 69.0 - - - +
721B PRO* 1.4 69.8 - - + +
723B HIS* 3.8 3.9 + - - +
724B GLU* 3.3 22.5 + - - +
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Residues in contact with PRO 721 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719B SER* 3.5 13.5 - - - -
720B GLN* 1.4 91.0 - - + +
722B LEU* 1.4 61.8 + - - +
724B GLU* 3.1 9.0 + - + +
725B GLU* 3.1 38.4 + - - +
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Residues in contact with LEU 722 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711B ILE* 5.1 18.2 - - + -
719B SER* 3.6 16.5 + - - +
720B GLN 3.7 0.2 - - - -
721B PRO* 1.4 78.5 - - - +
723B HIS* 1.4 57.8 + - + +
725B GLU* 3.4 15.2 + - - +
726B ILE* 3.1 40.1 + - + +
750B ILE* 5.4 10.5 - - + -
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Residues in contact with HIS 723 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719B SER 3.2 26.5 + - - +
720B GLN* 4.2 4.7 - - - +
721B PRO 3.3 0.8 - - - -
722B LEU* 1.4 73.7 - - + +
724B GLU* 1.4 61.2 + - - +
726B ILE* 4.1 11.4 - - + +
727B ALA* 3.3 22.9 + - - +
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Residues in contact with GLU 724 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720B GLN 3.3 15.2 + - - +
721B PRO* 3.1 11.8 + - + +
723B HIS* 1.4 72.2 - - - +
725B GLU* 1.4 60.4 + - + +
727B ALA* 3.4 6.4 + - - +
728B LEU* 3.0 30.5 + - - +
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Residues in contact with GLU 725 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721B PRO* 3.1 36.1 + - - +
722B LEU* 3.5 13.5 + - - +
724B GLU* 1.4 73.9 - - - +
726B ILE* 1.4 58.7 + - + +
728B LEU* 3.4 9.1 + - + +
729B HIS* 3.0 31.5 + - - +
823B PHE* 3.4 27.4 - - + +
824B GLY* 3.0 30.2 - - - +
826B SER 4.7 6.6 - - - +
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Residues in contact with ILE 726 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711B ILE* 5.6 0.7 - - + -
722B LEU* 3.1 26.4 + - + +
723B HIS* 4.1 10.5 - - + +
724B GLU 3.4 0.2 - - - -
725B GLU* 1.4 74.2 - - + +
727B ALA* 1.3 58.2 + - - +
729B HIS* 3.4 5.9 + - - +
730B LYS* 3.0 33.2 + - + +
740B TYR* 3.9 13.7 - - + +
743B SER* 3.5 23.6 - - - +
750B ILE* 4.2 18.2 - - + -
752B ILE* 4.0 33.7 - - + -
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Residues in contact with ALA 727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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924A ASP* 4.6 25.1 - - + +
723B HIS 3.3 17.8 + - - +
724B GLU* 3.4 8.3 + - - +
726B ILE* 1.3 78.2 - - - +
728B LEU* 1.3 58.4 + - - +
730B LYS* 3.4 13.0 - - + +
731B HIS* 3.1 30.5 - - - -
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Residues in contact with LEU 728 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724B GLU 3.0 17.8 + - - +
725B GLU* 3.5 8.1 - - - +
727B ALA* 1.3 78.1 - - - +
729B HIS* 1.3 62.1 + - - +
730B LYS 3.3 0.9 + - - -
731B HIS* 3.7 8.9 + - - +
732B LEU* 3.4 21.3 + - + +
799B ILE* 3.9 35.2 - - + -
823B PHE* 4.8 3.8 - - + +
826B SER* 3.7 36.3 - - - +
827B LYS* 4.0 14.1 - - - +
828B ARG* 4.4 13.5 - - + +
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Residues in contact with HIS 729 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725B GLU 3.0 17.9 + - - +
726B ILE* 3.9 4.5 - - - +
728B LEU* 1.3 73.3 - - - +
730B LYS* 1.3 64.5 + - - +
732B LEU* 3.4 24.5 + - + +
737B ILE* 4.6 2.2 - - + -
738B VAL* 3.0 30.0 + - - +
740B TYR* 3.4 37.9 + + + +
752B ILE* 5.2 4.3 - - + -
754B MET* 4.3 20.7 - - - -
822B ASP 6.0 0.2 + - - -
823B PHE* 3.5 43.4 - + + -
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Residues in contact with LYS 730 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726B ILE* 3.0 20.5 + - + +
727B ALA* 3.4 14.8 - - - +
728B LEU 3.2 0.2 - - - -
729B HIS* 1.3 78.2 - - - +
731B HIS* 1.3 81.6 + - + +
732B LEU 3.4 4.5 + - - +
739B GLN* 5.1 3.3 + - - -
740B TYR* 3.7 36.2 - - + +
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Residues in contact with HIS 731 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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924A ASP* 3.1 25.5 + - - -
727B ALA* 3.1 26.4 + - - -
728B LEU* 3.7 5.6 + - - +
729B HIS 3.5 0.2 - - - -
730B LYS* 1.3 92.8 - - + +
732B LEU* 1.4 62.1 + - - +
733B LYS* 3.7 5.8 + - - +
793B TYR* 3.7 5.9 + - - -
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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