Contacts of the helix formed by residues 788 - 794 (chain A) in PDB entry 3BWT
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 ARG 788 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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750A ASP* 3.7 44.9 + - - +
753A THR* 5.6 0.2 - - - -
754A LEU* 5.2 9.3 - - - +
784A LEU 4.7 9.6 + - - +
785A LEU* 2.9 16.1 + - - +
786A LYS 2.9 1.4 - - - -
787A PRO* 1.3 87.9 - - + +
789A ALA* 1.3 66.7 + - - +
790A ILE 3.2 2.7 - - - -
791A GLU* 2.9 52.0 + - - +
792A LEU* 2.8 55.9 + - + +
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Residues in contact with ALA 789 (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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785A LEU 3.5 1.1 + - - -
786A LYS 2.9 15.0 + - - +
787A PRO 3.6 0.6 - - - -
788A ARG* 1.3 76.7 - - - +
790A ILE* 1.3 55.6 + - + +
793A SER* 2.7 37.3 + - - -
802A ILE* 3.9 15.2 - - - +
815A MET* 3.5 24.2 - - - -
818A GLU* 3.9 14.8 - - + +
819A ILE* 4.0 15.9 - - + +
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Residues in contact with ILE 790 (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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788A ARG 3.2 0.6 - - - -
789A ALA* 1.3 73.7 - - + +
791A GLU* 1.3 69.3 + - - +
793A SER* 2.9 15.0 + - - -
794A ILE* 3.3 19.6 + - + +
818A GLU 5.6 0.4 - - - +
819A ILE* 4.4 18.8 - - + +
822A ASN 4.8 2.7 - - - +
823A GLY* 3.8 31.0 - - - +
827A GLY* 3.9 24.2 - - - +
830A SER* 4.9 5.8 - - - -
831A LEU* 4.0 29.2 - - + -
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Residues in contact with GLU 791 (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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754A LEU* 5.4 5.0 - - - +
788A ARG* 2.9 55.2 + - + +
790A ILE* 1.3 82.0 - - - +
792A LEU* 1.3 63.0 + - + +
794A ILE* 3.3 24.2 + - + +
795A HIS* 3.9 8.1 + - - +
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Residues in contact with LEU 792 (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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753A THR* 4.1 14.8 - - + -
754A LEU* 3.6 30.1 - - + -
785A LEU* 3.7 47.6 - - + +
788A ARG* 2.8 44.7 + - + +
791A GLU* 1.3 74.4 - - - +
793A SER* 1.3 62.8 + - - +
794A ILE 3.1 3.0 + - - -
795A HIS* 3.3 9.5 + - + +
798A GLY 3.2 4.7 - - - +
799A SER* 2.9 27.9 + - - -
801A VAL* 6.4 0.2 - - + -
802A ILE* 3.7 20.6 - - + -
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Residues in contact with SER 793 (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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789A ALA 2.7 23.6 + - - -
790A ILE* 2.9 9.5 + - - -
792A LEU* 1.3 77.5 - - - +
794A ILE* 1.3 57.2 + - - +
795A HIS 3.4 0.9 - - - -
799A SER* 3.6 16.2 - - - +
802A ILE* 3.5 12.1 - - - +
819A ILE* 4.3 5.7 - - - +
831A LEU* 3.9 20.0 - - - -
837A GLY* 3.0 24.9 + - - -
840A VAL* 3.4 25.1 - - - +
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Residues in contact with ILE 794 (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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790A ILE* 3.7 17.3 - - + +
791A GLU* 3.3 20.4 - - + +
793A SER* 1.3 81.0 - - - +
795A HIS* 1.3 57.7 + - - +
830A SER* 4.6 11.7 - - - +
831A LEU* 3.9 19.3 - - + -
834A ASP* 3.5 41.0 - - + +
836A TYR* 3.8 12.5 - - - -
837A GLY* 4.6 0.2 - - - -
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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