Contacts of the helix formed by residues 787 - 796 (chain A) in PDB entry 3B7B
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 HIS 787 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A SO4 3.3 21.3 + - - +
750A ALA 3.5 5.8 - - - -
751A GLU 2.9 28.5 + - - -
752A ALA* 3.3 16.5 - - - -
753A GLY* 3.2 25.9 - - - -
782A ALA 3.1 12.2 + - - +
785A ASN* 3.5 27.1 + - + +
786A ASN* 1.3 76.2 + - - +
788A LEU* 1.3 64.0 + - - +
789A GLU 3.5 0.9 - - - -
790A ALA* 3.2 6.8 + - + -
791A VAL* 3.0 25.0 + - - +
823A VAL* 4.5 0.2 - - - +
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Residues in contact with LEU 788 (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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8A SO4 3.0 13.5 + - - +
786A ASN* 3.3 5.3 + - - +
787A HIS* 1.3 70.5 - - - +
789A GLU* 1.3 59.3 + - - +
791A VAL* 2.8 27.7 + - + +
792A LYS* 2.9 41.5 + - + +
822A GLU* 3.7 38.1 - - + +
823A VAL* 4.4 14.6 - - + +
826A TYR* 4.1 22.0 - - + -
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Residues in contact with GLU 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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8A SO4 2.8 24.8 + - - +
755A VAL* 3.9 23.3 - - + +
788A LEU* 1.3 76.1 - - - +
790A ALA* 1.3 54.9 + - - +
792A LYS* 3.3 32.8 + - - +
793A TYR* 2.9 27.5 + - - +
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Residues in contact with ALA 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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8A SO4 4.2 0.8 + - - -
750A ALA 4.5 2.0 - - - +
753A GLY* 3.9 33.4 - - - +
755A VAL* 4.1 9.2 - - + +
758A CYS* 4.9 13.2 - - - -
782A ALA* 4.3 9.0 - - + -
787A HIS* 3.2 11.0 + - + +
788A LEU 3.2 0.6 - - - -
789A GLU* 1.3 76.9 - - - +
791A VAL* 1.3 64.4 + - - +
793A TYR* 3.9 5.0 - - - +
794A LEU* 3.1 32.2 + - + +
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Residues in contact with VAL 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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779A LEU* 4.0 14.7 - - + +
782A ALA* 3.7 28.7 - - + +
783A ALA* 3.8 9.9 - - - +
787A HIS 3.0 21.9 + - - +
788A LEU* 2.8 15.3 + - + +
790A ALA* 1.3 75.9 - - - +
792A LYS* 1.3 66.5 + - - +
794A LEU* 3.9 1.6 - - - +
795A ILE* 3.0 27.2 + - + +
823A VAL* 4.3 10.3 - - + -
826A TYR* 4.7 5.8 - - + -
827A LEU* 3.9 31.2 - - + -
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Residues in contact with LYS 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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788A LEU* 2.9 35.0 + - + +
789A GLU* 3.4 30.7 + - - +
790A ALA 3.3 0.2 - - - -
791A VAL* 1.3 74.7 - - - +
793A TYR* 1.3 57.3 + - - +
795A ILE* 3.0 1.2 + - - +
796A LYS* 2.6 41.4 + - + +
826A TYR* 3.2 51.4 - - + +
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Residues in contact with TYR 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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755A VAL* 3.7 23.6 - - + -
758A CYS* 4.4 12.1 - - + -
759A HIS* 3.5 48.1 + + + -
762A VAL* 2.9 40.0 - - + +
763A GLN* 4.5 0.5 + - - -
789A GLU 2.9 17.5 + - - +
790A ALA* 3.9 4.3 - - - +
791A VAL 3.4 0.2 - - - -
792A LYS* 1.3 78.7 - - - +
794A LEU* 1.3 81.4 + - + +
796A LYS* 3.1 11.4 + - - -
797A ALA* 3.0 36.6 - - + +
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Residues in contact with LEU 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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746A LEU* 4.5 12.8 - - + -
750A ALA* 4.2 9.6 - - + -
758A CYS* 5.0 4.9 - - - -
768A ILE* 3.7 28.8 - - + +
778A PRO* 3.8 33.9 - - + +
779A LEU* 3.8 17.7 - - + +
782A ALA* 4.0 10.8 - - + -
790A ALA* 3.1 19.8 + - + +
791A VAL 3.9 3.1 - - - +
793A TYR* 1.3 92.6 - - + +
795A ILE* 1.3 60.8 + - - +
797A ALA* 3.4 6.2 + - - +
798A GLY 3.5 0.5 + - - -
799A ALA* 2.8 37.1 + - + +
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Residues in contact with ILE 795 (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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779A LEU* 3.9 11.7 - - + -
791A VAL* 3.0 21.4 + - + +
792A LYS 3.5 1.6 - - - +
794A LEU* 1.3 73.3 - - - +
796A LYS* 1.3 54.8 + - - +
797A ALA 2.6 18.1 + - - -
798A GLY* 3.1 11.4 + - - -
799A ALA* 4.0 6.9 + - - +
801A VAL* 4.2 17.3 - - + -
826A TYR* 3.5 37.7 - - + +
827A LEU* 3.3 34.3 - - + -
830A ASN 4.4 10.8 - - - +
831A GLY* 4.4 10.5 - - - -
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Residues in contact with LYS 796 (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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792A LYS* 2.6 21.8 + - + +
793A TYR* 3.1 9.5 - - - +
795A ILE* 1.3 71.0 - - - +
797A ALA* 1.3 56.6 + - - +
826A TYR* 4.4 9.6 - - - +
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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