Contacts of the helix formed by residues 777 - 785 (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 THR 777 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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747A HIS* 3.9 2.8 - - - -
769A ASP* 4.0 24.0 - - + +
770A THR 3.8 2.2 - - - +
771A CYS* 4.5 8.7 - - - -
776A ARG* 1.3 77.1 - - - +
778A PRO* 1.3 76.0 - - - +
779A LEU* 3.8 10.2 + - - +
780A MET* 2.9 39.9 + - + +
781A GLU* 3.1 10.9 + - - +
800A LEU 4.7 2.7 + - - -
803A PRO* 3.5 35.3 - - + +
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Residues in contact with PRO 778 (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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744A SER* 5.1 0.2 - - - +
746A LEU* 3.8 38.8 - - + +
747A HIS* 3.8 20.6 - - + +
750A ALA* 3.3 24.7 - - + +
767A ASN 5.1 0.2 - - - +
768A ILE 3.7 17.5 - - - +
770A THR* 3.6 15.9 - - - +
777A THR* 1.3 85.9 - - - +
779A LEU* 1.3 61.9 + - - +
781A GLU* 3.0 5.2 + - + +
782A ALA* 2.9 21.1 + - - +
794A LEU* 3.9 9.9 - - + -
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Residues in contact with LEU 779 (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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768A ILE 5.4 1.2 + - - +
769A ASP* 6.1 0.2 - - - +
777A THR* 3.0 9.1 - - - +
778A PRO* 1.3 80.0 - - - +
780A MET* 1.3 57.7 + - - +
782A ALA* 3.2 2.8 + - - +
783A ALA* 2.8 31.9 + - + +
791A VAL* 4.0 26.9 - - + +
794A LEU* 3.8 16.2 - - + +
795A ILE* 3.9 21.5 - - + -
799A ALA* 4.1 13.7 - - + -
800A LEU 3.5 15.0 - - - +
801A VAL* 3.1 37.9 - - + -
811A CYS* 4.0 18.6 - - + -
827A LEU* 4.8 2.0 - - + -
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Residues in contact with MET 780 (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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775A GLN 4.2 4.3 - - - +
776A ARG* 3.6 22.4 - - + +
777A THR* 2.9 31.1 + - + +
779A LEU* 1.3 78.6 - - - +
781A GLU* 1.3 64.0 + - - +
783A ALA 3.1 0.3 + - - -
784A GLU* 3.0 28.8 + - - +
803A PRO* 3.1 50.9 - - + +
804A LYS 3.8 14.1 - - - +
805A ASP* 3.9 7.0 - - - +
809A SER 4.1 4.3 - - - +
810A THR* 4.8 0.4 - - - -
811A CYS* 4.0 28.7 - - + +
814A LEU* 4.1 17.1 - - + +
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Residues in contact with GLU 781 (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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743A ARG* 4.1 10.7 + - - -
747A HIS* 3.7 33.3 - - - +
750A ALA* 4.1 0.2 - - + -
751A GLU* 3.4 46.7 - - + +
772A SER* 5.3 1.9 - - - -
776A ARG* 2.9 46.2 + - - +
777A THR 3.1 6.8 + - - +
778A PRO* 3.0 14.8 + - + +
780A MET* 1.3 78.7 - - - +
782A ALA* 1.3 61.2 + - - +
784A GLU* 4.3 0.4 - - - +
785A ASN* 2.9 32.5 + - - +
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Residues in contact with ALA 782 (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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750A ALA 3.7 21.5 + - - +
778A PRO 2.9 18.0 + - - +
779A LEU* 3.7 3.4 - - - +
781A GLU* 1.3 71.7 - - - +
783A ALA* 1.3 66.7 + - - +
785A ASN 3.6 0.9 + - - -
786A ASN 3.6 2.3 + - - -
787A HIS* 3.1 29.0 + - - +
790A ALA* 4.3 10.8 - - + -
791A VAL* 3.7 16.5 - - + +
794A LEU* 4.0 17.5 - - + -
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Residues in contact with ALA 783 (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* 2.8 17.1 + - + +
780A MET* 3.1 3.6 + - - +
782A ALA* 1.3 76.2 - - - +
784A GLU* 1.3 58.6 + - - +
785A ASN 3.0 0.2 - - - -
786A ASN* 2.8 25.3 + - - -
791A VAL* 3.8 12.7 - - + +
811A CYS* 3.8 32.1 - - + +
815A ALA* 4.4 3.1 - - + -
820A HIS* 3.7 7.1 - - - -
823A VAL* 4.0 20.1 - - + +
827A LEU* 4.4 2.5 - - + -
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Residues in contact with GLU 784 (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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776A ARG* 2.6 34.4 + - - +
780A MET 3.0 13.2 + - - +
781A GLU 4.3 2.5 - - - +
783A ALA* 1.3 77.8 - - - +
785A ASN* 1.3 63.2 + - - +
786A ASN 3.3 0.9 - - - -
814A LEU* 3.7 42.0 - - + +
817A LYS* 4.9 4.9 - - - +
818A LYS* 3.9 35.6 + - + +
820A HIS* 3.1 21.4 + - - -
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Residues in contact with ASN 785 (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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751A GLU* 3.5 33.9 + - - +
776A ARG* 5.9 0.4 - - - +
781A GLU* 2.9 28.6 + - - +
782A ALA 3.6 0.2 + - - -
783A ALA 2.9 1.8 + - - -
784A GLU* 1.3 85.6 + - - +
786A ASN* 1.3 68.9 + - - +
787A HIS* 3.1 35.2 + - + +
820A HIS* 4.2 0.9 - - - -
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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