Contacts of the helix formed by residues 787 - 800 (chain B) in PDB entry 3V53
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 GLU 787 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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776B ASN* 5.3 0.4 + - - -
779B ILE* 4.3 17.8 - - + +
783B ILE* 5.1 11.2 - - + +
785B GLU* 3.6 7.6 + - - +
786B GLU* 1.3 76.3 - - - +
788B ALA* 1.3 65.0 + - - +
789B THR* 3.2 28.0 + - - +
790B LEU* 3.2 35.8 + - + +
791B VAL* 3.5 10.8 - - - +
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Residues in contact with ALA 788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772B ARG* 4.1 7.8 + - - +
776B ASN* 5.7 0.2 - - - -
786B GLU* 4.1 16.3 - - + +
787B GLU* 1.3 72.8 + - - +
789B THR* 1.3 60.3 + - + +
790B LEU 3.3 0.2 - - - -
791B VAL* 3.3 9.4 + - - +
792B ASP* 2.9 43.7 + - - +
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Residues in contact with THR 789 (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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787B GLU* 3.2 24.1 + - - +
788B ALA* 1.3 75.0 - - + +
790B LEU* 1.3 72.1 + - - +
792B ASP* 4.0 6.4 - - - +
793B PHE* 3.0 24.8 + - - +
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Residues in contact with LEU 790 (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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779B ILE* 3.9 32.3 - - + -
783B ILE* 4.6 10.1 - - + -
787B GLU* 3.2 31.4 + - + +
789B THR* 1.3 87.0 + - - +
791B VAL* 1.3 60.8 + - - +
793B PHE* 3.7 8.3 - - + +
794B VAL* 3.3 30.8 + - + +
811B VAL* 5.2 4.9 - - + -
814B VAL* 3.7 38.8 - - + -
815B LEU* 4.4 11.9 - - + -
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Residues in contact with VAL 791 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772B ARG* 3.7 40.2 - - + +
775B ILE* 3.9 18.4 - - + -
776B ASN* 4.0 29.4 - - - +
779B ILE* 4.1 13.7 - - + -
787B GLU 3.5 16.4 - - - +
788B ALA* 3.3 8.7 + - - +
789B THR 3.2 0.4 - - - -
790B LEU* 1.3 74.8 - - - +
792B ASP* 1.3 60.6 + - - +
794B VAL* 3.1 2.9 + - - +
795B CYS* 2.8 44.8 + - - -
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Residues in contact with ASP 792 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A ALA* 5.4 4.6 - - - +
751A GLU* 4.2 14.4 - - - +
772B ARG* 2.6 29.9 + - - -
788B ALA* 2.9 28.7 + - - +
789B THR* 4.0 6.5 - - - +
791B VAL* 1.3 76.1 - - - +
793B PHE* 1.3 57.0 + - - +
795B CYS* 3.7 6.3 - - - +
796B SER* 3.0 31.7 + - - -
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Residues in contact with PHE 793 (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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789B THR 3.0 18.8 + - - +
790B LEU* 3.7 9.9 - - + +
791B VAL 3.1 0.2 - - - -
792B ASP* 1.3 74.1 - - - +
794B VAL* 1.3 75.2 + - + +
796B SER* 2.8 23.2 + - - -
797B LYS* 3.2 40.8 + - + +
807B ILE* 6.0 0.2 - - - -
810B ASP* 3.6 40.4 - - + -
811B VAL* 4.3 13.5 - - + -
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Residues in contact with VAL 794 (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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775B ILE* 4.0 16.4 - - + -
779B ILE* 5.4 2.5 - - + -
790B LEU* 3.3 16.5 + - + +
791B VAL 3.1 6.1 + - - +
793B PHE* 1.3 80.2 - - + +
795B CYS* 1.3 66.6 + - - +
797B LYS* 3.1 8.2 + - - +
798B VAL* 3.0 22.1 + - + +
807B ILE* 6.0 4.3 - - + -
811B VAL* 3.9 27.6 - - + -
822B PHE* 4.0 18.4 - - + -
823B ILE* 5.1 3.8 - - + -
826B MET* 3.6 33.9 - - + -
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Residues in contact with CYS 795 (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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767B MET* 4.2 19.2 - - + +
772B ARG* 3.5 39.3 - - - +
775B ILE* 3.8 19.1 - - - -
791B VAL* 2.8 28.6 + - - +
792B ASP* 3.7 7.2 - - - +
794B VAL* 1.3 74.7 - - - +
796B SER* 1.3 51.5 + - - +
798B VAL* 3.0 8.0 + - - +
799B MET* 2.8 38.4 + - + +
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Residues in contact with SER 796 (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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792B ASP 3.0 16.9 + - - -
793B PHE* 2.8 23.0 + - - -
795B CYS* 1.3 75.1 - - - +
797B LYS* 1.3 58.4 + - - +
799B MET* 3.1 11.2 + - - +
800B ALA* 2.7 34.4 + - - +
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Residues in contact with LYS 797 (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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793B PHE* 3.2 46.2 + - + +
794B VAL* 3.1 11.7 + - - +
796B SER* 1.3 82.1 + - - +
798B VAL* 1.3 65.1 + - + +
800B ALA* 3.1 14.0 + - - +
802B SER* 3.0 54.5 + - - +
806B SER* 5.1 3.7 + - - +
807B ILE* 5.0 14.8 - - + -
810B ASP* 4.0 15.0 - - - +
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Residues in contact with VAL 798 (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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759B TRP* 3.3 22.2 - - + -
762B VAL* 4.3 2.0 - - + -
767B MET* 3.7 22.2 - - + -
771B ILE* 5.2 0.4 - - + -
794B VAL* 3.0 14.3 + - + +
795B CYS* 3.0 8.8 + - - +
797B LYS* 1.3 75.1 - - + +
799B MET* 1.3 59.7 + - - +
801B HIS* 3.1 16.3 + - - +
802B SER 4.9 0.7 - - - +
826B MET* 3.3 35.0 - - + -
827B TRP* 5.2 5.4 - - + -
830B LEU* 3.9 33.7 - - + -
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Residues in contact with MET 799 (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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762B VAL* 3.3 35.0 - - + +
763B ASP* 4.6 7.0 - - - +
764B SER* 5.1 3.4 - - - -
767B MET* 3.5 42.2 - - + -
795B CYS* 2.8 19.2 + - + +
796B SER* 3.1 14.3 + - - +
798B VAL* 1.3 76.8 - - - +
800B ALA* 1.3 57.4 + - - +
801B HIS* 3.2 18.7 + - - +
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Residues in contact with ALA 800 (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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796B SER 2.7 14.9 + - - +
797B LYS* 3.1 15.2 + - - +
799B MET* 1.3 74.9 - - - +
801B HIS* 1.3 73.3 + - - +
802B SER* 3.4 9.8 + - - +
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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