Contacts of the helix formed by residues 793 - 805 (chain B) in PDB entry 6V3O
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 GLY 793 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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609B GLY* 6.1 0.2 - - - -
611B LEU* 5.6 0.2 - - - -
724B ALA* 3.3 41.8 - - - +
727B GLU* 3.9 15.4 - - - +
728B TYR 4.5 0.7 - - - -
791B TRP* 5.1 0.4 - - - -
792B LEU* 1.3 81.2 - - - +
794B VAL* 1.3 61.3 + - - +
795B GLY 3.5 2.8 - - - +
796B ALA* 3.8 3.1 + - - +
797B ALA* 3.3 16.1 + - - +
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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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610B ARG* 5.5 0.9 - - + -
611B LEU* 3.9 31.4 - - + +
790B VAL 4.8 1.8 - - - +
791B TRP* 3.0 23.6 + - - +
792B LEU 4.7 1.8 - - - +
793B GLY* 1.3 76.8 - - - +
795B GLY* 1.3 59.8 + - - +
797B ALA* 3.3 5.9 + - - +
798B PHE* 3.0 64.1 + - + -
829B LEU* 3.9 27.8 - - + -
867B THR* 3.9 11.7 - - + -
871B LEU* 5.9 0.7 - - + -
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Residues in contact with GLY 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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793B GLY 3.5 0.8 - - - +
794B VAL* 1.3 79.2 - - - +
796B ALA* 1.3 61.5 + - - +
798B PHE* 3.4 5.6 + - - +
799B LYS* 3.0 26.4 + - - +
866B GLU* 4.7 12.6 - - - -
867B THR* 3.4 36.7 + - - +
870B LEU* 4.7 3.8 - - - +
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Residues in contact with ALA 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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723B VAL* 3.7 13.2 - - + +
727B GLU* 3.7 42.6 + - + +
793B GLY 3.8 3.2 + - - +
794B VAL 3.4 0.4 - - - -
795B GLY* 1.3 74.6 - - - +
797B ALA* 1.3 57.7 + - - +
799B LYS* 3.7 8.3 - - - +
800B PHE* 2.9 31.7 + - - +
866B GLU* 4.8 5.2 + - - +
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Residues in contact with ALA 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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611B LEU* 3.8 21.8 - - + -
720B MET* 3.5 39.0 - - + +
723B VAL* 3.9 12.0 - - - +
724B ALA* 4.1 1.8 - - + -
793B GLY 3.3 15.9 + - - +
794B VAL 3.3 4.7 + - - +
795B GLY 3.2 0.6 - - - -
796B ALA* 1.3 78.9 - - - +
798B PHE* 1.3 63.3 + - - +
800B PHE* 3.3 3.3 + - - +
801B ALA* 3.1 18.0 + - - +
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Residues in contact with PHE 798 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B LEU* 4.7 11.0 - - + -
720B MET* 3.3 24.7 - - + -
794B VAL* 3.0 44.8 + - + +
795B GLY* 3.9 3.8 - - - +
797B ALA* 1.3 75.7 - - + +
799B LYS* 1.3 64.3 + - - +
801B ALA* 3.2 4.0 + - - +
802B ILE* 3.0 30.0 + - + +
822B PHE* 4.4 10.3 - + - -
826B LEU* 3.4 35.7 - - + -
867B THR 4.9 2.7 - - - -
870B LEU* 4.2 15.7 - - + -
871B LEU* 4.1 27.6 - - + -
874B ILE* 3.7 28.9 - - + -
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Residues in contact with LYS 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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795B GLY 3.0 18.2 + - - +
796B ALA* 3.7 6.7 - - - +
798B PHE* 1.3 75.9 - - - +
800B PHE* 1.3 64.3 + - - +
802B ILE* 3.4 3.4 + - - +
803B ASP* 3.0 51.2 + - - +
866B GLU* 5.2 10.3 - - - +
870B LEU* 4.0 16.5 - - + +
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Residues in contact with PHE 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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716B LEU* 5.8 1.1 - - + -
719B GLU* 3.9 31.0 - - + -
720B MET* 4.9 2.0 - - + -
722B VAL* 6.0 1.1 - - + -
723B VAL* 3.6 35.0 - - + -
796B ALA 2.9 18.1 + - - +
797B ALA 3.6 5.8 - - - +
799B LYS* 1.3 75.4 - - - +
801B ALA* 1.3 64.3 + - + +
803B ASP* 3.9 4.5 - - - +
804B LYS* 3.0 61.3 + - + +
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Residues in contact with ALA 801 (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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716B LEU* 4.1 21.1 - - + -
720B MET* 3.7 28.0 - - + -
797B ALA 3.1 6.4 + - - +
798B PHE 3.7 6.3 - - - +
800B PHE* 1.3 81.6 - - + +
802B ILE* 1.3 66.5 + - - +
804B LYS* 3.4 6.4 + - - -
805B ASP 3.6 0.3 - - - +
808B ASN* 2.9 32.0 + - + +
812B LEU* 4.1 10.3 - - + -
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Residues in contact with ILE 802 (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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798B PHE* 3.0 19.2 + - + +
799B LYS* 3.9 6.1 - - - +
801B ALA* 1.3 74.4 - - - +
803B ASP* 1.3 66.9 + - - +
805B ASP 3.1 22.9 - - - +
806B VAL* 4.2 5.2 + - - +
808B ASN* 4.6 1.1 - - - -
809B PHE* 3.6 51.4 - - + +
812B LEU* 3.7 16.6 - - + -
870B LEU* 4.9 9.4 - - + -
874B ILE* 5.1 3.4 - - + -
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Residues in contact with ASP 803 (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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799B LYS* 3.0 47.5 + - - +
800B PHE* 4.0 5.1 - - - +
802B ILE* 1.3 84.5 - - - +
804B LYS* 1.3 64.3 + - - +
805B ASP* 3.5 0.7 + - - -
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Residues in contact with LYS 804 (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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715B LYS* 4.8 6.7 - - - +
716B LEU* 5.6 0.7 - - + -
719B GLU* 3.4 37.5 + - - +
800B PHE* 3.0 42.3 + - + +
801B ALA* 3.8 6.1 - - - +
802B ILE 3.3 0.4 - - - -
803B ASP* 1.3 78.8 - - - +
805B ASP* 1.3 61.1 + - + +
808B ASN* 4.1 11.0 - - - +
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Residues in contact with ASP 805 (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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801B ALA 3.6 1.8 + - - -
802B ILE 3.1 12.5 - - - +
803B ASP 3.3 2.1 - - - -
804B LYS* 1.3 83.2 - - + +
806B VAL* 1.3 84.8 + - - +
807B ARG* 3.0 52.7 + - - +
808B ASN* 3.0 35.9 + - - +
809B PHE 4.4 0.5 + - - -
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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