Contacts of the strand formed by residues 785 - 794 (chain B) in PDB entry 6CNB
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 CYS 785 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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710B ILE* 3.3 25.1 - - + -
726B TYR* 5.8 2.9 - - + -
727B LEU 3.9 4.9 - - - +
729B THR* 4.6 0.8 + - - -
783B GLY 4.1 0.7 - - - -
784B ARG* 1.3 77.1 - - - +
786B GLU* 1.3 70.3 + - - +
787B THR* 5.2 1.6 - - - +
903B ASN* 2.9 28.2 - - - +
904B ARG* 2.9 27.7 + - + +
1026B LYS* 2.6 44.9 - - - +
1030B MET* 4.4 3.8 - - + -
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Residues in contact with GLU 786 (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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718B PHE* 5.0 0.9 - - - -
726B TYR* 3.8 6.2 - - - +
727B LEU* 2.9 54.7 + - + +
729B THR* 4.3 10.5 + - - +
785B CYS* 1.3 82.6 - - - +
787B THR* 1.3 72.4 + - - +
788B ARG* 3.4 19.8 + - + +
901B ARG* 5.6 1.1 - - + -
902B GLN 3.2 9.4 - - - +
903B ASN* 4.1 8.3 - - + -
904B ARG 5.2 0.4 - - - -
93C GLN* 3.0 18.3 - - - +
95C GLU* 2.8 28.9 - - - +
96C VAL* 3.8 10.9 - - - +
1J MET* 5.4 4.0 - - - +
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Residues in contact with THR 787 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724B LEU* 4.9 5.4 - - + -
725B LEU 3.8 6.7 - - - +
726B TYR* 3.3 31.9 - - + +
785B CYS* 5.2 0.7 - - - +
786B GLU* 1.3 83.0 + - - +
788B ARG* 1.3 74.3 + - - +
789B ARG* 4.5 16.4 - - + +
900B LEU 4.2 0.4 - - - -
901B ARG* 3.1 27.0 - - - +
902B GLN* 2.9 21.5 + - + +
904B ARG* 4.0 26.6 + - - +
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Residues in contact with ARG 788 (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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717B GLN 5.7 3.4 - - - -
718B PHE* 4.1 25.5 + - - +
720B ARG 5.9 2.5 - - - -
722B ASP 4.6 3.3 - - - +
723B THR 3.4 1.0 - - - +
724B LEU* 3.3 5.9 - - - +
725B LEU* 2.8 54.1 + - + +
727B LEU* 3.4 27.2 - - + +
786B GLU* 3.4 9.2 + - - +
787B THR* 1.3 83.0 - - - +
789B ARG* 1.3 63.3 + - - +
882B ASP* 2.7 31.9 + - - +
899B LEU* 3.6 17.5 - - + +
900B LEU 3.3 5.4 - - - +
901B ARG* 4.2 9.8 - - + +
93C GLN* 3.0 39.7 + - - +
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Residues in contact with ARG 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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722B ASP 4.0 2.2 - - - -
723B THR 3.1 8.5 - - - +
724B LEU* 3.1 34.4 - - + +
787B THR* 4.5 12.6 - - + +
788B ARG* 1.3 80.1 - - - +
790B LYS* 1.3 65.1 + - - +
791B THR* 5.8 1.6 - - - +
873B TYR* 6.1 5.2 - - - -
899B LEU* 2.9 8.5 - - - +
900B LEU* 2.9 43.8 + - + +
902B GLN* 5.4 3.8 - - - +
904B ARG* 4.1 8.5 - - - +
1033B ASP* 3.8 24.5 + - - -
1054B ARG* 5.4 8.9 - - - +
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Residues in contact with LYS 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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122B ASP* 5.6 1.2 + - - -
721B ILE* 4.0 19.3 - - + +
722B ASP* 3.1 26.9 + - - +
723B THR* 3.1 38.1 + - - +
789B ARG* 1.3 78.6 - - - +
791B THR* 1.3 64.7 + - - +
792B THR* 4.1 26.6 + - - +
897B LYS* 4.4 22.3 - - + +
898B VAL 3.4 8.7 - - - +
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Residues in contact with THR 791 (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 ARG* 4.4 1.8 + - - +
790B LYS* 1.3 75.6 + - - +
792B THR* 1.3 69.5 + - - +
793B THR* 3.8 15.3 + - + +
842B TYR* 2.6 46.3 + - + +
871B VAL* 4.7 8.5 - - + -
896B ILE 4.1 0.2 - - - +
897B LYS* 3.6 3.8 - - - -
898B VAL* 2.9 34.9 + - + +
900B LEU* 4.9 4.2 - - - +
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Residues in contact with THR 792 (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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122B ASP* 4.3 8.4 + - - +
790B LYS* 4.0 19.4 + - - +
791B THR* 1.3 77.2 - - - +
793B THR* 1.3 68.8 + - - +
794B VAL* 4.1 2.5 + - - +
895B LEU* 3.7 20.1 - - - +
896B ILE 3.8 4.0 - - - -
897B LYS* 4.3 18.8 - - - +
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Residues in contact with THR 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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791B THR* 4.1 14.8 - - + +
792B THR* 1.3 78.6 - - - +
794B VAL* 1.3 63.6 + - - +
795B LEU* 3.7 4.3 + - - +
843B ILE* 3.2 45.8 - - + +
845B LYS* 4.8 20.2 - - + +
871B VAL* 4.3 9.6 - - + -
895B LEU* 4.1 1.8 - - - -
896B ILE* 2.9 35.8 + - - +
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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
----------------------------------------------------------
792B THR* 4.1 4.2 + - - +
793B THR* 1.3 74.3 - - - +
795B LEU* 1.3 72.2 + - - +
796B LYS* 4.0 19.9 + - + +
804B ASP* 4.0 1.9 - - - +
845B LYS* 3.7 19.6 + - - +
893B GLN* 3.6 29.2 - - + +
894B ALA 3.9 5.6 - - - +
895B LEU* 3.9 16.1 - - + +
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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