Contacts of the strand formed by residues 794 - 801 (chain B) in PDB entry 3HW2
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 LYS 794 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780B HIS* 3.3 2.9 - - - -
781B TYR* 2.7 59.4 + - + +
784B GLY 3.7 17.2 + - - +
792B HIS* 3.9 7.0 - - + -
793B TRP* 1.3 74.6 - - - +
795B THR* 1.3 70.4 + - - +
809B PRO* 5.6 6.9 - - - +
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Residues in contact with THR 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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778B MET* 5.1 8.3 - - + -
779B LEU 3.6 9.0 - - - -
780B HIS* 3.3 33.2 - - + +
781B TYR* 3.9 4.9 - - - -
793B TRP 5.6 0.2 - - - +
794B LYS* 1.3 87.2 - - - +
796B CYS* 1.3 61.1 + - - +
809B PRO 3.5 12.0 + - - +
810B ASP* 6.1 0.5 - - - +
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Residues in contact with CYS 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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778B MET* 3.7 9.6 - - - +
779B LEU* 2.9 36.0 + - - +
781B TYR* 3.2 32.5 - - + -
794B LYS 3.8 1.0 + - - -
795B THR* 1.3 71.0 - - - +
797B PHE* 1.3 61.0 + - - +
798B VAL* 3.6 24.2 - - - -
807B GLN* 3.3 24.2 - - + +
808B TYR 3.6 11.4 - - - +
809B PRO* 3.7 6.3 - - + +
810B ASP* 5.2 0.4 - - - -
854B LEU* 4.4 6.3 - - - -
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Residues in contact with PHE 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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776B GLU* 3.2 30.5 - - + -
777B GLY* 3.3 36.1 - - - -
778B MET* 3.7 22.2 - - + -
796B CYS* 1.3 72.6 - - - +
798B VAL* 1.3 58.7 + - - +
799B VAL* 3.3 25.4 - - + -
807B GLN* 3.4 1.9 - - - +
808B TYR* 2.5 63.5 + + - +
809B PRO 4.3 0.6 + - - -
810B ASP 3.8 16.8 - - - -
811B ARG* 4.2 25.8 - - + -
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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
----------------------------------------------------------
776B GLU* 3.2 4.9 - - - -
777B GLY 3.1 30.9 + - - +
779B LEU* 3.7 22.9 - - + -
796B CYS* 3.6 21.5 + - - -
797B PHE* 1.3 80.4 - - - +
799B VAL* 1.3 68.2 + - - +
805B LEU* 3.3 31.9 - - + -
806B TYR 3.4 3.1 - - - +
807B GLN* 3.7 16.6 - - + -
852B LEU* 5.5 2.0 - - + -
854B LEU* 4.6 9.0 - - + -
865B TRP* 3.6 16.9 - - + -
869B LEU* 6.4 0.2 - - + -
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Residues in contact with VAL 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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773B ILE* 3.8 28.5 - - + -
775B LYS 3.5 3.8 - - - +
776B GLU* 3.9 9.6 - - + +
797B PHE* 3.3 35.4 + - + -
798B VAL* 1.3 77.2 - - - +
800B LEU* 1.3 61.7 + - - +
801B SER* 3.9 13.9 - - - +
805B LEU* 3.5 1.4 - - - +
806B TYR* 2.7 50.2 + - + +
808B TYR* 4.1 15.3 - - + +
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Residues in contact with LEU 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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774B THR* 3.2 39.6 + - + +
775B LYS* 2.8 19.9 + - + +
798B VAL 4.3 0.2 - - - -
799B VAL* 1.3 71.5 - - - +
801B SER* 1.3 59.0 + - - +
802B ASN 4.7 4.7 - - - +
803B GLY 4.2 8.1 - - - +
804B ILE 3.3 23.8 - - - +
805B LEU* 4.0 15.5 - - + +
822B MET* 4.1 17.5 - - + -
865B TRP* 4.3 10.2 - - + -
868B HIS* 3.9 39.9 - - + +
869B LEU* 4.1 14.8 - - + +
872B ALA* 4.8 7.0 - - + -
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Residues in contact with SER 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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772B THR 3.7 13.3 + - - -
773B ILE* 4.1 11.8 - - - +
774B THR* 4.5 0.9 - - - +
799B VAL* 3.7 14.6 - - - -
800B LEU* 1.3 72.1 - - - +
802B ASN* 1.3 71.6 + - - +
804B ILE* 2.9 31.9 + - - +
806B TYR* 3.9 19.3 + - - -
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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