Contacts of the strand formed by residues 775 - 782 (chain B) in PDB entry 3H44
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 775 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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771B LEU* 6.1 0.2 - - - -
772B PRO* 2.9 32.9 + - - -
773B ASP 3.4 1.4 + - - -
774B ARG* 1.3 78.6 - - - +
776B TRP* 1.3 62.6 + - - +
777B PHE* 4.2 6.7 - - - -
951B ARG* 3.4 3.2 + - - +
953B LYS* 3.2 27.3 + - - +
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Residues in contact with TRP 776 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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774B ARG 3.9 1.9 + - - +
775B GLY* 1.3 74.6 - - - +
777B PHE* 1.3 73.5 + - - +
778B VAL* 3.5 18.5 - - + +
860B GLU* 3.6 21.8 - - + -
953B LYS* 3.1 46.6 - - + +
955B SER* 2.8 19.6 + - - -
957B HIS* 5.2 1.3 - - - -
986B LEU* 4.0 28.9 - - + -
987B PRO* 3.0 47.3 - - + -
988B GLN 5.3 1.1 - - - +
989B PRO* 3.4 27.2 - - + +
990B GLU* 2.9 26.9 + - - +
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Residues in contact with PHE 777 (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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771B LEU* 4.5 11.0 - - + -
772B PRO* 3.5 41.7 - - + -
775B GLY* 4.3 10.8 - - - -
776B TRP* 1.3 80.0 - - - +
778B VAL* 1.3 62.9 + - - +
953B LYS 3.0 12.2 + - - -
954B VAL* 3.3 11.4 - - + -
955B SER 2.9 25.0 + - - -
990B GLU* 3.2 46.9 - - + -
992B ILE* 3.6 21.5 - - + -
998B PHE* 3.8 24.9 - + + -
1002B LEU* 4.5 14.6 - - + -
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Residues in contact with VAL 778 (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 TRP* 3.5 28.7 - - + +
777B PHE* 1.3 78.5 - - - +
779B TYR* 1.3 72.7 + - - +
780B GLN* 4.5 6.5 - - + -
955B SER* 3.2 11.7 - - - +
957B HIS* 4.0 29.4 - - + +
989B PRO* 3.6 24.5 - - + -
990B GLU 3.0 6.8 + - - +
991B VAL* 3.4 15.0 - - + +
992B ILE* 3.1 23.4 + - - +
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Residues in contact with TYR 779 (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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685B TYR* 3.8 32.3 - + + -
689B LEU* 3.7 27.4 - - + -
778B VAL* 1.3 74.5 - - - +
780B GLN* 1.3 67.2 + - - +
781B GLN* 2.6 45.2 + - + -
955B SER 3.0 7.0 + - - +
956B VAL* 3.5 8.5 - - + -
957B HIS 3.1 22.0 + - - -
991B VAL* 5.9 0.2 - - - -
992B ILE* 3.8 37.5 - - + +
993B GLN 5.2 2.7 - - - -
994B ASN* 5.2 3.4 - - - -
995B MET* 3.2 34.7 - - + +
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Residues in contact with GLN 780 (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 VAL* 4.5 7.9 - - + -
779B TYR* 1.3 86.1 - - - +
781B GLN* 1.3 70.6 + - - +
956B VAL* 5.7 0.4 - - - -
957B HIS* 3.3 25.0 - - + +
959B LEU* 4.0 29.9 - - - +
964B ASP 5.5 2.0 + - - -
991B VAL* 5.5 10.5 - - + +
992B ILE 5.0 2.0 + - - -
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Residues in contact with GLN 781 (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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685B TYR* 3.6 43.4 + - + +
779B TYR* 2.6 37.2 + - + -
780B GLN* 1.3 83.0 - - - +
782B ARG* 1.3 60.8 + - - +
956B VAL* 6.0 0.2 - - - +
957B HIS 3.0 6.5 + - - +
958B VAL* 3.2 5.5 - - + -
959B LEU* 2.7 37.3 + - - +
995B MET* 5.3 0.2 - - - +
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Residues in contact with ARG 782 (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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681B HIS* 5.1 1.7 + - - -
685B TYR* 4.9 4.0 + - - -
781B GLN* 1.3 84.6 + - - +
783B ASN* 1.3 72.2 + - - +
784B GLU* 3.9 20.2 + - + +
958B VAL* 4.1 3.1 - - - +
959B LEU* 3.4 13.9 - - + +
960B ALA 3.7 6.1 + - - -
961B ARG* 3.5 20.9 + - - -
962B GLU 4.1 0.8 - - - -
963B MET* 2.5 45.1 + - - +
964B ASP 3.6 14.8 + - - -
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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