Contacts of the strand formed by residues 789 - 799 (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 SER 789 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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678B PRO* 3.8 3.1 - - - -
788B ASN* 1.3 74.6 - - - +
790B GLY* 1.3 59.3 + - - +
851B GLN* 3.3 9.5 - - - +
852B SER 2.7 35.5 + - - -
853B GLU* 4.9 0.4 - - - +
854B LYS 2.7 28.0 + - - -
856B PRO* 3.9 17.7 - - - +
859B LEU* 4.1 6.9 - - - +
958B VAL 3.2 14.4 - - - -
960B ALA* 3.6 13.3 - - - +
963B MET* 4.1 5.8 - - - -
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Residues in contact with GLY 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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678B PRO* 3.7 23.0 - - - +
679B HIS 4.3 1.1 - - - -
682B ALA* 4.5 2.7 - - - -
789B SER* 1.3 74.8 - - - +
791B ILE* 1.3 63.1 + - - +
850B ILE 3.4 10.1 - - - -
851B GLN* 4.3 1.6 - - - -
856B PRO* 4.3 2.9 - - - +
859B LEU* 5.7 0.2 - - - -
956B VAL 4.4 0.2 - - - -
957B HIS* 3.7 1.0 - - - -
958B VAL* 2.7 43.6 + - - +
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Residues in contact with ILE 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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679B HIS* 5.1 1.4 - - - +
682B ALA* 4.0 6.0 - - - +
790B GLY* 1.3 75.0 - - - +
792B GLU* 1.3 63.4 + - - +
793B ILE* 3.7 23.1 - - + -
848B PHE 3.6 1.4 - - - +
849B ILE* 3.4 6.3 - - - +
850B ILE* 3.0 51.4 + - + +
856B PRO* 4.6 8.7 - - + +
859B LEU* 4.1 19.1 - - + -
860B GLU* 3.6 39.5 - - + +
956B VAL 3.2 15.9 - - - +
957B HIS* 3.7 13.2 - - + +
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Residues in contact with GLU 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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682B ALA* 3.7 17.8 - - + +
683B MET* 3.1 34.7 - - - +
686B LEU* 3.3 31.2 - - + +
791B ILE* 1.3 75.1 - - - +
793B ILE* 1.3 71.2 + - - +
794B TYR 4.2 0.2 - - - -
838B ARG* 4.3 0.4 - - - -
847B ARG* 2.7 38.1 + - + +
848B PHE 3.3 8.5 - - - +
849B ILE* 3.8 14.6 - - + -
954B VAL 4.2 0.2 - - - +
955B SER* 3.4 3.1 - - - -
956B VAL* 2.9 35.4 + - + +
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Residues in contact with ILE 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 ILE* 3.7 31.6 - - + -
792B GLU* 1.3 74.4 - - - +
794B TYR* 1.3 63.7 + - - +
795B TYR* 3.3 36.7 - - + +
846B LEU 3.5 1.0 - - - +
847B ARG* 3.1 9.4 - - - +
848B PHE* 2.8 37.6 + - + +
850B ILE* 6.1 0.2 - - + -
860B GLU* 4.0 20.2 - - - +
863B VAL* 3.8 38.8 - - + -
864B GLU* 6.5 0.2 - - + -
953B LYS* 3.8 13.9 - - - -
954B VAL 3.7 4.3 - - - +
955B SER* 4.4 0.7 - - - +
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Residues in contact with TYR 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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686B LEU* 4.0 25.4 - - + -
690B MET* 4.2 19.3 - - + -
768B GLU* 2.8 28.7 + - - -
792B GLU 4.2 0.2 - - - -
793B ILE* 1.3 74.7 - - - +
795B TYR* 1.3 65.6 + - - +
796B GLN* 3.8 23.0 + - + +
838B ARG* 3.7 38.6 + - + -
843B ILE 4.6 0.2 - - - -
844B GLN* 3.3 21.7 + - - -
845B GLY* 3.8 16.8 - - - -
846B LEU 3.8 7.9 - - - -
847B ARG* 4.6 1.3 - - + -
952B HIS 3.5 1.0 - - - +
953B LYS* 3.2 5.4 - - - +
954B VAL* 2.7 59.4 + - + +
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Residues in contact with TYR 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 ILE* 3.3 24.0 - - + +
794B TYR* 1.3 71.8 - - - +
796B GLN* 1.3 62.2 + - - +
797B THR* 4.4 2.4 - - - +
845B GLY* 3.2 3.5 - - - -
846B LEU* 2.8 56.8 + - + +
848B PHE* 4.0 20.6 - + - -
863B VAL* 4.3 6.6 - - + +
864B GLU* 2.5 24.6 + - - +
867B LEU* 3.8 10.7 - - + +
943B MET 5.6 1.6 - - - +
944B LEU* 3.7 26.5 - - + -
951B ARG* 3.3 39.9 - - + -
952B HIS 3.2 6.7 - - - +
953B LYS* 3.4 31.0 + - + -
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Residues in contact with GLN 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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690B MET* 5.3 1.2 - - - -
768B GLU* 3.2 21.4 + - - +
769B VAL 3.2 21.0 + - - -
771B LEU* 3.2 41.3 + - + +
794B TYR* 3.7 25.2 - - + +
795B TYR* 1.3 72.8 - - - +
797B THR* 1.3 62.8 + - - +
843B ILE* 3.5 7.8 - - + +
844B GLN 3.7 7.9 - - - +
943B MET* 4.4 4.2 - - - +
944B LEU* 5.9 0.2 - - - +
950B ARG 4.7 0.2 - - - +
952B HIS* 2.9 45.1 + - + +
1005B PHE* 3.3 23.5 - - + -
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Residues in contact with THR 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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795B TYR 3.7 0.2 + - - -
796B GLN* 1.3 78.5 - - - +
798B ASP* 1.3 71.0 + - - +
804B GLU* 4.1 16.3 - - - +
808B LEU* 4.7 7.7 - - + +
844B GLN* 2.8 33.8 + - - +
845B GLY* 4.0 11.5 - - - -
939B PHE* 4.0 24.5 - - + -
943B MET* 3.2 30.6 - - + +
944B LEU* 4.3 19.1 - - + -
950B ARG* 4.3 2.1 + - - -
952B HIS* 4.2 7.4 - - - -
1005B PHE* 5.9 0.4 - - - -
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Residues in contact with ASP 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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797B THR* 1.3 82.8 + - - +
799B MET* 1.3 82.1 + - - +
804B GLU* 3.7 21.1 + - + +
843B ILE* 4.1 8.2 - - - +
844B GLN* 3.3 25.4 + - - +
950B ARG* 4.8 14.4 + - - +
1005B PHE* 3.3 25.7 - - - -
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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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798B ASP* 1.3 91.4 + - - +
800B GLN* 1.3 77.8 + - - +
801B SER* 3.4 5.8 + - - -
804B GLU* 3.6 14.2 - - - +
842B GLY 3.5 8.7 - - - +
843B ILE* 3.7 19.8 - - + +
1005B PHE* 4.1 11.9 - - + -
1006B PRO* 4.0 33.2 - - + +
1007B LEU 4.4 3.1 - - - +
1008B VAL* 3.8 24.5 - - + -
1009B LYS* 5.2 2.0 - - + +
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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