Contacts of the strand formed by residues 724 - 731 (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 HIS 724 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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553B ASP* 5.6 0.2 - - - -
554B THR 4.4 3.1 - - - -
555B ALA 3.2 23.4 + - - +
556B MET 3.3 4.0 + - - -
557B SER* 3.8 2.0 - - - -
558B LYS* 3.5 47.0 - - + +
578B PHE* 3.4 5.0 - - - +
579B PHE* 2.9 58.7 + + + -
723B LEU* 1.3 75.8 - - - +
725B ILE* 1.3 71.8 + - - +
726B GLU* 4.7 4.5 + - - -
758B LEU* 4.3 4.9 - - + +
763B LEU* 3.9 40.5 - - + +
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Residues in contact with ILE 725 (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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556B MET* 3.0 18.1 + - + +
557B SER* 3.2 5.8 - - - -
558B LYS 2.9 26.3 + - - +
576B PHE* 3.9 15.7 - - + -
577B GLU 3.4 9.6 - - - +
578B PHE* 3.5 33.9 - - + -
723B LEU* 4.9 6.3 - - + -
724B HIS* 1.3 83.9 - - - +
726B GLU* 1.3 70.1 + - - +
742B MET* 3.8 31.9 - - + -
745B VAL* 4.4 5.8 - - + -
746B GLU* 4.8 10.1 - - + -
749B LEU* 4.0 17.3 - - + -
755B THR* 6.5 0.4 - - + -
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Residues in contact with GLU 726 (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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558B LYS* 3.4 27.5 - - + +
560B TRP* 3.1 20.8 + - - +
576B PHE* 3.2 4.7 - - - -
577B GLU* 2.8 38.8 + - + +
579B PHE* 4.1 27.1 - - + -
724B HIS* 4.1 4.1 + - - +
725B ILE* 1.3 76.3 - - - +
727B ALA* 1.3 63.1 + - - +
908B TRP* 4.1 3.7 - - + -
911B ILE* 3.9 22.3 - - + +
912B ILE* 6.0 0.2 - - - -
914B GLN* 4.9 4.7 + - - +
916B TYR* 2.5 30.5 + - - -
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Residues in contact with ALA 727 (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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558B LYS 3.2 6.4 + - - +
559B LEU* 3.9 18.2 - - + -
560B TRP* 2.9 36.1 + - - +
575B ASN 3.0 13.5 - - - +
576B PHE* 3.8 22.2 - - + -
726B GLU* 1.3 76.9 - - - +
728B LEU* 1.3 60.7 + - - +
729B LEU* 4.4 2.9 - - + -
742B MET* 4.0 10.5 - - - -
908B TRP* 4.3 4.0 - - - -
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Residues in contact with LEU 728 (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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548B PRO* 4.3 18.2 - - + -
560B TRP* 3.3 17.5 - - + +
561B PHE* 4.6 1.1 - - - +
562B LYS* 4.9 1.6 - - + +
573B ASN* 3.9 1.5 - - + +
574B LEU* 3.6 0.5 - - - -
575B ASN* 2.7 40.7 + - + +
727B ALA* 1.3 74.1 - - - +
729B LEU* 1.3 68.1 + - - +
730B HIS* 3.9 26.9 - - + -
904B SER* 3.9 20.2 - - - +
907B TYR* 3.9 21.8 - - + -
908B TRP* 3.9 21.4 - - + +
911B ILE* 3.9 16.2 - - + -
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Residues in contact with LEU 729 (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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559B LEU* 3.8 22.4 - - + -
560B TRP 2.9 9.7 + - - +
561B PHE* 3.5 8.4 - - + -
562B LYS 3.2 23.4 + - - +
573B ASN 3.5 4.3 - - - -
574B LEU* 3.7 27.6 - - + -
575B ASN 4.4 1.6 - - - +
576B PHE* 3.7 28.5 - - + -
727B ALA* 4.4 2.0 - - + -
728B LEU* 1.3 86.1 - - - +
730B HIS* 1.3 59.4 + - - +
733B ILE* 4.2 10.5 - - + +
738B ALA* 3.7 37.0 - - + +
741B ILE* 4.2 14.4 - - + -
742B MET* 4.7 3.6 - - + +
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Residues in contact with HIS 730 (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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562B LYS* 3.3 38.1 + - + +
564B ASP* 4.2 11.7 - - - -
572B ALA* 3.6 0.9 - - - +
573B ASN* 2.7 40.2 + - + +
728B LEU* 3.9 19.2 - - + -
729B LEU* 1.3 73.0 - - - +
731B GLY* 1.3 63.7 + - - +
733B ILE* 4.6 2.7 - - - -
900B LEU* 3.5 24.5 - - + +
903B GLU* 3.4 27.9 + - - +
904B SER* 2.9 39.7 - - - +
907B TYR* 4.2 9.2 - + - -
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Residues in contact with GLY 731 (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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562B LYS 3.2 3.3 + - - +
563B GLN* 3.4 7.8 - - - +
564B ASP* 2.8 36.8 + - - -
571B LYS 3.8 8.7 - - - -
572B ALA* 4.2 1.6 - - - -
730B HIS* 1.3 83.4 + - - +
732B ASN* 1.3 58.0 + - - -
733B ILE* 3.0 15.4 + - - +
900B LEU* 3.9 7.9 - - - -
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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