Contacts of the helix formed by residues 726 - 740 (chain B) in PDB entry 5WRZ
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 ASP 726 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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720B VAL* 5.9 0.3 - - - +
725B SER* 1.3 76.8 + - - +
727B SER* 1.3 64.1 + - - +
728B GLN 3.3 0.2 - - - -
729B ILE* 3.4 30.7 - - + +
730B LEU* 3.0 22.8 + - + +
751B LEU* 4.7 7.1 - - + +
753B ASN* 3.5 33.0 + - + +
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Residues in contact with SER 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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725B SER* 3.2 6.1 + - - -
726B ASP* 1.3 80.9 - - - +
728B GLN* 1.3 63.0 + - - +
730B LEU* 3.5 6.2 - - - +
731B ASP* 3.3 22.8 + - - +
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Residues in contact with GLN 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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715B GLU* 3.4 20.6 + - - -
719B ALA* 3.5 19.4 - - + +
725B SER* 3.8 7.9 + - - +
727B SER* 1.3 79.0 - - - +
729B ILE* 1.3 58.7 + - + +
731B ASP* 3.2 10.6 + - + +
732B LEU* 2.9 62.4 + - - +
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Residues in contact with ILE 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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716B VAL* 4.0 14.6 - - + +
719B ALA* 3.2 35.7 - - + -
720B VAL* 3.9 19.3 - - + +
725B SER 3.6 14.6 - - - +
726B ASP* 3.4 25.8 - - + +
727B SER 3.4 0.4 - - - -
728B GLN* 1.3 79.1 - - - +
730B LEU* 1.3 55.8 + - - +
732B LEU* 3.3 5.7 + - - +
733B SER* 2.8 27.6 + - - -
751B LEU* 5.7 0.7 - - + -
752B LEU 3.1 24.7 - - - +
753B ASN* 3.5 19.5 - - + +
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Residues in contact with LEU 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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726B ASP* 3.0 24.1 + - + +
727B SER* 3.5 5.4 - - - +
729B ILE* 1.3 73.9 - - - +
731B ASP* 1.3 74.0 + - - +
733B SER* 3.0 7.6 + - - -
734B ASN* 2.7 57.0 + - - +
748B LYS* 5.6 7.6 - - + +
751B LEU* 4.4 17.3 - - + -
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Residues in contact with ASP 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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727B SER 3.3 8.6 + - - +
728B GLN* 3.2 14.6 + - + +
730B LEU* 1.3 94.1 - - - +
732B LEU* 1.3 59.1 + - + +
734B ASN* 3.3 9.3 + - - +
735B ARG* 2.9 55.3 + - - +
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Residues in contact with LEU 732 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712B ILE* 3.5 30.1 - - + +
715B GLU* 3.8 24.0 - - + +
716B VAL* 3.5 44.6 - - + +
719B ALA* 4.6 1.3 - - + -
728B GLN* 2.9 46.3 + - - +
729B ILE* 3.6 3.6 - - - +
731B ASP* 1.3 77.9 - - + +
733B SER* 1.3 62.1 + - - +
735B ARG* 3.4 29.0 + - - +
736B PHE* 3.1 19.5 + - - +
752B LEU* 5.4 0.2 - - - -
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Residues in contact with SER 733 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729B ILE 2.8 14.3 + - - -
730B LEU 3.3 8.7 - - - -
732B LEU* 1.3 73.6 - - - +
734B ASN* 1.3 65.9 + - - +
736B PHE* 3.2 11.1 + - - +
737B TYR* 3.1 30.3 + - - -
749B PRO 5.3 0.2 + - - -
751B LEU* 3.3 21.7 - - - +
752B LEU* 2.9 43.8 + - - +
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Residues in contact with ASN 734 (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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730B LEU* 2.7 49.2 + - - +
731B ASP* 3.6 10.2 + - - +
733B SER* 1.3 73.2 - - - +
735B ARG* 1.3 62.4 + - + +
737B TYR* 3.2 9.5 + - - +
738B THR* 2.8 27.2 + - - +
748B LYS* 4.6 24.4 - - - +
751B LEU* 5.6 1.6 - - - +
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Residues in contact with ARG 735 (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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712B ILE* 4.3 20.6 - - + +
731B ASP* 2.9 40.8 + - - +
732B LEU* 3.7 27.6 - - - +
733B SER 3.3 0.4 - - - -
734B ASN* 1.3 71.2 - - + +
736B PHE* 1.3 54.1 + - - +
738B THR* 3.1 9.8 + - - -
739B LEU* 2.8 39.4 + - + +
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Residues in contact with PHE 736 (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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709B ALA* 3.8 32.5 - - + -
712B ILE* 4.1 9.6 - - + +
713B LEU* 3.5 27.8 - - + -
732B LEU 3.1 12.7 + - - +
733B SER 3.2 9.8 + - - +
735B ARG* 1.3 73.8 - - - +
737B TYR* 1.3 69.0 + + - +
739B LEU* 3.2 8.3 + - - +
740B ILE* 2.9 36.3 + - + +
742B HIS* 4.4 4.9 - + - -
752B LEU* 3.7 17.3 - - + -
761B LYS* 3.8 26.0 - - + -
764B MET* 3.7 31.6 - - + -
765B LEU* 4.1 13.0 - - + -
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Residues in contact with TYR 737 (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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733B SER* 3.1 34.9 + - - -
734B ASN* 3.2 10.6 + - - +
735B ARG 3.2 0.6 - - - -
736B PHE* 1.3 76.2 - + + +
738B THR* 1.3 61.1 + - - +
740B ILE 3.2 14.6 - - - +
741B PRO* 3.7 9.9 - - - +
742B HIS* 3.5 39.3 + + + -
744B PHE* 4.7 3.0 - + - -
747B LYS* 4.3 12.6 - - + +
748B LYS* 5.2 4.3 - - - +
749B PRO* 3.5 47.0 - - + +
750B PRO* 2.4 34.5 + - - +
752B LEU* 4.1 7.0 - - + +
761B LYS* 3.4 28.8 + - - -
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Residues in contact with THR 738 (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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734B ASN* 2.8 17.2 + - - +
735B ARG* 3.1 12.3 + - - +
737B TYR* 1.3 79.1 - - - +
739B LEU* 1.3 63.8 + - - +
740B ILE 3.4 0.4 + - - -
741B PRO* 4.1 11.6 - - - +
747B LYS* 4.7 16.5 + - + +
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Residues in contact with LEU 739 (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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696B MET* 4.5 6.2 - - - +
705B GLN* 3.6 37.7 - - + +
708B ALA* 4.0 14.6 - - + +
709B ALA* 3.8 32.5 - - + +
712B ILE* 4.1 15.3 - - + -
735B ARG* 2.8 17.0 + - + +
736B PHE* 3.4 10.1 - - - +
738B THR* 1.3 75.7 - - - +
740B ILE* 1.3 66.6 + - + +
741B PRO* 3.5 7.4 - - - +
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Residues in contact with ILE 740 (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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691B ILE* 4.2 25.6 - - + -
696B MET* 4.3 17.9 - - + -
705B GLN* 4.8 11.0 - - + +
706B ILE* 5.3 3.1 - - + -
709B ALA* 4.0 24.9 - - + -
736B PHE* 2.9 29.8 + - + +
737B TYR* 3.2 12.3 - - - +
739B LEU* 1.3 83.5 - - + +
741B PRO* 1.3 59.1 - - + +
742B HIS* 2.7 44.8 + - + +
764B MET* 4.6 4.9 - - + -
765B LEU* 4.5 9.9 - - + -
768B LEU* 4.8 7.2 - - + -
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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