Contacts of the helix formed by residues 736 - 751 (chain B) in PDB entry 6UZA
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 736 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376B LYS* 6.2 3.4 - - - -
734B ILE* 3.2 5.4 - - + +
735B GLU* 1.3 77.3 - - - +
737B ASP* 1.3 61.4 + - - +
738B ALA 3.3 2.6 + - - -
739B ASP* 3.7 9.8 + - - +
740B VAL* 3.4 24.1 + - - +
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Residues in contact with ASP 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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376B LYS* 5.3 9.9 - - - +
629B ARG* 5.6 0.6 + - - -
733B GLU* 6.4 0.9 - - + -
734B ILE* 3.6 19.2 + - + +
735B GLU 3.5 0.2 - - - -
736B ASP* 1.3 75.3 - - - +
738B ALA* 1.3 58.9 + - - +
739B ASP 3.2 0.9 - - - -
740B VAL* 3.6 10.6 - - + +
741B GLU* 2.9 31.5 + - - +
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Residues in contact with ALA 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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622B PRO* 4.9 8.4 - - + +
625B ILE* 5.4 4.1 - - - +
629B ARG* 5.4 8.5 - - - +
734B ILE 4.0 6.5 + - - +
735B GLU* 4.2 13.5 - - - +
736B ASP 3.3 1.0 - - - -
737B ASP* 1.3 78.3 - - - +
739B ASP* 1.3 63.1 + - - +
741B GLU* 4.2 4.6 + - - +
742B TRP* 3.7 19.1 + - - +
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Residues in contact with ASP 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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622B PRO* 5.8 3.1 - - - +
735B GLU 4.6 9.5 + - - +
736B ASP* 3.7 11.0 + - - +
737B ASP 3.2 0.2 - - - -
738B ALA* 1.3 81.8 - - - +
740B VAL* 1.3 60.2 + - + +
742B TRP* 3.4 15.4 + - - -
743B LYS* 2.9 54.9 + - - +
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Residues in contact with VAL 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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375B LYS* 3.7 39.3 - - + +
376B LYS* 3.9 29.2 - - + +
379B ALA* 3.9 16.7 - - + +
736B ASP* 3.4 17.3 - - + +
737B ASP* 3.3 12.4 + - + +
739B ASP* 1.3 78.4 - - + +
741B GLU* 1.3 56.8 + - - +
743B LYS* 3.4 0.6 + - - +
744B PHE* 2.9 28.5 + - - +
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Residues in contact with GLU 741 (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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375B LYS* 4.8 18.8 - - + +
625B ILE* 4.5 22.0 - - + +
629B ARG* 4.6 9.6 - - - +
737B ASP 2.9 17.8 + - - +
738B ALA 4.6 2.0 - - - +
740B VAL* 1.3 78.5 - - - +
742B TRP* 1.3 56.5 + - - +
744B PHE* 3.4 6.8 + - - +
745B ALA* 3.0 28.6 + - - +
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Residues in contact with TRP 742 (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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615B PRO* 3.9 15.1 + - + -
617B ASN 3.3 16.9 + - - -
618B GLU* 3.6 34.5 - - + -
621B GLY* 3.8 11.0 - - - -
622B PRO* 3.6 36.8 - - + +
625B ILE* 4.3 12.4 - - + +
738B ALA 3.7 15.1 + - - +
739B ASP* 3.4 18.5 + - - +
740B VAL 3.4 0.2 - - - -
741B GLU* 1.3 80.1 - - - +
743B LYS* 1.3 90.5 + - + +
745B ALA* 3.2 3.4 + - + +
746B ARG* 2.9 59.0 + - - +
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Residues in contact with LYS 743 (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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378B VAL 5.2 0.4 - - - +
379B ALA* 3.7 33.1 + - + +
384B GLN* 3.6 31.6 + - + +
739B ASP* 2.9 42.8 + - - +
740B VAL* 6.3 0.2 - - - +
742B TRP* 1.3 103.7 - - + +
744B PHE* 1.3 57.6 + - - +
746B ARG* 3.4 13.5 + - - +
747B ALA* 2.9 29.5 + - - +
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Residues in contact with PHE 744 (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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369B ALA 4.2 2.7 - - - -
370B ILE* 3.7 47.3 - - + -
373B GLU* 4.1 27.4 - - + -
374B VAL 4.3 3.6 - - - -
375B LYS* 3.9 34.3 - - + +
378B VAL* 4.0 25.6 - - + -
379B ALA* 4.6 1.9 - - - +
740B VAL 2.9 17.7 + - - +
741B GLU* 3.7 5.4 - - - +
743B LYS* 1.3 77.2 - - - +
745B ALA* 1.3 57.6 + - - +
747B ALA* 3.4 2.5 + - - -
748B LYS* 2.9 56.6 + - + +
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Residues in contact with ALA 745 (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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615B PRO* 4.9 15.4 - - + +
625B ILE* 4.2 20.2 - - + -
741B GLU 3.0 17.4 + - - +
742B TRP* 3.2 5.6 + - + +
744B PHE* 1.3 76.7 - - - +
746B ARG* 1.3 58.6 + - - +
748B LYS* 3.4 15.4 + - - +
749B LEU* 2.9 27.2 + - - +
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Residues in contact with ARG 746 (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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384B GLN* 3.1 30.7 - - - +
388B LEU* 5.6 4.2 - - - +
615B PRO 3.6 25.5 + - - +
616B ALA* 4.2 18.1 + - - -
618B GLU* 5.0 6.7 - - - +
742B TRP* 2.9 49.0 + - - +
743B LYS* 3.8 14.8 - - - +
745B ALA* 1.3 78.1 - - - +
747B ALA* 1.3 55.6 + - - +
749B LEU* 3.2 5.0 + - + +
750B TRP* 2.9 65.6 + - + +
1005B Y01 5.7 3.8 + - - -
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Residues in contact with ALA 747 (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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370B ILE* 4.6 2.9 - - + -
378B VAL* 3.7 28.5 - - + -
384B GLN* 4.6 6.5 - - - +
387B LEU* 4.2 15.7 - - + -
743B LYS 2.9 18.0 + - - +
744B PHE 3.9 2.5 - - - +
746B ARG* 1.3 74.1 - - - +
748B LYS* 1.3 61.2 + - - +
750B TRP* 3.2 12.1 + - + +
751B PHE* 2.9 36.5 + - - -
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Residues in contact with LYS 748 (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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370B ILE* 3.8 26.9 - - + +
744B PHE* 2.9 48.7 + - + +
745B ALA* 3.6 11.9 - - - +
747B ALA* 1.3 75.2 - - - +
749B LEU* 1.3 63.8 + - - +
751B PHE* 3.8 6.4 + - - +
752B SER* 3.7 18.0 + - - -
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Residues in contact with LEU 749 (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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391B TRP* 4.4 5.6 - - + -
443B PHE* 4.6 3.6 - - + -
612B TYR* 3.3 27.4 - - - +
613B ILE* 4.9 1.1 - - - -
615B PRO* 3.7 23.8 - - + -
616B ALA* 3.7 31.6 - - + +
745B ALA 2.9 14.3 + - - +
746B ARG* 3.2 8.9 + - - +
748B LYS* 1.3 75.1 - - - +
750B TRP* 1.3 75.9 + - + +
752B SER* 2.8 23.7 + - - +
753B TYR* 3.2 29.0 - - + -
1003B S9Y 6.1 1.6 - - - -
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Residues in contact with TRP 750 (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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384B GLN* 4.3 16.2 - - - -
387B LEU* 3.8 38.4 - - + -
388B LEU* 3.6 37.5 - - + -
391B TRP* 3.6 39.9 - + + -
616B ALA* 5.3 0.6 - - - +
746B ARG* 2.9 63.1 + - + +
747B ALA* 3.2 17.2 + - + +
749B LEU* 1.3 84.0 - - + +
751B PHE* 1.3 58.2 + - + +
753B TYR* 3.0 19.9 + - - +
754B PHE* 3.4 26.5 + - + -
1005B Y01 3.7 21.8 + - - -
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Residues in contact with PHE 751 (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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363B LEU* 4.2 19.7 - - + -
366B LEU* 4.0 25.1 - - + -
367B LYS* 3.6 38.7 - - + -
370B ILE* 3.6 25.1 - - + -
378B VAL* 5.5 0.2 - - + -
387B LEU* 3.7 41.1 - - + -
747B ALA 2.9 27.1 + - - +
748B LYS* 3.8 5.8 + - - +
749B LEU 3.3 0.4 - - - -
750B TRP* 1.3 76.6 - - + +
752B SER* 1.3 59.7 + - - +
753B TYR 3.3 0.6 + - - -
754B PHE* 3.7 25.2 + + + +
755B GLU* 3.9 15.2 - - - +
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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