Contacts of the helix formed by residues 736 - 751 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A LYS* 6.2 3.1 - - - -
734A ILE* 3.2 5.4 - - + +
735A GLU* 1.3 77.4 - - - +
737A ASP* 1.3 61.3 + - - +
738A ALA 3.3 2.4 + - - -
739A ASP* 3.7 9.5 + - - +
740A VAL* 3.4 22.6 + - - +
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Residues in contact with ASP 737 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A LYS* 5.3 10.1 - - - +
629A ARG* 5.6 0.6 + - - -
733A GLU* 6.4 0.9 - - + -
734A ILE* 3.6 20.2 + - + +
735A GLU 3.5 0.4 - - - -
736A ASP* 1.3 74.2 - - - +
738A ALA* 1.3 59.8 + - - +
739A ASP 3.2 1.1 - - - -
740A VAL* 3.6 10.7 - - + +
741A GLU* 2.9 32.1 + - - +
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Residues in contact with ALA 738 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622A PRO* 4.9 8.4 - - + +
625A ILE* 5.4 4.0 - - - +
629A ARG* 5.4 9.0 - - - +
734A ILE 4.0 6.5 + - - +
735A GLU* 4.2 13.9 - - - +
736A ASP 3.3 1.2 - - - -
737A ASP* 1.3 78.7 - - - +
739A ASP* 1.3 63.1 + - - +
741A GLU* 4.6 3.5 - - - +
742A TRP* 3.7 19.4 + - - +
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Residues in contact with ASP 739 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622A PRO* 5.8 3.3 - - - +
735A GLU 4.6 8.9 - - - +
736A ASP* 3.7 10.8 + - - +
737A ASP 3.2 0.4 - - - -
738A ALA* 1.3 81.5 - - - +
740A VAL* 1.3 60.5 + - + +
742A TRP* 3.4 14.7 + - - -
743A LYS* 2.9 54.8 + - - +
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Residues in contact with VAL 740 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A LYS* 3.7 39.3 - - + +
376A LYS* 3.9 28.9 - - + +
379A ALA* 3.9 17.2 - - + +
736A ASP 3.4 15.7 + - - +
737A ASP* 3.3 13.8 + - + +
739A ASP* 1.3 79.0 - - + +
741A GLU* 1.3 57.4 + - - +
743A LYS* 3.8 0.8 - - - +
744A PHE* 2.9 28.9 + - - +
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Residues in contact with GLU 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A LYS* 4.8 18.2 - - + +
625A ILE* 4.5 22.5 - - + +
629A ARG* 4.6 9.0 - - - +
737A ASP 2.9 17.4 + - - +
738A ALA 4.6 2.0 - - - +
740A VAL* 1.3 78.1 - - - +
742A TRP* 1.3 57.1 + - - +
744A PHE* 3.4 6.4 + - - +
745A ALA* 3.0 28.6 + - - +
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Residues in contact with TRP 742 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615A PRO* 3.9 15.3 + - + -
617A ASN 3.3 16.9 + - - -
618A GLU* 3.6 34.8 - - + -
621A GLY* 3.8 11.0 - - - -
622A PRO* 3.6 36.1 - - + +
625A ILE* 4.3 12.7 - - + +
738A ALA 3.7 14.0 + - - +
739A ASP* 3.4 19.6 + - - +
741A GLU* 1.3 79.4 - - - +
743A LYS* 1.3 92.5 + - + +
745A ALA* 3.2 3.3 + - + +
746A ARG* 2.9 58.7 + - - +
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Residues in contact with LYS 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378A VAL 5.2 0.4 - - - +
379A ALA* 3.7 32.9 + - + +
384A GLN* 3.6 31.3 + - + +
739A ASP* 2.9 43.3 + - - +
740A VAL* 6.3 0.2 - - - +
742A TRP* 1.3 103.4 - - + +
744A PHE* 1.3 57.5 + - - +
746A ARG* 3.8 13.6 - - - +
747A ALA* 2.9 29.3 + - - +
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Residues in contact with PHE 744 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A ALA 4.2 2.7 - - - -
370A ILE* 3.7 47.3 - - + -
373A GLU* 4.1 27.6 - - + -
374A VAL 4.3 3.4 - - - -
375A LYS* 3.9 34.1 - - + +
378A VAL* 4.0 25.8 - - + -
379A ALA* 4.6 1.5 - - - +
740A VAL 2.9 18.3 + - - +
741A GLU* 3.7 6.1 - - - +
742A TRP 3.3 0.2 - - - -
743A LYS* 1.3 76.6 - - - +
745A ALA* 1.3 58.0 + - - +
747A ALA* 3.4 3.1 + - - -
748A LYS* 2.9 56.1 + - + +
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Residues in contact with ALA 745 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615A PRO* 4.9 15.6 - - + +
625A ILE* 4.2 19.7 - - + -
741A GLU 3.0 17.8 + - - +
742A TRP* 3.2 5.6 + - + +
744A PHE* 1.3 76.5 - - - +
746A ARG* 1.3 57.5 - - - +
748A LYS* 3.4 15.9 + - - +
749A LEU* 2.9 26.9 + - - +
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Residues in contact with ARG 746 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A GLN* 3.1 30.1 - - - +
388A LEU* 5.6 5.0 - - - +
615A PRO 3.6 25.5 + - - +
616A ALA* 4.2 18.0 + - - -
618A GLU* 5.0 6.5 - - - +
742A TRP* 2.9 47.9 + - - +
743A LYS* 3.8 15.2 - - - +
745A ALA* 1.3 77.2 - - - +
747A ALA* 1.3 56.9 + - - +
749A LEU* 3.2 5.3 + - - +
750A TRP* 2.9 65.6 + - + +
1004A Y01 5.2 3.4 + - - -
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Residues in contact with ALA 747 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A ILE* 4.6 3.1 - - + -
378A VAL* 3.7 29.4 - - + -
384A GLN* 4.6 6.1 - - - +
387A LEU* 4.2 15.5 - - + -
743A LYS 2.9 17.8 + - - +
744A PHE 3.9 2.5 - - - +
746A ARG* 1.3 73.6 - - - +
748A LYS* 1.3 60.5 + - - +
750A TRP* 3.2 12.5 + - + +
751A PHE* 2.9 36.0 + - - -
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Residues in contact with LYS 748 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A ILE* 3.8 27.1 - - + +
744A PHE* 2.9 47.2 + - + +
745A ALA* 3.6 12.1 - - - +
747A ALA* 1.3 75.2 - - - +
749A LEU* 1.3 61.9 + - - +
751A PHE* 3.8 5.8 + - - +
752A SER* 3.7 17.7 + - - -
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Residues in contact with LEU 749 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A TRP* 4.4 4.9 - - + -
443A PHE* 4.6 4.0 - - + -
612A TYR 3.3 27.1 - - - +
613A ILE* 4.9 0.9 - - - -
615A PRO* 3.7 23.6 - - + -
616A ALA* 3.7 31.6 - - + +
745A ALA 2.9 13.8 + - - +
746A ARG* 3.4 9.6 - - - +
748A LYS* 1.3 76.2 - - - +
750A TRP* 1.3 75.4 + - + +
752A SER* 2.8 23.0 + - - +
753A TYR* 3.2 30.3 - - + -
1002A S9Y 6.1 1.3 - - - -
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Residues in contact with TRP 750 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A GLN* 4.3 15.5 - - - -
387A LEU* 3.8 37.7 - - + -
388A LEU* 3.6 37.9 - - + -
391A TRP* 3.6 40.5 - + + -
746A ARG* 2.9 62.6 + - + +
747A ALA* 3.2 17.2 + - - +
749A LEU* 1.3 83.7 - - + +
751A PHE* 1.3 58.1 + - + +
753A TYR* 3.0 20.1 + - - +
754A PHE* 3.4 26.3 + - + -
1004A Y01 3.7 21.8 + - - -
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Residues in contact with PHE 751 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A LEU* 4.2 19.5 - - + -
366A LEU* 4.0 26.2 - - + -
367A LYS* 3.6 39.8 - - + -
370A ILE* 3.6 23.6 - - + -
378A VAL* 5.5 0.4 - - + -
387A LEU* 3.7 41.7 - - + -
747A ALA 2.9 25.1 + - - +
748A LYS* 4.2 5.2 - - - +
749A LEU 3.3 0.4 - - - -
750A TRP* 1.3 75.5 - - + +
752A SER* 1.3 59.6 + - - +
753A TYR 3.3 0.8 + - - -
754A PHE* 3.7 26.2 + + + +
755A GLU* 3.9 14.6 - - - +
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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