Contacts of the helix formed by residues 774 - 786 (chain Z) in PDB entry 5L4K
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 GLY 774 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310Z ASP* 4.4 15.3 - - - -
312Z GLU* 4.4 4.9 - - - -
764Z LEU* 5.7 1.6 - - - +
766Z GLN* 4.5 14.6 - - - +
772Z GLY 3.9 1.4 + - - -
773Z LYS* 1.3 77.2 - - - +
775Z THR* 1.3 64.1 + - - -
776Z LEU 3.3 3.8 - - - -
777Z THR* 3.7 2.3 + - - -
778Z LEU* 3.3 31.7 + - - +
804Z LEU* 5.9 1.6 - - - -
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Residues in contact with THR 775 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312Z GLU* 2.7 29.5 + - - +
313Z GLU* 2.9 35.3 + - - +
490Z ALA* 3.4 33.8 + - + +
527Z VAL* 4.8 8.4 - - + +
528Z GLY* 3.9 2.9 + - - -
774Z GLY* 1.3 74.0 - - - +
776Z LEU* 1.3 66.2 + - + +
777Z THR 3.3 0.9 + - - -
778Z LEU* 5.2 2.0 - - - -
779Z CYS* 3.7 31.8 + - + +
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Residues in contact with LEU 776 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313Z GLU* 3.7 27.8 + - - +
420Z TRP* 4.7 14.1 - - + -
453Z SER* 6.3 2.0 - - - -
456Z ARG* 4.9 11.0 - - - +
774Z GLY 3.3 0.6 - - - -
775Z THR* 1.3 79.7 - - + +
777Z THR* 1.3 57.4 + - - +
780Z PRO* 3.0 12.9 - - - +
802Z SER* 2.4 52.3 - - - +
803Z PHE* 3.8 20.2 - - - +
804Z LEU* 3.7 31.0 - - + +
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Residues in contact with THR 777 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680Z ARG* 5.4 0.3 + - - -
683Z GLU* 6.4 0.2 - - + -
761Z MET 5.2 0.5 + - - -
762Z VAL* 4.2 7.4 - - + -
763Z ARG 3.7 35.3 + - - +
764Z LEU* 4.3 14.8 - - + +
766Z GLN* 4.1 9.1 + - - -
774Z GLY* 3.7 4.4 + - - -
775Z THR 3.3 0.2 - - - -
776Z LEU* 1.3 78.5 - - - +
778Z LEU* 1.3 63.6 + - - +
779Z CYS 3.3 2.2 - - - -
780Z PRO* 4.1 1.7 - - - +
781Z TYR* 3.3 22.8 + - + +
803Z PHE* 3.8 24.8 - - + -
804Z LEU* 4.0 15.6 + - - +
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Residues in contact with LEU 778 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312Z GLU* 5.4 2.7 - - + -
527Z VAL* 6.1 0.7 - - + -
564Z LEU* 5.6 1.8 - - + -
567Z LEU* 4.4 18.8 - - + -
681Z TYR* 4.2 25.4 - - + +
764Z LEU* 3.8 25.6 - - + -
773Z LYS* 3.8 23.6 - - + -
774Z GLY 3.3 35.2 + - - +
775Z THR* 4.8 2.0 - - - +
777Z THR* 1.3 77.8 - - - +
779Z CYS* 1.3 56.3 + - - +
781Z TYR* 3.8 3.2 - - - +
782Z HIS* 2.8 51.9 + - + -
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Residues in contact with CYS 779 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490Z ALA* 5.6 1.6 - - - -
524Z MET* 4.0 34.8 - - + -
527Z VAL* 4.4 21.8 - - - -
564Z LEU* 4.6 10.1 - - - -
775Z THR* 3.7 19.4 + - - +
778Z LEU* 1.3 77.5 - - - +
780Z PRO* 1.3 76.5 - - + +
781Z TYR 3.1 0.8 + - - -
782Z HIS* 3.2 4.8 + - - +
783Z SER* 2.9 27.1 + - - +
799Z VAL* 4.3 8.1 - - + -
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Residues in contact with PRO 780 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680Z ARG* 3.7 3.8 + - - +
775Z THR 4.3 0.2 - - - +
776Z LEU 3.0 28.7 - - - +
777Z THR 4.1 0.7 - - - +
779Z CYS* 1.3 92.9 - - + +
781Z TYR* 1.3 62.2 + - - +
783Z SER* 3.6 2.0 + - - -
784Z ASP* 3.0 23.6 + - - +
799Z VAL* 3.6 31.3 - - + +
800Z LEU* 4.4 3.1 - - - +
802Z SER* 3.2 27.1 - - - +
803Z PHE* 3.6 26.2 - - + -
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Residues in contact with TYR 781 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632Z LYS* 3.6 20.7 - - - +
677Z HIS* 3.2 38.1 + + + +
680Z ARG* 3.4 28.1 - - + +
681Z TYR* 3.4 47.9 - + + +
762Z VAL* 6.2 0.4 - - + -
777Z THR* 3.3 20.7 + - + +
778Z LEU* 3.8 5.4 - - - +
779Z CYS 3.1 1.2 - - - -
780Z PRO* 1.3 74.5 - - - +
782Z HIS* 1.3 81.9 + + - +
784Z ASP* 2.5 25.7 + - + +
785Z ARG* 2.8 41.6 + - + +
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Residues in contact with HIS 782 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520Z LEU* 5.3 6.0 - - + +
560Z LEU* 4.0 36.8 - - + +
564Z LEU* 3.7 32.0 - - + +
567Z LEU* 5.2 5.2 - - + -
632Z LYS* 4.1 20.7 + - - -
681Z TYR* 4.6 9.1 + - - -
778Z LEU* 2.8 32.6 + - + +
779Z CYS* 4.0 4.4 - - - +
781Z TYR* 1.3 105.6 - + - +
783Z SER* 1.3 60.1 + - - +
785Z ARG* 3.4 16.7 + - + +
786Z GLN* 4.0 4.0 + - - +
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Residues in contact with SER 783 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483Z PHE* 5.4 2.6 - - - -
520Z LEU* 4.7 16.1 - - - +
524Z MET* 5.1 6.8 - - - -
779Z CYS* 2.9 18.2 + - - +
780Z PRO* 3.7 4.5 - - - -
782Z HIS* 1.3 79.4 - - - +
784Z ASP* 1.3 59.7 + - - +
785Z ARG 3.4 0.3 + - - -
786Z GLN 3.7 10.4 - - - +
796Z LEU 5.4 1.2 + - - -
797Z LEU* 3.2 38.4 - - - +
799Z VAL* 4.0 29.0 - - - +
800Z LEU* 5.6 0.4 - - - -
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Residues in contact with ASP 784 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677Z HIS* 2.9 29.1 + - - -
680Z ARG* 3.4 35.4 - - - +
709Z THR* 5.2 0.2 - - - -
712Z LYS* 2.5 39.5 + - - +
780Z PRO 3.0 17.4 + - - +
781Z TYR* 2.5 12.6 + - + +
783Z SER* 1.3 70.1 - - - +
785Z ARG* 1.3 58.8 - - - -
787Z LEU* 3.5 13.8 - - - +
797Z LEU* 5.2 3.0 - - - +
800Z LEU* 4.4 15.8 - - + +
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Residues in contact with ARG 785 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560Z LEU* 5.9 1.6 - - + -
628Z ASP* 2.9 38.4 + - - +
629Z LYS* 4.0 3.6 - - - +
632Z LYS* 3.6 24.7 - - - +
673Z ARG* 3.7 7.5 - - - +
674Z THR* 3.3 30.4 + - - +
677Z HIS* 2.7 58.3 + - + -
781Z TYR* 2.8 36.3 + - + +
782Z HIS* 3.5 17.9 - - + +
783Z SER 3.2 0.8 - - - -
784Z ASP* 1.3 76.7 - - - +
786Z GLN* 1.3 91.6 + - + +
787Z LEU 3.6 0.9 + - - -
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Residues in contact with GLN 786 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556Z ARG* 3.2 52.2 + - + +
557Z TRP* 5.1 15.8 + - + +
560Z LEU* 5.5 10.3 - - + -
590Z PHE* 5.1 10.5 - - + -
628Z ASP* 5.7 1.8 - - - +
673Z ARG* 3.0 21.9 + - - +
782Z HIS 4.0 6.2 + - - +
783Z SER 3.7 10.5 - - - +
785Z ARG* 1.3 113.7 - - + +
787Z LEU* 1.3 59.2 + - - +
793Z VAL* 4.8 3.8 - - - +
797Z LEU* 4.6 5.4 - - - +
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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