Contacts of the helix formed by residues 725 - 738 (chain N) in PDB entry 5GJQ
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 MET 725 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681N ASN* 3.8 12.1 - - + -
682N TYR* 3.8 15.0 - - + +
685N GLN* 2.8 44.6 + - - +
723N ASP* 3.4 15.0 - - + +
724N VAL* 1.3 75.9 - - - +
726N ALA* 1.3 68.2 + - - +
728N PHE* 2.9 8.3 - - - +
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Residues in contact with ALA 726 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681N ASN* 3.6 19.0 - - + +
684N ARG* 4.8 6.5 - - - -
685N GLN* 4.4 9.9 - - - +
688N LEU* 4.8 2.8 - - - +
716N VAL* 3.5 21.8 - - + -
722N ASP* 3.6 6.7 - - + -
723N ASP 3.0 23.5 + - - +
725N MET* 1.3 81.9 - - - +
727N LYS* 1.3 64.5 + - - +
729N GLY* 3.3 1.2 + - - -
730N ALA* 3.0 19.8 + - - +
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Residues in contact with LYS 727 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359N ALA* 4.0 1.9 + - - +
360N VAL* 2.7 44.8 - - + +
365N CYS* 5.7 7.9 - - + -
716N VAL* 3.2 36.3 - - + +
717N ILE* 3.0 36.0 + - - +
718N ASN 5.2 0.6 + - - -
719N ASP 3.6 12.9 + - - +
720N LYS* 6.0 0.8 - - - +
722N ASP 4.3 6.7 - - - +
723N ASP 2.6 17.1 + - - +
724N VAL* 4.7 3.4 - - - -
726N ALA* 1.3 74.7 - - - +
728N PHE* 1.3 53.6 + - - +
730N ALA* 3.7 3.4 - - - -
731N ILE* 2.5 53.6 + - + +
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Residues in contact with PHE 728 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364N VAL* 4.3 17.3 - - + -
365N CYS* 4.9 4.4 - - - +
367N THR* 4.8 7.9 - - + -
368N ALA* 3.3 43.3 - - + +
685N GLN* 3.1 20.4 - - + +
689N ILE* 5.3 2.0 - - + -
724N VAL* 2.8 27.3 + - - +
725N MET 2.9 6.7 + - - +
727N LYS* 1.3 76.6 - - - +
729N GLY* 1.3 61.9 + - - +
731N ILE* 3.7 2.2 - - - +
732N LEU* 2.8 38.5 + - + +
766N PHE* 5.1 6.3 - + - -
769N PHE* 4.3 24.7 - + + -
773N PHE* 5.1 17.7 - + + -
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Residues in contact with GLY 729 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685N GLN* 3.6 19.7 - - - +
688N LEU* 4.3 3.1 - - - -
689N ILE* 3.9 16.1 - - - +
725N MET 3.2 6.7 + - - -
728N PHE* 1.3 84.9 - - - +
730N ALA* 1.3 54.8 + - - +
732N LEU* 3.0 2.9 + - - -
733N ALA* 2.3 43.8 + - - +
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Residues in contact with ALA 730 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688N LEU* 4.2 10.8 - - + +
713N TYR* 3.5 42.5 - - + +
716N VAL* 4.2 4.5 - - + -
717N ILE* 4.0 5.4 - - + -
726N ALA 3.0 15.3 + - - +
727N LYS* 3.3 13.9 - - - +
729N GLY* 1.3 72.8 - - - +
731N ILE* 1.3 54.3 + - - +
733N ALA* 4.4 2.0 - - - -
734N GLN* 2.6 37.1 + - - +
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Residues in contact with ILE 731 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353N LEU* 4.2 10.7 - - + +
356N THR* 3.8 20.9 - - - +
365N CYS* 5.5 9.4 - - + +
368N ALA* 4.9 3.6 - - + -
369N THR* 2.9 43.1 - - - +
372N ALA* 3.6 17.4 - - + +
717N ILE* 3.6 26.0 - - + +
727N LYS* 2.5 42.4 + - + +
728N PHE* 3.8 4.0 - - - +
730N ALA* 1.3 71.7 - - - +
732N LEU* 1.3 52.3 + - - +
734N GLN* 3.3 4.7 - - - +
735N GLY 2.7 28.8 + - - -
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Residues in contact with LEU 732 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368N ALA* 5.3 7.3 - - + +
371N ILE* 5.7 3.1 - - + -
372N ALA* 4.4 9.2 - - - +
375N PHE* 3.7 24.0 - - + -
689N ILE* 5.0 7.9 - - + -
728N PHE* 2.8 31.4 + - + +
729N GLY* 3.4 6.3 - - - +
731N ILE* 1.3 71.9 - - - +
733N ALA* 1.3 53.6 + - - +
735N GLY 2.7 5.4 + - - -
736N ILE* 2.3 49.6 + - + +
766N PHE* 6.0 4.0 - - + -
776N SER* 6.1 2.7 - - - -
779N LEU* 5.9 3.8 - - + -
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Residues in contact with ALA 733 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688N LEU* 3.6 34.8 - - + +
689N ILE* 3.7 4.7 - - - +
692N ALA* 3.1 16.9 - - + +
713N TYR* 4.9 4.9 - - + -
729N GLY 2.3 32.1 + - - +
730N ALA* 3.8 3.1 - - - +
732N LEU* 1.3 67.9 - - - +
734N GLN* 1.3 65.1 + - - +
736N ILE* 3.1 15.5 - - - +
737N LEU* 2.9 17.0 + - - +
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Residues in contact with GLN 734 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349N ASP 5.6 0.2 + - - -
352N ILE* 3.4 36.8 + - - +
353N LEU* 4.0 11.0 - - + +
356N THR* 3.1 24.6 + - - -
376N MET* 6.1 1.6 - - - -
710N ARG* 5.9 7.9 - - + +
713N TYR* 4.5 10.5 - - + +
714N SER* 4.5 6.7 + - - -
717N ILE* 3.1 17.5 - - - +
730N ALA 2.6 21.8 + - - +
731N ILE* 3.3 5.8 - - - +
733N ALA* 1.3 70.1 - - - +
735N GLY* 1.3 64.8 + - - +
737N LEU* 2.8 20.3 + - - +
738N ASP* 2.9 23.5 + - - -
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Residues in contact with GLY 735 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353N LEU* 5.4 0.4 - - - -
372N ALA* 3.7 20.9 - - - -
375N PHE* 3.2 11.9 - - - +
376N MET* 4.9 3.6 - - - -
731N ILE 2.7 13.5 + - - -
732N LEU 2.7 10.0 + - - -
734N GLN* 1.3 74.5 - - - +
736N ILE* 1.3 49.4 + - - -
738N ASP* 3.1 10.1 - - - -
739N ALA* 2.5 36.0 + - - -
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Residues in contact with ILE 736 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375N PHE* 3.6 12.3 - - + -
689N ILE* 3.8 28.9 - - + +
692N ALA* 3.6 27.8 - - + +
693N LEU* 3.9 12.8 - - + +
696N ILE* 3.3 20.8 - - + +
732N LEU* 2.3 40.3 + - + +
733N ALA* 3.1 24.2 - - - +
735N GLY* 1.3 66.8 - - - +
737N LEU* 1.3 65.7 + - - +
739N ALA* 2.8 21.9 + - - +
746N ILE* 5.9 1.1 - - + -
779N LEU* 5.7 7.4 - - + -
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Residues in contact with LEU 737 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692N ALA* 4.8 6.7 - - + +
695N MET* 4.9 3.1 - - + +
696N ILE* 3.5 32.6 - - + +
697N GLN 5.3 0.9 - - - +
699N THR* 4.5 16.6 - - + -
710N ARG* 5.5 11.2 - - + -
733N ALA 2.9 11.0 + - - +
734N GLN* 2.8 14.3 + - - +
736N ILE* 1.3 74.6 - - - +
738N ASP* 1.3 60.7 + - - +
739N ALA 3.7 0.2 + - - -
742N HIS* 3.4 18.0 - - - +
814N PRO* 4.5 21.8 - - + -
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Residues in contact with ASP 738 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347N ASN 4.9 0.4 - - - +
348N THR 4.9 8.7 - - - +
376N MET* 3.2 41.3 - - + +
734N GLN* 2.9 28.7 + - - +
735N GLY* 3.1 4.7 - - - +
737N LEU* 1.3 84.4 - - - +
739N ALA* 1.3 65.4 + - - +
741N GLY 3.5 0.5 + - - -
742N HIS* 2.9 26.2 + - + -
814N PRO* 5.7 6.5 - - - -
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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