Contacts of the helix formed by residues 720 - 729 (chain G) in PDB entry 5JLH
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 720 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G PHE* 3.9 8.0 - - - -
503G GLN* 3.5 19.4 + - - -
599G TYR* 4.1 10.1 - - - -
717G ARG 3.4 10.7 + - - -
718G CYS 3.3 4.9 + - - -
719G ASN* 1.3 79.7 + - - +
721G VAL* 1.3 56.8 + - - -
722G LEU 3.2 3.1 - - - -
723G GLU* 2.9 10.8 + - - +
724G GLY* 2.8 23.9 + - - -
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Residues in contact with VAL 721 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121G VAL* 4.9 10.3 - - + -
138G SER* 3.9 24.6 + - - +
141G PHE* 3.7 25.4 - - + -
143G VAL* 4.7 6.5 - - + -
694G ARG* 4.0 13.5 - - + -
716G LEU* 3.8 20.4 - - + -
719G ASN* 2.8 38.6 + - - +
720G GLY* 1.3 76.1 - - - +
722G LEU* 1.3 59.7 + - + +
724G GLY* 2.9 15.1 + - - -
725G ILE* 2.9 17.4 + - + +
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Residues in contact with LEU 722 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G GLU* 3.7 38.8 - - + +
121G VAL* 5.5 0.9 - - + -
599G TYR 6.0 2.0 - - - +
600G ALA 5.8 0.2 - - - +
713G LEU 4.4 0.4 - - - +
716G LEU* 3.4 31.7 + - + +
717G ARG* 3.7 50.3 - - + +
720G GLY 3.2 0.2 - - - -
721G VAL* 1.3 79.2 - - + +
723G GLU* 1.3 60.6 + - - +
725G ILE* 2.9 36.9 - - + +
726G ARG* 2.9 13.7 + - - +
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Residues in contact with GLU 723 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503G GLN* 2.7 33.9 - - - +
507G ASN* 2.5 32.7 + - - +
533G ASP* 4.9 2.4 - - - +
534G LEU* 3.7 10.7 - - - +
599G TYR* 3.3 25.0 + - + +
720G GLY* 2.9 14.4 + - - +
722G LEU* 1.3 79.5 - - - +
724G GLY* 1.3 50.1 + - - +
726G ARG* 3.2 34.1 + - - +
727G ILE* 2.7 41.8 + - + +
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Residues in contact with GLY 724 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G PHE* 4.2 15.7 - - - -
506G PHE* 4.3 11.6 - - - -
510G MET* 4.2 5.4 - - - +
720G GLY 2.8 12.9 + - - -
721G VAL 2.9 5.5 + - - -
723G GLU* 1.3 77.5 - - - +
725G ILE* 1.3 61.8 + - - +
727G ILE* 3.2 8.8 + - - +
728G CYS* 3.0 25.3 + - - +
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Residues in contact with ILE 725 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G MET* 5.8 2.2 - - + -
116G LEU* 4.7 17.0 - - + -
117G ASN* 4.0 20.2 - - - +
118G GLU 4.0 1.1 - - - +
121G VAL* 3.9 28.7 - - + -
138G SER* 4.0 19.1 - - - +
721G VAL* 2.9 15.0 + - + +
722G LEU* 2.9 48.2 - - + +
724G GLY* 1.3 78.0 - - - +
726G ARG* 1.3 61.4 + - + +
728G CYS* 3.1 14.3 - - - -
729G ARG* 3.0 33.3 + - - +
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Residues in contact with ARG 726 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533G ASP* 4.7 20.8 + - - +
534G LEU* 5.0 2.0 - - - +
599G TYR* 4.2 23.4 + - - +
722G LEU* 2.9 15.5 + - - +
723G GLU* 3.2 47.1 + - - +
725G ILE* 1.3 78.3 - - + +
727G ILE* 1.3 59.9 + - - +
729G ARG* 4.1 14.5 - - - +
730G GLN* 3.0 42.7 + - - +
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Residues in contact with ILE 727 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506G PHE* 4.5 3.6 - - + -
507G ASN* 3.2 45.8 - - + +
510G MET* 3.8 21.3 - - + -
530G PHE* 3.7 37.4 - - + -
533G ASP* 4.6 7.6 - - - +
723G GLU* 2.7 33.7 + - + +
724G GLY* 3.4 10.8 - - - +
725G ILE 3.1 0.4 - - - -
726G ARG* 1.3 74.0 - - + +
728G CYS* 1.3 61.6 + - - +
730G GLN* 2.9 38.1 + - - +
731G GLY 3.7 2.1 + - - -
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Residues in contact with CYS 728 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G ALA* 5.5 9.6 - - + -
116G LEU* 3.4 24.0 - - - -
139G GLY* 6.0 4.0 - - - -
510G MET* 3.7 20.0 - - + -
514G GLU* 4.4 8.9 - - - +
530G PHE* 5.9 0.4 - - - -
724G GLY 3.0 17.5 + - - -
725G ILE* 3.1 29.8 - - - -
727G ILE* 1.3 73.1 - - - +
729G ARG* 1.3 64.6 + - - +
731G GLY* 3.0 21.5 + - - +
733G PRO* 3.5 19.3 - - + +
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Residues in contact with ARG 729 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G LEU* 3.1 46.7 + - + +
117G ASN* 4.6 9.3 - - - +
725G ILE* 3.0 31.1 + - - +
726G ARG* 4.1 13.8 - - - +
727G ILE 3.2 0.2 - - - -
728G CYS* 1.3 78.9 - - - +
730G GLN* 1.3 61.3 + - + +
731G GLY 3.0 9.5 - - - +
733G PRO* 4.6 8.3 - - - +
788G ARG* 4.3 12.1 + - - -
789G ALA* 4.8 17.1 + - + +
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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