Contacts of the helix formed by residues 720 - 731 (chain W) in PDB entry 5O9G
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 720 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-20I C 3.2 7.0 - - - -
657W LYS* 3.7 44.9 - - + +
660W ASN* 4.2 14.4 - - - +
664W LEU* 5.6 6.5 - - + -
718W SER* 4.3 6.9 - - - -
719W GLN* 1.3 97.7 - - - +
721W VAL* 1.3 63.0 + - - +
722W ARG* 3.3 5.1 + - + +
723W MET* 3.7 34.0 + - + +
724W LEU* 3.6 17.9 + - - +
789W PHE* 5.5 3.6 - - + -
790W ASP* 3.9 23.6 - - - +
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Residues in contact with VAL 721 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-21I C 5.7 0.9 - - - -
-20I C 3.1 31.2 + - + +
-19I G 4.9 11.7 - - - +
719W GLN 4.3 3.4 - - - +
720W MET* 1.3 72.1 - - - +
722W ARG* 1.3 80.8 + - + +
724W LEU* 3.6 24.6 + - + +
725W ASP* 3.5 17.4 + - - +
740W ARG* 4.1 4.9 + - - +
742W ASP* 5.3 11.0 - - + +
743W GLY 6.3 0.2 - - - +
770W SER* 5.5 2.9 - - - +
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Residues in contact with ARG 722 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B HIS 4.4 5.9 + - - -
19B ARG* 4.3 8.1 - - - +
20B LYS* 3.8 41.7 + - - +
657W LYS* 5.7 6.7 - - - +
664W LEU* 4.5 19.6 + - + -
720W MET* 3.3 3.7 - - + +
721W VAL* 1.3 90.0 - - + +
723W MET* 1.3 60.5 + - - +
724W LEU 3.2 0.4 - - - -
725W ASP* 3.0 19.9 + - - +
726W ILE* 2.9 33.7 + - + +
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Residues in contact with MET 723 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661W HIS* 3.8 48.7 - - + +
664W LEU* 5.3 4.3 - - + +
696W LYS* 6.4 1.1 - - + -
697W MET* 3.9 21.8 - - - -
718W SER* 4.7 3.6 - - - +
720W MET* 3.7 30.1 + - + +
721W VAL 3.4 0.4 - - - -
722W ARG* 1.3 77.6 - - - +
724W LEU* 1.3 57.1 + - - +
726W ILE* 3.5 12.6 - - + +
727W LEU* 2.9 36.4 + - + +
789W PHE* 3.8 39.3 - - + -
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Residues in contact with LEU 724 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716W ILE 5.0 2.7 - - - +
718W SER* 3.8 26.9 - - - +
719W GLN 5.8 0.4 - - - +
720W MET 3.6 14.1 - - - +
721W VAL* 3.6 11.0 + - + +
722W ARG 3.2 0.6 - - - -
723W MET* 1.3 79.2 - - - +
725W ASP* 1.3 56.6 + - - +
727W LEU* 3.5 10.1 + - + +
728W GLY* 2.9 22.5 + - - -
740W ARG* 3.4 36.5 + - + +
741W LEU 5.0 1.3 - - - +
742W ASP* 4.4 5.8 - - + -
768W LEU* 4.0 22.2 - - + +
769W LEU 3.3 28.0 - - - +
770W SER* 3.4 15.5 - - - +
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Residues in contact with ASP 725 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ARG* 3.6 30.9 - - + +
18B HIS 5.4 4.0 - - - +
721W VAL 3.5 13.8 + - - +
722W ARG* 3.0 21.8 + - - +
724W LEU* 1.3 75.7 - - - +
726W ILE* 1.3 60.3 + - + +
728W GLY* 3.0 4.4 + - - +
729W ASP* 2.9 35.2 + - - +
740W ARG* 3.3 28.3 + - - +
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Residues in contact with ILE 726 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B HIS 5.7 4.3 - - - +
661W HIS* 3.4 35.9 - - + +
663W TYR* 3.3 31.0 - - + +
664W LEU* 4.8 3.6 - - + -
690W LEU* 4.4 19.5 - - + +
697W MET* 5.9 2.0 - - + -
722W ARG* 2.9 23.5 + - + +
723W MET* 3.5 19.5 - - + +
725W ASP* 1.3 77.0 - - + +
727W LEU* 1.3 57.5 + - + +
729W ASP* 3.1 9.5 + - - +
730W TYR* 2.9 27.9 + - + +
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Residues in contact with LEU 727 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697W MET* 4.0 28.7 - - + -
700W LEU* 4.7 6.1 - - + -
716W ILE* 3.8 17.9 - - + -
718W SER* 4.7 2.5 - - - +
723W MET* 2.9 33.3 + - + +
724W LEU* 3.8 7.4 - - + +
726W ILE* 1.3 76.4 - - + +
728W GLY* 1.3 57.8 + - - +
730W TYR* 4.3 7.2 - - + +
731W LEU* 2.9 45.2 + - + +
738W PHE* 4.2 1.1 - - - -
768W LEU* 4.2 20.9 - - + -
789W PHE* 3.6 32.5 - - + -
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Residues in contact with GLY 728 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724W LEU 2.9 15.8 + - - -
725W ASP* 3.0 8.6 + - - -
727W LEU* 1.3 79.2 - - - +
729W ASP* 1.3 61.1 + - - +
730W TYR 3.5 0.2 - - - -
732W SER* 3.0 24.4 + - - -
738W PHE* 3.5 24.2 - - - -
740W ARG* 5.1 4.3 - - - -
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Residues in contact with ASP 729 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LYS 3.4 12.9 - - - +
17B ARG* 2.9 26.5 - - - +
18B HIS* 3.3 32.7 - - + +
690W LEU* 5.4 5.9 - - + +
725W ASP 2.9 15.3 + - - +
726W ILE* 3.1 9.4 + - - +
728W GLY* 1.3 81.0 - - - +
730W TYR* 1.3 57.0 + - - +
732W SER* 3.4 6.0 + - - -
733W ILE* 3.3 31.2 - - - +
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Residues in contact with TYR 730 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687W LEU* 3.6 41.2 - - + +
690W LEU* 4.0 23.1 - - + +
691W ILE* 3.3 38.1 - - + +
697W MET* 3.8 27.8 - - + -
700W LEU* 6.2 2.2 - - + -
701W ASP* 3.5 23.2 + - + +
704W LEU* 6.1 1.1 - - + -
726W ILE* 2.9 16.3 + - + +
727W LEU* 4.1 7.4 - - + +
729W ASP* 1.3 76.3 - - - +
731W LEU* 1.3 87.3 + - + +
732W SER 3.3 1.9 + - - -
733W ILE* 3.5 8.4 + - - -
734W LYS* 3.6 25.4 + - + +
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Residues in contact with LEU 731 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700W LEU* 6.2 3.8 - - + -
704W LEU* 4.5 11.0 - - + -
716W ILE* 5.4 3.6 - - + -
727W LEU* 2.9 34.8 + - + +
730W TYR* 1.3 98.6 - - + +
732W SER* 1.3 61.4 + - - +
733W ILE 3.3 0.2 - - - -
734W LYS* 3.7 4.5 + - + +
736W ILE* 3.1 54.9 + - + +
738W PHE* 3.9 19.7 - - + -
766W VAL* 3.9 30.5 - - + -
768W LEU* 4.6 7.9 - - + -
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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