Contacts of the helix formed by residues 683 - 692 (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 ARG 683 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263W THR* 5.9 4.9 - - - +
265W GLU* 5.5 4.6 + - - -
681W MET 5.1 1.8 - - - +
682W THR* 1.3 78.8 + - - +
684W GLU* 1.3 64.3 + - - +
685W ASN 3.3 1.6 - - - -
686W VAL* 3.6 7.1 + - - +
687W LEU* 3.5 19.8 + - - +
733W ILE* 4.3 33.5 - - + +
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Residues in contact with GLU 684 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682W THR* 3.8 1.7 + - - +
683W ARG* 1.3 78.1 - - - +
685W ASN* 1.3 66.0 + - - +
687W LEU* 3.6 16.0 + - - +
688W ARG* 2.9 36.6 + - + +
733W ILE* 6.1 1.4 - - - +
734W LYS* 5.4 5.4 + - - -
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Residues in contact with ASN 685 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673W LEU* 4.0 11.8 - - + +
675W LYS* 3.5 39.8 + - + +
676W PHE 5.4 2.0 - - - -
682W THR* 3.0 32.0 + - + +
683W ARG 3.3 0.4 - - - -
684W GLU* 1.3 81.3 - - - +
686W VAL* 1.3 59.4 + - - +
688W ARG* 3.8 13.4 + - - +
689W GLY* 2.9 25.3 + - - -
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Residues in contact with VAL 686 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B HIS* 6.2 2.0 - - - +
669W GLU* 6.0 4.0 - - + +
673W LEU* 4.3 26.2 - - + +
681W MET* 5.2 5.8 - - + -
682W THR* 3.8 34.3 - - + +
683W ARG* 3.9 6.3 - - - +
684W GLU 3.3 0.8 - - - -
685W ASN* 1.3 76.8 - - - +
687W LEU* 1.3 56.9 + - - +
689W GLY 3.4 2.4 + - - -
690W LEU* 2.9 32.9 + - + +
733W ILE* 6.3 3.4 - - + -
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Residues in contact with LEU 687 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683W ARG 3.5 13.6 + - - +
684W GLU* 4.1 17.9 - - - +
685W ASN 3.4 0.2 - - - -
686W VAL* 1.3 76.9 - - - +
688W ARG* 1.3 63.4 + - - +
690W LEU* 3.1 8.9 + - + +
691W ILE* 2.9 39.1 + - + +
730W TYR* 3.6 36.6 - - + +
733W ILE* 3.8 38.3 - - + +
734W LYS* 3.8 33.2 - - + +
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Residues in contact with ARG 688 (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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675W LYS* 3.1 29.9 - - - +
684W GLU* 2.9 26.8 + - + +
685W ASN* 3.8 14.1 + - - +
687W LEU* 1.3 79.1 - - - +
689W GLY* 1.3 68.1 + - - +
690W LEU 3.4 0.5 + - - -
691W ILE* 3.4 9.2 - - + +
692W MET* 3.4 62.6 + - + +
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Residues in contact with GLY 689 (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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663W TYR* 3.1 18.8 + - - -
672W VAL* 4.2 17.5 - - - +
673W LEU* 5.3 5.4 - - - -
685W ASN 2.9 18.0 + - - -
686W VAL 3.6 2.9 - - - -
688W ARG* 1.3 85.6 - - - +
690W LEU* 1.3 58.2 + - - +
692W MET* 4.4 3.8 - - - -
693W SER* 3.8 12.8 + - - -
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Residues in contact with LEU 690 (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* 4.3 11.3 - - + +
663W TYR* 3.6 35.2 - - + -
686W VAL* 2.9 21.2 + - + +
687W LEU* 3.1 9.8 + - + +
689W GLY* 1.3 77.4 - - - +
691W ILE* 1.3 62.0 + - - +
692W MET 3.4 0.2 - - - -
693W SER* 2.8 20.8 + - - -
697W MET* 4.2 11.0 - - + +
726W ILE* 4.4 14.6 - - + +
729W ASP* 5.4 4.0 - - + +
730W TYR* 4.0 36.3 - - + +
733W ILE* 6.5 0.9 - - + -
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Residues in contact with ILE 691 (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* 2.9 23.7 + - + +
688W ARG* 3.4 14.6 - - + +
690W LEU* 1.3 76.7 - - - +
692W MET* 1.3 70.1 + - + +
693W SER 3.2 2.1 + - - -
694W SER 3.1 21.5 - - - +
697W MET* 3.3 28.3 - - + +
698W VAL* 3.3 16.9 - - + +
701W ASP* 3.8 24.0 - - + +
730W TYR* 3.3 30.9 - - + +
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Residues in contact with MET 692 (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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619W SER* 4.9 6.9 + - - -
620W ASP* 5.6 1.4 - - - +
621W VAL* 5.8 0.5 - - - +
688W ARG* 3.4 52.9 + - + +
689W GLY* 4.7 3.6 - - - -
691W ILE* 1.3 83.4 - - + +
693W SER* 1.3 61.6 + - - +
694W SER* 3.3 3.1 + - - +
698W VAL* 4.1 12.8 - - + -
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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