Contacts of the helix formed by residues 3152 - 3163 (chain D) in PDB entry 1G24
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 LYS3152 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3150D ILE* 2.8 17.4 + - - +
3151D ASN* 1.3 79.7 - - - +
3153D THR* 1.3 63.6 + - - +
3154D ALA 3.3 1.5 - - - +
3155D PHE* 3.3 26.1 - - + +
3156D GLU* 3.2 47.5 + - + +
3159D LYS* 5.1 1.8 - - - +
3230D LEU* 4.1 21.6 - - + +
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Residues in contact with THR3153 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2153C THR* 4.2 19.6 + - + +
3151D ASN* 2.7 30.8 + - - +
3152D LYS* 1.3 71.0 - - - +
3154D ALA* 1.3 63.1 + - - +
3156D GLU* 3.2 21.1 + - - +
3157D LYS* 3.5 20.8 + - - +
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Residues in contact with ALA3154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3139D PHE* 3.1 30.4 - - + -
3142D THR* 4.0 23.8 - - + +
3143D LEU* 4.2 8.3 - - + -
3151D ASN* 2.7 23.6 - - + +
3152D LYS 3.3 0.2 - - - -
3153D THR* 1.3 70.8 - - - +
3155D PHE* 1.3 54.2 + - - +
3157D LYS* 2.9 11.1 + - + +
3158D ALA 2.8 31.7 + - - -
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Residues in contact with PHE3155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3143D LEU* 5.1 0.7 - - - -
3150D ILE* 3.3 23.8 - - + +
3152D LYS* 3.3 29.4 + - + +
3154D ALA* 1.3 79.9 - - - +
3156D GLU* 1.3 67.5 + - - +
3158D ALA* 3.2 8.8 + - + +
3159D LYS* 2.9 74.4 + - + +
3228D MET* 3.7 15.9 - - + -
3229D ARG* 3.7 14.1 - - - -
3230D LEU* 3.7 31.9 - - + -
3237D ILE* 3.8 27.1 - - + -
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Residues in contact with GLU3156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3152D LYS* 3.2 40.7 + - + +
3153D THR* 3.5 10.8 - - - +
3154D ALA 3.1 0.6 - - - -
3155D PHE* 1.3 77.8 - - - +
3157D LYS* 1.3 60.8 + - + +
3159D LYS* 3.4 30.7 + - - +
3160D ALA* 3.0 28.1 + - - +
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Residues in contact with LYS3157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3138D GLU* 5.6 5.6 - - - +
3139D PHE* 3.9 13.6 - - + -
3153D THR* 3.9 22.2 - - - +
3154D ALA* 2.9 12.9 + - - +
3156D GLU* 1.3 78.2 - - + +
3158D ALA* 1.3 59.2 + - - +
3160D ALA* 3.5 6.7 + - - +
3161D LYS* 3.0 29.5 + - - +
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Residues in contact with ALA3158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3135D LEU* 4.0 23.3 - - + -
3139D PHE* 3.6 19.7 - - + -
3143D LEU* 5.2 0.2 - - + -
3154D ALA 2.8 11.8 + - - +
3155D PHE* 3.4 15.7 - - + +
3157D LYS* 1.3 78.6 - - - +
3159D LYS* 1.3 56.3 + - - +
3161D LYS* 3.3 3.2 + - - -
3162D PHE* 3.0 36.3 + - - +
3228D MET* 4.0 11.5 - - + +
3237D ILE* 5.2 0.4 - - + -
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Residues in contact with LYS3159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3152D LYS* 5.1 1.8 - - - +
3155D PHE* 2.9 52.7 + - + +
3156D GLU* 3.5 39.6 + - - +
3157D LYS 3.3 0.2 - - - -
3158D ALA* 1.3 72.4 - - - +
3160D ALA* 1.3 60.9 + - - +
3161D LYS 2.9 4.9 - - - -
3163D LEU* 2.8 51.1 + - + +
3228D MET* 3.8 29.9 + - + +
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Residues in contact with ALA3160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3156D GLU 3.0 17.3 + - - +
3157D LYS* 3.8 8.1 - - - +
3159D LYS* 1.3 75.1 - - - +
3161D LYS* 1.3 58.7 + - - +
3163D LEU 4.9 0.8 - - - +
3165D LYS* 3.8 16.8 + - - -
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Residues in contact with LYS3161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3135D LEU 3.2 17.1 + - - +
3136D GLY* 4.2 7.1 - - - -
3138D GLU* 3.0 28.3 + - - +
3139D PHE* 4.4 7.4 - - + -
3157D LYS 3.0 16.5 + - - +
3158D ALA 3.4 5.4 - - - +
3159D LYS 2.9 0.8 - - - -
3160D ALA* 1.3 80.2 - - - +
3162D PHE* 1.3 90.3 + - + +
3165D LYS* 3.3 24.2 + - - +
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Residues in contact with PHE3162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3134D TYR* 4.5 0.4 - + - -
3135D LEU* 3.4 53.8 - - + -
3158D ALA* 3.0 24.8 + - - +
3161D LYS* 1.3 106.1 - - + +
3163D LEU* 1.3 68.1 + - - +
3164D ASN 3.3 0.5 + - - -
3165D LYS* 3.2 23.4 + - - +
3167D ARG* 3.2 45.8 - - + -
3225D ILE* 3.6 29.9 - - + +
3228D MET* 4.1 5.8 - - + -
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Residues in contact with LEU3163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3159D LYS* 2.8 45.5 + - + +
3160D ALA 5.3 0.5 - - - +
3162D PHE* 1.3 73.1 - - - +
3164D ASN* 1.3 94.5 + - - +
3165D LYS* 3.4 11.6 - - - +
3225D ILE* 4.1 2.7 - - - +
3226D ASP 3.8 24.2 - - - +
3227D ASP* 3.9 15.5 - - - +
3228D MET* 3.9 16.8 - - + +
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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