Contacts of the helix formed by residues 12 - 25 (chain G) in PDB entry 5G04
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 LYS 12 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10G GLU* 3.7 8.7 + - + +
11G LEU* 1.3 80.2 - - - +
13G LEU* 1.3 59.9 + - - +
14G ASP* 3.1 15.7 - - + +
15G ASP* 2.8 43.7 + - - +
16G ILE* 3.2 7.4 + - - +
514J PHE* 4.1 7.6 - - - -
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Residues in contact with LEU 13 (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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12G LYS* 1.3 72.8 - - - +
14G ASP* 1.3 64.2 + - - +
16G ILE* 2.9 44.2 + - + +
17G GLU* 3.3 4.2 + - - +
513J THR* 5.5 7.4 - - - +
514J PHE* 5.4 7.9 - - + +
517J THR* 4.9 9.2 - - + -
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Residues in contact with ASP 14 (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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12G LYS* 4.1 13.3 - - + +
13G LEU* 1.3 80.7 - - - +
15G ASP* 1.3 63.5 + - - +
17G GLU* 3.1 30.0 + - - +
18G GLU* 3.8 2.1 + - - +
457J LYS* 4.8 3.3 + - - +
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Residues in contact with ASP 15 (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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10G GLU 3.9 4.7 - - - +
11G LEU* 3.6 15.2 - - + -
12G LYS* 2.8 38.9 + - - +
14G ASP* 1.3 79.1 - - - +
16G ILE* 1.3 57.1 + - - -
18G GLU* 3.0 12.2 + - - +
413J PHE* 6.0 1.2 - - - -
453J HIS* 4.5 1.9 - - - -
456J ARG* 3.3 23.8 + - - +
457J LYS* 3.5 27.1 + - - +
487J TYR* 2.2 30.5 + - + +
514J PHE* 5.0 0.9 - - + -
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Residues in contact with ILE 16 (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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12G LYS 3.2 0.8 + - - -
13G LEU* 2.9 38.5 + - + +
15G ASP* 1.3 72.0 - - - +
17G GLU* 1.3 63.5 + - - +
19G PHE* 3.0 15.9 + - + +
20G GLU* 3.4 21.3 + - + +
487J TYR* 3.9 7.2 - - - -
514J PHE* 3.8 25.6 - - + -
517J THR* 3.9 30.3 - - + +
518J MET* 4.5 17.0 - - + -
521J HIS* 5.1 14.8 - - + +
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Residues in contact with GLU 17 (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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13G LEU 3.3 5.0 + - - +
14G ASP* 3.1 21.1 + - - +
16G ILE* 1.3 76.9 - - - +
18G GLU* 1.3 61.2 + - - +
20G GLU* 3.1 22.2 + - + +
21G ASN* 3.4 25.8 + - - +
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Residues in contact with GLU 18 (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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14G ASP 3.8 1.6 + - - +
15G ASP* 3.0 13.5 + - - +
17G GLU* 1.3 76.2 + - - +
19G PHE* 1.3 62.0 + - - +
21G ASN* 3.2 29.4 + - - +
22G ILE* 3.5 5.7 + - - +
456J ARG* 2.8 35.9 + - - +
457J LYS* 3.4 42.9 + - - +
459J LYS* 3.5 38.9 + - - +
487J TYR* 3.6 2.9 - - - +
491J LEU* 4.4 8.2 - - + +
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Residues in contact with PHE 19 (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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16G ILE* 3.0 13.0 + - + +
18G GLU* 1.3 78.8 - - - +
20G GLU* 1.3 78.1 + - - +
22G ILE* 3.3 15.8 + - + +
23G ARG* 3.2 32.3 + - + +
487J TYR* 3.6 11.7 + - + +
490J SER* 4.0 14.8 - - - -
491J LEU* 3.6 30.5 - - + -
495J PHE* 3.7 26.5 - + - -
518J MET* 4.5 13.7 - - + -
521J HIS* 4.0 30.7 - + + -
522J CYS 5.1 0.2 - - - -
525J MET* 3.6 23.8 - - + -
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Residues in contact with GLU 20 (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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16G ILE* 3.4 17.0 + - + +
17G GLU* 3.1 17.3 + - + +
19G PHE* 1.3 94.7 - - - +
21G ASN* 1.3 64.1 + - - +
23G ARG* 3.2 24.6 + - - +
24G LYS* 3.2 19.4 + - - +
521J HIS* 4.3 16.9 + - - -
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Residues in contact with ASN 21 (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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17G GLU* 3.4 27.0 + - - +
18G GLU* 3.2 18.8 + - - +
19G PHE 3.2 0.6 - - - -
20G GLU* 1.3 76.7 - - - +
22G ILE* 1.3 62.0 + - - +
24G LYS* 3.2 22.6 + - - +
25G ASP* 3.7 4.3 + - - +
459J LYS* 5.5 5.6 - - - +
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Residues in contact with ILE 22 (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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18G GLU 3.5 4.3 + - - +
19G PHE* 3.3 35.1 + - + +
21G ASN* 1.3 74.9 - - - +
23G ARG* 1.3 63.9 + - - +
25G ASP* 3.3 25.3 + - + +
459J LYS* 5.2 4.5 - - + +
461J TYR* 3.9 27.1 - - + +
490J SER 5.2 0.7 - - - +
491J LEU* 3.6 33.7 - - + +
495J PHE* 6.0 2.2 - - + -
525J MET* 6.4 0.4 - - + -
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Residues in contact with ARG 23 (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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19G PHE* 3.2 30.9 + - + +
20G GLU* 3.2 31.6 + - - +
22G ILE* 1.3 75.4 - - - +
24G LYS* 1.3 66.3 + - - +
25G ASP 3.4 6.6 + - - +
521J HIS* 5.3 8.9 - - - -
524J GLU* 6.4 0.2 - - - +
525J MET* 3.4 37.7 - - + +
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Residues in contact with LYS 24 (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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20G GLU 3.2 6.6 + - - +
21G ASN* 3.2 15.5 + - - +
23G ARG* 1.3 80.0 - - - +
25G ASP* 1.3 61.4 + - - +
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Residues in contact with ASP 25 (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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21G ASN 3.7 4.3 + - - +
22G ILE* 3.3 25.2 + - + +
23G ARG 3.3 7.1 - - - +
24G LYS* 1.3 81.2 - - - +
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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