Contacts of the helix formed by residues 1030 - 1037 (chain W) in PDB entry 6G0L
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 ILE1030 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1024W PHE* 3.6 42.8 - - + -
1026W ASN 4.7 2.0 - - - +
1027W LEU* 3.2 27.7 + - + +
1029W GLU* 1.3 90.7 - - + +
1031W LEU* 1.3 65.7 + - - +
1032W ASP 3.2 3.1 + - - -
1033W GLU* 3.4 24.3 + - + +
1034W LEU* 3.8 19.1 + - + +
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Residues in contact with LEU1031 (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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1027W LEU* 4.0 23.6 - - + +
1028W LYS* 3.3 24.2 - - + +
1029W GLU 3.3 4.8 + - - +
1030W ILE* 1.3 77.4 - - - +
1032W ASP* 1.3 60.9 + - - +
1034W LEU* 4.0 6.7 + - + +
1035W ILE* 3.5 25.2 + - + +
1040W LEU* 4.8 6.4 - - + +
1045W PHE* 3.3 57.2 - - + +
1048W TYR* 4.1 27.8 - - + -
1049W GLY* 5.0 6.5 - - - +
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Residues in contact with ASP1032 (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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345W LYS 4.4 11.7 - - - +
346W ILE* 5.5 2.9 - - - +
350W TYR* 5.2 16.5 - - - -
1030W ILE 3.5 0.6 - - - -
1031W LEU* 1.3 75.3 - - - +
1033W GLU* 1.3 68.7 + - + +
1034W LEU 3.2 0.4 - - - -
1035W ILE* 3.1 13.7 + - - +
1036W ALA* 2.9 24.1 + - - +
1045W PHE* 4.0 23.5 - - + -
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Residues in contact with GLU1033 (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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343W ASN* 2.8 47.9 + - - +
344W SER* 4.0 4.1 + - - -
345W LYS* 3.0 37.9 + - - +
1030W ILE* 3.4 19.2 + - + +
1032W ASP* 1.3 77.5 - - + +
1034W LEU* 1.3 64.3 + - + +
1036W ALA 3.7 0.7 + - - -
1037W ASP* 3.8 3.5 + - - +
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Residues in contact with LEU1034 (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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1020W ALA* 4.8 7.2 - - + -
1024W PHE* 3.6 34.1 - - + -
1027W LEU* 4.9 10.8 - - + -
1030W ILE* 3.8 31.3 + - + +
1031W LEU* 4.2 7.6 - - - +
1032W ASP 3.2 0.4 - - - -
1033W GLU* 1.3 76.4 - - + +
1035W ILE* 1.3 54.7 + - - +
1037W ASP* 2.3 35.4 + - - +
1039W THR* 3.5 22.7 + - + +
1040W LEU* 3.4 35.0 + - + -
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Residues in contact with ILE1035 (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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349W GLN* 5.7 1.6 - - - +
350W TYR* 4.5 11.9 - - + +
1031W LEU* 3.5 21.0 + - + +
1032W ASP* 3.1 13.3 + - - +
1034W LEU* 1.3 73.1 - - - +
1036W ALA* 1.3 68.7 + - - +
1037W ASP 2.9 7.4 - - - +
1040W LEU* 3.3 40.7 - - + +
1041W PRO 3.6 10.3 - - - +
1042W VAL* 3.8 28.7 - - + -
1043W LYS 4.3 12.1 - - - +
1045W PHE* 4.5 12.1 - - + -
1048W TYR* 4.0 16.6 - - + -
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Residues in contact with ALA1036 (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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345W LYS* 2.2 67.8 + - + +
347W LEU* 5.2 4.2 - - - +
349W GLN* 3.9 26.9 - - - +
350W TYR* 6.0 6.1 - - - -
1032W ASP* 2.9 16.5 + - - +
1034W LEU 3.3 0.2 - - - -
1035W ILE* 1.3 79.5 - - - +
1037W ASP* 1.3 52.6 + - - +
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Residues in contact with ASP1037 (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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345W LYS* 2.8 39.9 + - + +
349W GLN* 5.6 1.1 - - - -
472W TYR* 5.9 2.6 - - - -
1033W GLU 3.8 3.1 + - - +
1034W LEU* 2.3 29.2 + - - +
1035W ILE 2.9 9.7 - - - +
1036W ALA* 1.3 74.2 - - - +
1038W GLY* 1.3 72.9 + - - +
1039W THR* 3.3 8.2 + - - -
1040W LEU 3.8 1.2 + - - +
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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