Contacts of the helix formed by residues 100 - 108 (chain G) in PDB entry 1ZWS
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 GLU 100 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98G GLY 4.6 0.3 - - - +
99G GLY* 1.3 72.2 - - - -
101G LEU* 1.3 70.5 + - - +
102G PHE* 4.4 3.3 - - + +
103G ASP* 2.8 45.7 + - - +
104G PHE* 3.1 8.7 + - - +
142G PRO 3.8 9.7 - - - +
143G GLU* 3.2 36.1 + - - +
145G ILE 3.8 4.0 - - - +
146G MET* 3.6 18.4 - - + -
147G LEU* 4.6 0.7 - - - -
53H ARG* 4.8 5.9 + - - -
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Residues in contact with LEU 101 (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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99G GLY 3.4 4.0 + - - -
100G GLU* 1.3 68.1 - - - +
102G PHE* 1.3 72.8 + - + +
104G PHE* 2.7 35.6 + - + +
105G LEU* 3.0 32.3 + - + -
119G PHE* 3.9 27.4 - - + -
123G ILE* 4.5 11.2 - - + -
145G ILE* 2.8 46.3 + - + +
147G LEU* 3.7 25.0 - - + +
157G ILE* 3.8 12.3 - - + -
206G ILE* 6.1 0.9 - - + -
210G LEU* 5.5 3.6 - - + -
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Residues in contact with PHE 102 (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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100G GLU* 4.4 3.8 - - + +
101G LEU* 1.3 99.7 - - + +
103G ASP* 1.3 65.7 + - - +
105G LEU* 3.4 15.9 + - + +
106G ALA* 3.2 17.8 + - - +
142G PRO* 3.5 51.8 - - + +
145G ILE* 4.5 1.3 + - + -
206G ILE* 4.3 17.3 - - + -
209G ILE* 3.6 32.1 - - + -
210G LEU* 4.3 19.7 - - + -
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Residues in contact with ASP 103 (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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100G GLU* 2.8 45.9 + - - +
102G PHE* 1.3 71.8 - - - +
104G PHE* 1.3 63.4 + - - +
106G ALA* 2.7 30.6 - - - +
107G GLN* 3.4 7.3 + - - +
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Residues in contact with PHE 104 (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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98G GLY 5.0 0.7 - - - +
100G GLU 3.1 5.1 + - - +
101G LEU* 2.7 20.7 + - + +
103G ASP* 1.3 71.4 - - - +
105G LEU* 1.3 80.2 + - + -
106G ALA 2.7 10.6 + - - -
107G GLN* 2.9 27.4 + - - +
108G LYS* 3.2 47.0 + - + +
119G PHE* 4.3 4.0 - + - -
147G LEU* 3.5 26.5 - - + -
150G LYS* 4.0 34.5 - - + +
152G ILE 4.7 1.8 - - - -
153G PRO 4.7 2.2 - - - -
155G PRO* 3.8 31.4 - - + -
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Residues in contact with LEU 105 (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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101G LEU* 3.0 30.7 + - + +
102G PHE* 3.7 16.2 - - + +
104G PHE* 1.3 93.9 - - + +
106G ALA* 1.3 56.5 + - - +
108G LYS* 2.8 32.2 - - + +
111G LEU* 4.0 25.9 - - + +
119G PHE* 3.9 24.7 - - + -
210G LEU* 4.3 26.9 - - + +
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Residues in contact with ALA 106 (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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102G PHE 3.2 8.9 + - - +
103G ASP* 2.7 23.7 + - - +
104G PHE 2.7 1.0 + - - -
105G LEU* 1.3 73.9 - - - +
107G GLN* 1.3 59.3 + - + +
108G LYS 2.6 19.9 - - - +
109G GLU* 4.7 0.5 - - - -
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Residues in contact with GLN 107 (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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103G ASP 4.1 7.0 - - - +
104G PHE* 2.9 14.6 + - - +
106G ALA* 1.3 77.5 - - + +
108G LYS* 1.3 64.4 + - - +
109G GLU* 3.0 14.0 + - - +
150G LYS* 4.0 19.4 + - - -
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Residues in contact with LYS 108 (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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104G PHE* 3.2 41.8 + - + +
105G LEU* 2.8 24.3 - - + +
106G ALA 2.6 19.3 - - - +
107G GLN* 1.3 76.7 - - - +
109G GLU* 1.3 60.5 + - - +
110G SER 3.4 21.3 + - - +
111G LEU* 4.2 9.0 - - + -
115G GLU* 3.2 32.0 + - - +
119G PHE* 4.5 7.4 - - - -
153G PRO* 3.9 12.7 + - - +
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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