Contacts of the helix formed by residues 100 - 111 (chain G) in PDB entry 2VKZ
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 ASP 100 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96G LEU* 4.9 2.4 - - - +
99G ASN* 1.3 81.4 + - - +
101G ILE* 1.3 82.9 + - - +
102G HIS* 2.7 32.5 - - + +
103G ALA* 2.8 18.9 + - + +
104G LEU* 3.2 9.2 + - - +
126G TYR* 5.8 0.3 - - - -
137G PHE* 5.3 5.9 - - - -
255G LEU* 3.5 12.6 - - - +
548G PHE* 3.3 38.9 + - + +
549G ASP* 5.1 0.4 + - - -
550G VAL* 4.5 2.6 - - - +
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Residues in contact with ILE 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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91G PHE* 4.9 4.7 - - + -
96G LEU* 4.9 8.7 - - + +
99G ASN 4.1 0.6 + - - -
100G ASP* 1.3 84.7 + - - +
102G HIS* 1.3 65.6 + - + +
104G LEU* 3.0 10.2 + - - +
105G ALA* 2.9 28.6 + - - +
122G LEU* 4.1 26.1 - - + +
123G ILE* 4.2 15.0 - - + +
126G TYR* 3.6 44.9 - - + -
127G ILE* 3.2 41.3 - - + -
137G PHE* 5.2 2.5 - - + -
255G LEU* 5.1 1.6 - - + -
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Residues in contact with HIS 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 ASP* 2.7 31.6 - - + +
101G ILE* 1.3 87.8 - - + +
103G ALA* 1.3 60.3 + - - +
105G ALA* 3.4 8.2 + - - +
106G ALA* 3.1 22.5 + - - +
123G ILE* 3.5 21.2 - - + +
180G TYR* 2.8 37.8 + + - -
255G LEU* 3.5 20.9 - - + +
533G LEU* 4.0 7.4 - - + +
544G LYS* 4.0 18.1 - - + +
545G GLN* 3.7 27.4 - - + +
548G PHE* 4.3 10.6 - + + -
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Residues in contact with ALA 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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99G ASN* 3.8 18.4 - - + +
100G ASP* 2.8 15.7 + - + +
102G HIS* 1.3 78.1 - - - +
104G LEU* 1.3 60.7 + - - +
106G ALA* 3.5 7.1 + - - +
107G LYS* 3.1 31.6 + - + +
545G GLN* 4.8 6.4 - - + +
549G ASP* 3.7 28.5 - - + +
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Residues in contact with LEU 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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58G ALA* 4.8 7.0 - - + -
91G PHE* 3.7 19.3 - - + -
95G TYR* 4.2 20.9 - - + +
96G LEU* 3.4 31.2 - - + -
99G ASN* 5.6 1.9 - - - +
100G ASP 3.2 4.7 + - - +
101G ILE* 3.0 12.2 + - + +
103G ALA* 1.3 77.5 - - - +
105G ALA* 1.3 54.0 + - - +
107G LYS* 3.0 11.8 + - + +
108G LEU* 2.7 62.7 + - + +
122G LEU* 4.0 10.8 - - + -
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Residues in contact with ALA 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 ILE 2.9 12.1 + - - +
102G HIS 3.4 4.2 + - - +
104G LEU* 1.3 77.7 - - - +
106G ALA* 1.3 57.2 + - - +
108G LEU* 3.2 10.0 + - - +
109G LEU* 2.8 33.3 + - - +
119G THR* 3.4 35.4 + - + +
122G LEU* 5.8 4.0 - - + -
123G ILE* 4.1 7.6 - - + -
533G LEU* 3.5 16.6 - - + -
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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 HIS 3.1 10.6 + - - +
103G ALA* 3.6 10.5 - - - +
105G ALA* 1.3 77.1 - - - +
107G LYS* 1.3 61.9 + - + +
109G LEU* 3.1 7.9 + - - +
110G GLN* 2.8 32.9 + - - +
533G LEU* 4.8 4.0 - - + +
535G ILE* 3.9 8.2 - - + +
545G GLN* 3.6 28.0 - - + +
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Residues in contact with LYS 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 ALA* 3.1 23.5 + - - +
104G LEU* 3.0 15.8 + - + +
106G ALA* 1.3 75.0 - - - +
108G LEU* 1.3 60.7 + - + +
110G GLN* 4.6 4.7 - - + -
111G GLU* 2.9 64.8 + - - +
112G ASN* 4.8 0.6 - - - +
553G ASN* 4.5 16.6 + - - +
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Residues in contact with LEU 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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56G THR* 3.9 15.3 - - + +
58G ALA* 4.4 10.1 - - + -
59G GLU* 4.2 26.9 - - + +
104G LEU* 2.7 48.9 + - + +
105G ALA* 3.6 8.7 - - - +
106G ALA 3.2 0.2 - - - -
107G LYS* 1.3 73.8 - - + +
109G LEU* 1.3 63.1 + - + +
112G ASN* 3.2 54.9 - - + +
113G ASP 3.6 7.7 + - - +
119G THR* 5.2 4.0 - - - +
122G LEU* 4.5 13.9 - - + -
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Residues in contact with LEU 109 (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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105G ALA 2.8 10.9 + - - +
106G ALA* 3.4 8.5 - - - +
108G LEU* 1.3 80.1 - - - +
110G GLN* 1.3 68.8 + - - +
112G ASN 3.4 2.3 - - - +
113G ASP 5.0 0.2 - - - +
114G THR* 2.9 36.3 + - + +
115G THR 3.3 33.9 - - - +
116G LEU* 3.3 30.5 - - + -
119G THR* 3.4 25.4 - - + +
533G LEU* 5.2 2.7 - - + +
534G ASP* 5.0 3.8 - - - +
535G ILE* 3.5 27.4 - - + -
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Residues in contact with GLN 110 (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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106G ALA 2.8 20.9 + - - +
107G LYS* 4.0 4.5 - - + +
109G LEU* 1.3 77.8 - - - +
111G GLU* 1.3 72.0 + - + +
112G ASN 4.1 0.3 - - - +
114G THR* 4.7 1.2 + - - -
535G ILE* 3.8 23.9 - - + +
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Residues in contact with GLU 111 (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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107G LYS* 2.9 44.3 + - + +
110G GLN* 1.3 83.1 - - + +
112G ASN* 1.3 80.4 + - - +
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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