Contacts of the helix formed by residues 107 - 118 (chain G) in PDB entry 4U0Z
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 ARG 107 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106G ALA* 1.4 76.7 - - - +
108G ALA* 1.3 60.7 + - - +
109G ALA 3.3 0.2 - - - -
110G LEU* 3.4 2.0 + - - +
111G ASN* 2.7 42.1 + - - +
139G PHE* 3.9 20.6 - - + -
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Residues in contact with ALA 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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106G ALA 4.1 8.0 - - - +
107G ARG* 1.3 78.2 - - - +
109G ALA* 1.4 59.0 + - - +
111G ASN* 3.6 6.0 + - - +
112G GLN* 3.2 23.6 + - - +
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Residues in contact with ALA 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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106G ALA* 3.4 14.8 + - - +
107G ARG 3.3 0.2 - - - -
108G ALA* 1.4 76.9 - - - +
110G LEU* 1.4 54.3 + - - +
112G GLN* 3.3 0.9 + - - -
113G ALA* 2.8 36.5 + - - +
128G LEU* 3.4 25.1 - - + +
131G HIS* 3.8 26.9 - - + +
132G ALA* 3.8 13.7 - - + -
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Residues in contact with LEU 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 3.6 2.0 + - - -
107G ARG 3.4 6.1 + - - +
109G ALA* 1.4 73.8 - - - +
111G ASN* 1.3 63.2 + - - +
113G ALA* 3.5 3.7 + - - +
114G LEU* 3.1 39.3 + - + +
129G PHE* 3.6 28.5 - - + -
132G ALA* 4.2 5.3 - - + +
139G PHE* 3.5 37.7 - - + -
141G ASP* 3.6 27.1 - - + +
142G ALA* 3.6 20.2 - - + +
145G GLU* 3.7 8.1 - - + -
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Residues in contact with ASN 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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282C ILE* 6.1 4.5 - - + -
107G ARG* 2.7 32.7 + - - +
108G ALA* 4.1 6.5 - - - +
109G ALA 3.4 0.2 - - - -
110G LEU* 1.3 80.3 - - - +
112G GLN* 1.4 55.6 + - - +
114G LEU* 3.8 6.9 + - - +
115G GLU* 3.3 25.1 + - - +
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Residues in contact with GLN 112 (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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108G ALA 3.2 18.3 + - - +
109G ALA* 3.5 4.9 - - - +
110G LEU 3.2 0.2 - - - -
111G ASN* 1.4 73.7 - - - +
113G ALA* 1.4 56.7 + - - +
115G GLU* 3.3 7.0 + - - +
116G MET* 3.0 38.5 + - - +
128G LEU* 3.8 20.0 - - + -
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Residues in contact with ALA 113 (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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109G ALA 2.8 20.2 + - - +
110G LEU* 3.7 7.0 - - - +
112G GLN* 1.4 72.0 - - - +
114G LEU* 1.4 56.6 + - - +
116G MET 3.4 0.5 + - - -
117G LYS* 3.0 25.1 + - - +
125G ALA* 3.4 13.2 - - - +
128G LEU* 3.6 27.3 - - + +
129G PHE* 3.9 36.2 - - + +
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Residues in contact with LEU 114 (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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110G LEU* 3.1 47.2 + - + +
111G ASN* 3.9 7.9 - - - +
113G ALA* 1.4 74.7 - - - +
115G GLU* 1.4 61.8 + - - +
117G LYS* 3.4 11.6 - - + +
118G ARG* 3.3 19.6 + - - +
129G PHE* 4.6 10.5 - - + -
145G GLU* 3.9 16.4 - - + +
148G ILE* 5.7 8.1 - - + -
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Residues in contact with GLU 115 (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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111G ASN 3.3 15.2 + - - +
112G GLN* 3.3 8.4 + - - +
114G LEU* 1.4 76.9 - - - +
116G MET* 1.4 63.2 + - - +
118G ARG* 3.2 26.0 + - - +
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Residues in contact with MET 116 (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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112G GLN* 3.0 28.1 + - - +
113G ALA* 3.6 6.3 - - - +
115G GLU* 1.4 75.4 - - - +
117G LYS* 1.4 54.3 + - - +
118G ARG 3.3 4.9 - - - +
120G GLY 2.8 32.0 - - - +
121G LYS* 3.6 24.2 - - + +
124G LYS* 3.8 18.4 - - + -
125G ALA* 3.8 13.7 - - + -
128G LEU* 3.3 20.2 - - + -
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Residues in contact with LYS 117 (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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113G ALA 3.0 13.7 + - - +
114G LEU* 3.4 21.1 - - + +
116G MET* 1.4 73.9 - - - +
118G ARG* 1.4 61.5 + - - +
119G GLN 3.6 2.8 + - - -
120G GLY 3.6 12.4 + - - +
121G LYS 4.9 0.2 - - - -
122G ARG* 5.3 9.6 + - - +
125G ALA* 4.0 10.0 - - + +
129G PHE* 5.0 2.5 - - + -
149G PHE* 4.6 18.8 - - + -
152G GLU* 5.9 0.7 - - - +
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Residues in contact with ARG 118 (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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114G LEU 3.3 9.4 + - - +
115G GLU* 3.2 22.8 + - - +
116G MET 3.3 3.8 - - - +
117G LYS* 1.4 76.1 - - - +
119G GLN* 1.3 58.6 + - + +
120G GLY 2.9 12.6 + - - -
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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