Contacts of the helix formed by residues 116 - 134 (chain G) in PDB entry 7RDB
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 PHE 116 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ARG* 4.5 28.0 - - + +
134A ASN* 3.4 17.7 - - - +
141A PHE* 4.0 11.7 - - + -
115G THR* 1.3 79.0 + - - +
117G ARG* 1.3 66.1 + - - +
118G GLN 3.2 0.9 - - - -
119G GLN* 3.0 26.7 + - - +
120G THR* 3.1 21.5 + - + +
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Residues in contact with ARG 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ASP* 3.0 30.1 + - - +
140A ASP* 3.8 20.7 + - - +
141A PHE* 3.7 15.1 - - + -
115G THR 2.6 14.0 + - - +
116G PHE* 1.3 73.7 - - - +
118G GLN* 1.3 56.6 + - - +
120G THR* 3.2 6.1 + - - +
121G ILE* 3.0 56.1 + - + +
221G ASN* 3.4 23.8 + - - +
224G ILE* 4.3 9.9 - - - +
225G ILE* 6.0 1.0 - - - +
190I THR 5.0 2.8 + - - -
191I THR 3.4 24.0 + - - -
192I GLU 4.9 2.2 + - - -
193I VAL* 4.2 23.2 - - - +
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Residues in contact with GLN 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G THR* 3.5 25.1 + - + +
116G PHE 3.2 0.8 - - - -
117G ARG* 1.3 76.8 - - + +
119G GLN* 1.3 61.6 + - - +
121G ILE* 4.2 22.1 - - - +
122G ASP* 2.8 56.5 + - - +
195J ASN* 6.3 0.7 - - - +
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Residues in contact with GLN 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ARG* 5.1 12.5 - - - +
115G THR* 3.6 22.0 + - - +
116G PHE* 3.0 19.1 + - - +
118G GLN* 1.3 78.0 - - - +
120G THR* 1.3 62.4 + - + +
122G ASP* 3.5 7.6 + - - +
123G PHE* 2.8 26.7 + - - +
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Residues in contact with THR 120 (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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141A PHE* 5.9 5.1 - - + -
116G PHE* 3.1 15.6 + - + +
117G ARG* 3.2 10.5 + - - +
119G GLN* 1.3 76.1 - - + +
121G ILE* 1.3 65.6 + - - +
123G PHE* 3.1 12.2 + - - +
124G LEU* 2.8 40.4 + - - +
224G ILE* 5.6 5.2 - - - +
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Residues in contact with ILE 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G ARG* 3.0 60.0 + - + +
118G GLN* 4.1 23.3 - - - +
120G THR* 1.3 84.6 + - - +
122G ASP* 1.3 66.9 + - - +
124G LEU* 3.4 3.8 + - - +
125G ASN* 2.8 33.4 + - - +
158G GLU* 5.3 3.1 - - - +
220G THR* 4.1 18.2 - - + -
221G ASN* 4.7 14.1 - - + +
224G ILE* 5.2 11.4 - - + -
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Residues in contact with ASP 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G GLN* 2.8 46.1 + - - +
119G GLN* 3.5 8.1 - - - +
120G THR 3.3 0.2 - - - -
121G ILE* 1.3 73.5 - - - +
123G PHE* 1.3 50.9 + - - +
125G ASN* 2.4 36.0 + - - +
126G ASP* 2.7 33.2 + - - +
197J MET* 4.3 19.7 - - - +
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Residues in contact with PHE 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119G GLN 2.8 17.2 + - - +
120G THR* 3.2 14.1 - - - +
122G ASP* 1.3 69.2 - - - +
124G LEU* 1.3 90.0 + - + +
126G ASP* 3.2 8.7 + - - +
127G ASN* 3.2 58.5 + - - +
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Residues in contact with LEU 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G THR* 2.8 25.1 + - - +
123G PHE* 1.3 98.7 - - + +
125G ASN* 1.3 64.2 + - - +
127G ASN* 3.5 5.4 + - - +
128G ILE* 3.3 28.9 + - + +
220G THR* 3.6 35.2 - - + +
223G VAL* 6.0 4.5 - - + -
224G ILE* 3.9 23.1 - - + -
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Residues in contact with ASN 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G GLN* 6.0 0.2 - - - +
121G ILE* 2.8 26.9 + - - +
122G ASP* 2.4 28.9 + - - +
124G LEU* 1.3 69.8 - - - +
126G ASP* 1.3 64.1 + - - +
127G ASN 3.3 0.2 - - - -
128G ILE* 4.3 3.8 - - - +
129G ARG* 3.2 44.6 + - - +
157G GLY* 3.3 7.7 - - - -
158G GLU* 3.6 37.3 + - - +
220G THR* 2.4 34.9 + - - -
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Residues in contact with ASP 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122G ASP* 2.7 41.6 + - - +
123G PHE* 3.2 7.9 + - + +
124G LEU 3.2 0.2 - - - -
125G ASN* 1.3 78.3 - - - +
127G ASN* 1.3 67.1 + - - +
129G ARG* 4.1 17.0 + - - +
130G ARG* 3.2 21.8 + - - +
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Residues in contact with ASN 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G PHE* 3.2 46.5 + - - +
124G LEU* 3.9 6.0 - - - +
126G ASP* 1.3 82.3 - - - +
128G ILE* 1.3 68.0 + - + +
130G ARG* 3.3 8.5 + - - +
131G GLY* 3.3 15.6 + - - -
141G PHE* 4.2 3.3 - - - -
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Residues in contact with ILE 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G LEU* 3.3 18.4 + - + +
125G ASN 4.3 3.4 - - - +
127G ASN* 1.3 78.1 - - + +
129G ARG* 1.3 66.2 + - + +
132G ILE* 2.9 36.3 + - + +
141G PHE* 3.1 10.7 - - + -
145G MET* 3.8 28.9 - - - -
156G GLY 3.2 10.8 - - - +
157G GLY* 3.1 41.5 - - - +
219G CYS* 5.2 3.1 - - + -
220G THR* 5.0 4.7 - - - +
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Residues in contact with ARG 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G ASN* 3.2 39.9 + - - +
126G ASP* 4.1 18.0 + - - +
127G ASN 3.3 0.2 - - - -
128G ILE* 1.3 80.0 - - + +
130G ARG* 1.3 67.3 + - - +
131G GLY 3.1 0.9 + - - -
132G ILE* 3.4 10.4 + - + +
133G GLU* 3.3 27.1 + - - +
158G GLU* 4.7 8.9 - - - +
162G ASP* 4.1 24.4 + - - +
165G LYS* 3.9 38.9 - - + +
176J PRO* 6.1 3.4 - - - +
200J TYR* 6.3 1.0 - - - -
201J LYS* 5.5 7.5 - - - +
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Residues in contact with ARG 130 (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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116C PHE* 5.9 4.7 - - + -
126G ASP 3.2 16.2 + - - +
127G ASN* 3.4 12.8 - - - +
129G ARG* 1.3 76.9 - - - +
131G GLY* 1.3 57.2 + - - +
133G GLU* 3.3 28.9 - - - +
134G ASN* 3.3 17.4 + - - +
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Residues in contact with GLY 131 (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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116C PHE* 5.8 2.2 - - - -
127G ASN 3.3 3.8 + - - -
128G ILE 3.3 0.8 + - - -
129G ARG 3.0 0.6 - - - -
130G ARG* 1.3 77.4 - - - +
132G ILE* 1.3 51.6 + - - +
133G GLU 2.8 2.5 - - - -
134G ASN* 2.5 25.7 + - - -
135G TYR 2.6 8.1 + - - -
141G PHE* 1.7 55.4 - - - -
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Residues in contact with ILE 132 (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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128G ILE* 2.9 37.1 + - + +
129G ARG* 3.7 9.0 - - - +
131G GLY* 1.3 72.2 - - - +
133G GLU* 1.3 52.0 + - - +
135G TYR* 3.3 10.8 - - - +
141G PHE* 2.3 13.9 - - + -
145G MET* 4.8 3.1 - - + -
156G GLY* 4.5 2.7 - - - -
162G ASP* 3.9 35.9 - - + +
163G TRP* 3.9 37.2 - - + -
165G LYS* 4.2 6.3 - - + -
166G ASN* 2.5 57.6 + - + +
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Residues in contact with GLU 133 (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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129G ARG* 3.3 15.3 + - - +
130G ARG* 3.3 18.2 - - - +
131G GLY 2.8 0.8 - - - -
132G ILE* 1.3 79.5 - - - +
134G ASN* 1.3 61.6 + - - +
135G TYR 3.3 1.0 + - - -
136G TYR 5.1 0.3 + - - -
137G ASP* 4.6 7.3 - - - +
165G LYS* 3.6 35.3 - - + +
166G ASN* 3.4 16.5 + - - +
167G GLN* 5.4 2.6 + - - +
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Residues in contact with ASN 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C THR* 4.1 11.3 + - - +
116C PHE* 3.7 28.2 - - + +
130G ARG* 3.3 18.5 + - - +
131G GLY* 2.5 16.1 + - - +
133G GLU* 1.3 74.1 - - - +
135G TYR* 1.3 62.1 + - - +
136G TYR 3.4 2.2 - - - -
137G ASP* 3.7 20.8 - - + +
138G ASP* 3.0 27.9 + - + +
141G PHE* 3.7 7.8 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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