Contacts of the helix formed by residues 139 - 152 (chain G) in PDB entry 3IYD
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 VAL 139 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138G ASP* 1.3 78.6 - - - +
140G THR* 1.3 62.9 + - - +
142G ARG* 3.3 23.2 - - - +
143G ILE* 3.1 53.0 + - + +
176G VAL* 5.4 0.7 - - + -
178G CYS* 4.4 17.9 - - + -
182G THR* 3.8 27.6 - - + +
186G ILE* 5.1 6.7 - - + -
19I G 3.3 38.6 + - - +
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Residues in contact with THR 140 (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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138G ASP* 3.3 13.6 + - - -
139G VAL* 1.3 78.9 - - - +
141G GLY* 1.3 57.6 + - - +
143G ILE* 4.3 2.5 - - - +
144G ALA* 3.1 30.1 + - + +
186G ILE* 4.1 30.3 - - + +
189G MET* 6.1 0.3 - - - -
190G LEU* 5.0 19.1 - - + -
19I G 4.7 4.2 + - - -
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Residues in contact with GLY 141 (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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137G LEU* 4.2 16.1 - - - +
138G ASP* 2.9 17.0 + - - -
140G THR* 1.3 76.9 - - - +
142G ARG* 1.3 63.1 + - - +
144G ALA* 3.4 6.6 + - - +
145G GLN* 3.3 27.9 + - - +
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Residues in contact with ARG 142 (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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133G ASN* 3.2 29.6 - - + +
134G LEU* 3.3 26.0 + - - +
137G LEU* 3.8 19.2 + - + -
138G ASP* 2.9 23.5 + - - +
139G VAL* 3.3 36.9 - - - +
141G GLY* 1.3 75.3 - - - +
143G ILE* 1.3 61.4 + - - +
145G GLN* 3.4 7.8 + - - +
146G THR* 3.0 22.5 + - - -
176G VAL* 2.9 46.9 + - + +
177G GLY 4.0 13.1 + - - -
178G CYS* 4.7 1.8 - - - +
19I G 4.7 1.4 + - - -
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Residues in contact with ILE 143 (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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139G VAL* 3.1 37.0 + - + +
140G THR* 4.3 2.9 - - - +
142G ARG* 1.3 72.6 - - - +
144G ALA* 1.3 66.8 + - - +
146G THR* 3.0 17.9 + - - -
147G LEU* 3.1 28.2 + - + +
172G ILE* 4.1 15.9 - - + -
176G VAL* 3.8 21.3 - - + -
183G VAL* 3.8 39.5 - - + +
186G ILE* 5.6 5.8 - - + -
187G LEU* 6.4 1.8 - - + -
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Residues in contact with ALA 144 (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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140G THR* 3.1 23.9 + - + +
141G GLY* 3.5 8.7 - - - +
142G ARG 3.3 0.2 - - - -
143G ILE* 1.3 78.9 - - - +
145G GLN* 1.3 63.3 + - + +
147G LEU* 3.4 18.1 + - + +
148G LEU* 3.2 24.4 - - + +
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Residues in contact with GLN 145 (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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137G LEU* 4.6 16.3 - - + +
141G GLY 3.3 15.0 + - - +
142G ARG* 3.7 7.4 - - - +
143G ILE 3.2 0.4 - - - -
144G ALA* 1.3 77.2 - - - +
146G THR* 1.3 62.9 + - - +
148G LEU* 3.3 11.5 + - - +
149G ASN* 2.9 39.0 + - - +
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Residues in contact with THR 146 (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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142G ARG 3.0 13.9 + - - -
143G ILE* 3.0 14.1 + - - -
145G GLN* 1.3 76.1 - - - +
147G LEU* 1.3 66.4 + - + +
149G ASN* 3.1 11.3 + - + +
150G LEU* 3.0 47.8 + - + +
167G ILE* 5.5 3.4 - - + -
172G ILE* 5.3 11.0 - - + -
175G ILE* 4.3 22.3 - - + +
176G VAL* 3.9 12.9 - - - +
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Residues in contact with LEU 147 (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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143G ILE* 3.1 27.0 + - + +
144G ALA* 3.5 17.0 - - + +
145G GLN 3.2 0.4 - - - -
146G THR* 1.3 79.4 - - + +
148G LEU* 1.3 66.3 + - + +
150G LEU* 3.8 3.7 + - + +
151G ALA* 3.4 20.1 + - - +
163G MET* 5.7 0.3 - - - +
165G ILE* 3.9 29.2 - - + +
172G ILE* 5.9 4.7 - - + -
187G LEU* 5.8 3.4 - - + -
190G LEU* 5.9 3.8 - - + -
196G ILE* 4.9 16.8 - - + -
203G ILE* 4.3 21.1 - - + -
205G VAL* 3.9 30.4 - - + +
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Residues in contact with LEU 148 (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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144G ALA 3.2 19.5 - - - +
145G GLN* 3.3 13.6 + - - +
146G THR 3.2 0.6 - - - -
147G LEU* 1.3 81.8 - - + +
149G ASN* 1.3 67.6 + - - +
151G ALA* 3.3 13.1 + - + +
152G LYS* 3.3 30.8 + - - +
205G VAL* 5.4 7.2 - - + -
208G THR* 3.9 28.9 - - + +
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Residues in contact with ASN 149 (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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145G GLN* 2.9 27.7 + - - +
146G THR* 3.1 13.2 + - + +
148G LEU* 1.3 82.1 - - - +
150G LEU* 1.3 63.5 + - + +
152G LYS* 3.3 25.2 + - - +
153G GLN* 3.4 22.7 + - - +
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Residues in contact with LEU 150 (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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146G THR* 3.0 34.9 + - + +
147G LEU* 4.2 2.2 - - + +
149G ASN* 1.3 78.5 - - + +
151G ALA* 1.3 63.3 + - - +
153G GLN* 3.3 24.7 + - + +
155G ASP* 4.3 2.0 - - - +
156G ALA* 3.2 16.3 - - - +
165G ILE* 3.8 27.5 - - + +
167G ILE* 3.8 46.0 - - + -
172G ILE* 5.9 0.7 - - + -
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Residues in contact with ALA 151 (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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147G LEU 3.4 13.5 + - - +
148G LEU* 3.3 17.2 + - + +
149G ASN 3.2 0.4 - - - -
150G LEU* 1.3 81.5 - - - +
152G LYS* 1.3 58.3 + - + +
153G GLN 3.9 0.5 - - - +
156G ALA* 3.3 20.5 - - - +
163G MET* 3.6 42.1 - - + +
165G ILE* 4.3 4.2 - - + +
205G VAL* 6.0 0.2 - - + -
208G THR* 5.5 1.6 - - + -
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Residues in contact with LYS 152 (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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148G LEU* 3.3 25.7 - - - +
149G ASN* 3.3 17.5 + - - +
150G LEU 3.2 0.6 - - - -
151G ALA* 1.3 76.4 - - + +
153G GLN* 1.3 66.2 + - - +
154G PRO* 3.8 3.3 - - - +
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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