Contacts of the helix formed by residues 137 - 150 (chain G) in PDB entry 1I43
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 SER 137 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110E ARG* 4.3 10.7 - - - -
292E GLY* 3.1 28.8 + - - -
294E ALA* 5.5 2.0 - - - -
135G MET* 3.2 2.5 - - - +
136G ALA* 1.3 83.8 - - - +
138G GLY* 1.3 63.8 + - - +
139G MET* 3.4 0.7 + - - +
140G CYS* 3.2 14.2 + - - +
141G ALA 3.1 15.4 + - - -
270G LEU* 4.6 5.6 - - - -
271G ALA* 3.5 10.1 - - - +
272G GLY* 3.1 16.3 - - - -
500G PLP 3.2 15.2 + - - -
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Residues in contact with GLY 138 (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 SER* 1.3 72.9 - - - +
139G MET* 1.3 58.0 + - - -
141G ALA* 3.2 5.2 + - - +
142G SER* 2.8 27.5 + - - -
256G LEU* 4.4 3.4 - - - +
257G HIS 4.3 4.9 - - - -
258G SER* 4.0 12.1 - - - -
271G ALA 3.5 3.6 + - - -
272G GLY* 3.9 10.1 - - - -
500G PLP 2.6 33.7 + - - -
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Residues in contact with MET 139 (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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110E ARG* 3.3 39.0 - - - +
290E ILE* 3.3 30.5 - - + +
291E LEU 4.0 0.4 - - - -
292E GLY* 4.4 0.9 - - - -
137G SER* 3.9 2.7 - - - +
138G GLY* 1.3 68.9 - - - +
140G CYS* 1.3 60.5 + - - +
142G SER* 3.4 6.9 + - - +
143G THR* 2.9 43.0 + - - +
163G TYR* 3.9 17.7 - - - -
165G LYS* 3.9 10.3 - - + -
166G THR* 3.7 37.9 - - + +
169G PHE* 5.1 3.1 - - + -
500G PLP 2.6 19.8 + - - +
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Residues in contact with CYS 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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291E LEU 3.1 13.6 + - - -
292E GLY 3.1 25.6 - - - +
293E GLY* 5.2 0.9 - - - -
135G MET* 3.8 18.8 - - + -
136G ALA 4.4 0.2 - - - -
137G SER* 3.2 16.9 + - - +
139G MET* 1.3 78.3 - - - +
141G ALA* 1.3 59.3 + - - +
143G THR* 4.2 1.1 - - - -
144G VAL* 2.9 51.0 + - - +
288G HIS* 5.1 0.2 - - - -
291G LEU* 6.4 0.2 - - - -
293G GLY* 4.0 23.1 - - - -
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Residues in contact with ALA 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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135G MET* 3.5 18.8 - - - -
137G SER 3.1 8.0 + - - +
138G GLY* 3.3 10.1 - - - +
140G CYS* 1.3 77.0 - - - +
142G SER* 1.3 66.8 + - - +
144G VAL* 3.9 0.5 - - - +
145G MET* 2.8 26.3 + - - +
256G LEU* 4.5 4.7 - - + -
273G CYS 4.0 16.8 - - - +
274G ILE* 3.4 28.5 - - + +
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Residues in contact with SER 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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138G GLY 2.8 17.0 + - - -
139G MET* 3.7 12.6 + - - -
141G ALA* 1.3 77.4 - - - +
143G THR* 1.3 65.1 + - - +
145G MET* 3.3 4.3 - - - +
146G LEU* 2.8 32.6 + - - +
166G THR* 4.6 21.5 + - - -
205G PHE* 4.8 8.4 - - - -
256G LEU* 4.1 25.8 - - - +
500G PLP 5.1 4.5 - - - -
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Residues in contact with THR 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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290E ILE 3.8 14.4 + - - -
291E LEU* 3.5 34.4 - - + +
139G MET* 2.9 29.6 + - - +
140G CYS* 3.6 5.2 - - - +
142G SER* 1.3 76.5 - - - +
144G VAL* 1.3 70.6 + - + +
146G LEU* 3.1 2.6 + - - +
147G LEU* 3.0 33.4 + - + +
169G PHE* 3.9 26.8 - - + -
291G LEU* 5.4 1.8 - - + -
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Residues in contact with VAL 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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135G MET* 3.4 24.9 - - + -
140G CYS* 2.9 39.1 + - - +
143G THR* 1.3 77.4 - - + +
145G MET* 1.3 63.7 + - - +
147G LEU* 3.3 1.6 + - - -
148G ALA* 2.9 27.4 + - - +
284G ILE* 3.7 20.0 - - + +
287G LEU* 3.7 20.6 - - + +
288G HIS* 4.1 14.4 - - - +
291G LEU* 3.9 20.4 - - + -
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Residues in contact with MET 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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141G ALA 2.8 20.2 + - - +
142G SER* 3.3 4.9 - - - +
144G VAL* 1.3 75.8 - - - +
146G LEU* 1.3 97.0 + - + +
148G ALA 3.8 0.2 - - - -
149G LEU* 3.0 48.2 + - + +
203G LEU* 3.8 27.4 - - + -
205G PHE* 4.4 8.7 - - + -
234G CYS* 3.6 28.7 - - - -
254G LEU* 4.7 3.4 - - + -
256G LEU* 4.3 9.2 - - + -
274G ILE* 4.0 14.6 - - + -
284G ILE* 4.0 20.8 - - + +
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Residues in contact with LEU 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 SER* 2.8 20.7 + - - +
143G THR 3.5 6.1 - - - +
145G MET* 1.3 94.4 - - + +
147G LEU* 1.3 62.2 + - - +
148G ALA 3.0 4.8 + - - -
150G VAL* 3.1 33.9 + - + +
156G ILE* 3.4 32.5 - - + -
166G THR* 4.7 9.0 - - + -
169G PHE* 3.6 33.4 - - + -
170G ILE* 4.2 18.2 - - + -
174G LEU* 4.3 10.4 - - + +
179G ILE* 5.5 0.2 - - - +
203G LEU* 4.1 2.5 - - + -
205G PHE* 5.2 9.2 - - + -
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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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147E LEU* 5.2 16.2 - - + -
173E ILE* 5.7 9.6 - - + -
176E LYS* 4.1 18.7 + - - -
291E LEU* 5.3 1.6 - - + -
143G THR* 3.0 28.0 + - + +
146G LEU* 1.3 76.0 - - - +
148G ALA* 1.3 58.6 + - - +
150G VAL 4.2 6.8 - - - +
169G PHE* 3.8 26.2 - - + -
173G ILE* 5.5 5.8 - - + -
174G LEU* 4.5 8.1 - - + -
177G MET* 3.8 35.0 - - + +
287G LEU* 3.8 17.8 - - + +
291G LEU* 4.4 16.6 - - + -
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Residues in contact with ALA 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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176E LYS* 5.9 0.3 + - - -
144G VAL 2.9 17.5 + - - +
145G MET 3.9 2.2 - - - +
147G LEU* 1.3 81.1 - - - +
149G LEU* 1.3 64.2 + - - +
150G VAL 4.9 0.8 - - - -
283G GLU* 4.3 15.2 - - - +
284G ILE* 4.0 28.9 - - + +
287G LEU* 3.6 19.1 - - + -
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Residues in contact with LEU 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 MET* 3.0 37.3 + - + +
146G LEU 4.6 0.2 - - - +
148G ALA* 1.3 83.0 - - - +
150G VAL* 1.3 66.5 + - + +
151G PRO* 3.5 9.9 - - - +
202G ASN* 5.4 0.7 + - - +
203G LEU* 4.5 8.7 - - + -
232G LEU* 4.6 11.7 - - + -
254G LEU* 3.4 32.5 - - + -
280G LEU* 4.0 24.2 - - + +
283G GLU* 4.6 13.9 - - + -
284G ILE* 4.0 17.0 - - + -
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Residues in contact with VAL 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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176E LYS* 5.2 1.9 + - - -
146G LEU* 3.1 23.9 + - + +
147G LEU 4.2 8.7 - - - +
148G ALA 4.9 0.6 - - - -
149G LEU* 1.3 77.3 - - + +
151G PRO* 1.3 80.7 - - + +
154G GLY 4.6 5.6 - - - -
155G HIS 4.7 2.0 - - - +
156G ILE* 4.1 13.9 - - + -
174G LEU* 6.0 1.3 - - + -
177G MET* 4.5 4.0 - - - +
179G ILE* 3.5 34.6 - - + +
202G ASN* 4.5 11.2 - - + -
203G LEU* 3.9 34.3 - - + -
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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