Contacts of the helix formed by residues 277 - 292 (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 PRO 277 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130G GLU* 3.8 16.2 - - + +
248G LEU* 5.1 2.2 - - + -
253G ASP* 2.9 30.1 - - + +
254G LEU* 4.5 0.2 - - + -
276G GLY* 1.3 79.1 - - - +
278G LEU* 1.3 61.9 + - - +
279G LYS* 4.5 7.4 - - + +
280G LEU* 3.3 28.8 + - + +
281G VAL* 2.9 27.4 + - - +
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Residues in contact with LEU 278 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G GLU* 2.9 44.3 + - + +
131G SER* 4.4 9.2 - - - +
277G PRO* 1.3 66.5 - - - +
279G LYS* 1.3 68.7 + - - +
280G LEU 2.9 2.4 + - - -
281G VAL* 3.7 7.6 - - + -
282G SER* 2.9 41.2 + - - +
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Residues in contact with LYS 279 (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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130G GLU* 4.4 1.2 + - - -
277G PRO* 3.4 6.0 - - + +
278G LEU* 1.3 78.4 - - - +
280G LEU* 1.3 69.9 + - + +
282G SER* 3.8 7.2 + - - -
283G GLU* 3.7 17.8 - - - +
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Residues in contact with LEU 280 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149G LEU* 4.0 22.5 - - + +
232G LEU* 3.9 25.8 - - + -
253G ASP* 4.0 15.7 - - + +
254G LEU* 3.7 35.9 - - + -
277G PRO* 3.3 22.6 + - + +
278G LEU 2.9 2.0 + - - -
279G LYS* 1.3 87.8 - - + +
281G VAL* 1.3 67.3 + - - +
282G SER 3.1 1.3 - - - -
283G GLU* 2.9 24.1 + - + +
284G ILE* 3.5 9.3 + - - +
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Residues in contact with VAL 281 (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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131G SER* 3.2 41.5 - - - +
133G LEU* 3.8 32.5 - - + +
254G LEU* 4.5 4.0 - - + +
274G ILE* 4.2 16.4 - - + +
276G GLY* 4.2 6.5 - - - +
277G PRO 2.9 24.4 + - - +
278G LEU* 3.6 7.0 - - + +
280G LEU* 1.3 73.6 - - - +
282G SER* 1.3 61.9 + - - +
284G ILE* 3.2 12.3 + - + +
285G ARG* 3.0 28.0 + - - +
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Residues in contact with SER 282 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278G LEU* 2.9 34.8 + - - +
279G LYS* 3.8 7.4 + - - -
281G VAL* 1.3 78.7 - - - +
283G GLU* 1.3 69.4 + - - +
285G ARG* 3.4 12.6 + - - +
286G ASN* 3.1 29.3 + - - +
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Residues in contact with GLU 283 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148G ALA* 4.3 17.3 - - - +
149G LEU* 4.6 14.8 - - + -
279G LYS 3.7 15.9 - - - +
280G LEU* 2.9 12.4 + - + +
282G SER* 1.3 81.4 + - - +
284G ILE* 1.3 64.3 + - - +
286G ASN* 3.3 27.7 + - - +
287G LEU* 3.6 4.7 + - - +
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Residues in contact with ILE 284 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G LEU* 3.7 20.0 - - + -
135G MET* 3.9 5.4 - - + -
144G VAL* 3.7 20.6 - - + +
145G MET* 4.0 37.2 - - + -
148G ALA* 4.0 14.1 - - + -
149G LEU* 4.0 16.6 - - + -
254G LEU* 4.6 5.8 - - + -
274G ILE* 4.2 21.5 - - + -
280G LEU 4.1 11.2 - - - +
281G VAL* 3.2 12.9 + - - +
283G GLU* 1.3 75.1 - - - +
285G ARG* 1.3 66.6 + - - +
287G LEU* 3.0 5.4 + - - +
288G HIS* 2.8 19.8 + - - +
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Residues in contact with ARG 285 (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 TYR 5.2 5.2 + - - -
120G GLU* 3.0 34.2 + - - -
131G SER* 3.4 24.0 + - - -
132G THR 3.4 11.9 + - - -
133G LEU* 3.4 25.8 - - + +
281G VAL* 3.0 17.1 + - - +
282G SER* 3.6 14.9 - - - +
284G ILE* 1.3 78.0 - - - +
286G ASN* 1.3 58.4 + - - +
288G HIS* 3.2 10.0 + - - +
289G HIS* 2.9 57.3 + - + +
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Residues in contact with ASN 286 (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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282G SER* 3.1 18.0 + - - +
283G GLU* 3.5 22.9 + - - +
284G ILE 3.1 0.8 - - - -
285G ARG* 1.3 81.0 - - - +
287G LEU* 1.3 61.1 + - - +
289G HIS* 3.5 25.5 + - - +
290G ILE* 3.8 14.0 + - - +
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Residues in contact with LEU 287 (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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173E ILE* 4.0 31.2 - - + -
144G VAL* 3.7 13.2 - - + +
147G LEU* 3.8 17.9 - - + +
148G ALA* 3.6 37.2 - - + +
283G GLU 3.6 2.5 + - - +
284G ILE 3.0 7.2 + - - +
286G ASN* 1.3 77.1 - - - +
288G HIS* 1.3 62.0 + - - +
290G ILE* 3.0 15.4 + - + +
291G LEU* 2.9 53.3 + - + +
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Residues in contact with HIS 288 (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 ARG 4.9 5.0 + - - +
133G LEU* 4.0 26.7 - - + -
134G LEU 3.8 11.3 + - - -
135G MET* 3.5 21.6 - - + +
144G VAL* 4.1 14.6 - - + +
284G ILE 2.8 13.8 + - - +
285G ARG* 3.2 12.1 - - - +
287G LEU* 1.3 77.7 - - - +
289G HIS* 1.3 71.8 + + - +
291G LEU* 4.5 3.1 - - - +
292G GLY* 2.8 30.7 + - - -
293G GLY* 3.3 42.0 + - - -
294G ALA* 3.6 10.3 - - - +
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Residues in contact with HIS 289 (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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165E LYS* 4.6 6.2 - - - +
110G ARG* 2.9 54.3 + - - +
111G TYR* 3.5 45.5 + + + -
285G ARG* 2.9 47.4 + - + +
286G ASN* 3.5 18.9 + - - +
287G LEU 3.2 0.2 - - - -
288G HIS* 1.3 84.0 - + - +
290G ILE* 1.3 59.5 + - + +
292G GLY 4.3 0.9 - - - -
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Residues in contact with ILE 290 (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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139E MET* 3.3 28.0 - - + +
143E THR* 3.9 1.0 + - - -
165E LYS* 4.3 28.5 - - + +
168E ILE* 3.9 28.0 - - + -
169E PHE* 4.1 36.3 - - + +
172E THR* 5.4 2.5 - - - +
173E ILE* 5.5 3.8 - - + -
286G ASN 3.9 13.7 - - - +
287G LEU* 3.0 19.8 + - + +
289G HIS* 1.3 81.6 - - + +
291G LEU* 1.3 68.2 + - + +
292G GLY 3.1 2.3 + - - -
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Residues in contact with LEU 291 (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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139E MET 3.8 0.5 - - - +
140E CYS* 3.1 29.8 - - - +
143E THR* 3.5 32.2 + - + +
147E LEU* 5.2 3.1 - - + -
169E PHE* 3.9 20.4 - - + -
173E ILE* 5.9 0.9 - - + -
140G CYS* 6.4 0.2 - - - -
143G THR* 5.4 1.8 - - + -
144G VAL* 3.9 24.9 - - + -
147G LEU* 4.4 17.0 - - + -
287G LEU* 2.9 48.9 + - + +
288G HIS* 4.2 3.6 - - - +
290G ILE* 1.3 75.3 - - + +
292G GLY* 1.3 60.0 - - - +
293G GLY* 3.7 2.9 - - - +
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Residues in contact with GLY 292 (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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136E ALA* 3.6 5.7 - - - +
137E SER* 3.0 26.8 + - - -
139E MET* 4.4 0.7 - - - -
140E CYS* 3.4 11.4 - - - +
110G ARG* 3.8 18.8 - - - -
288G HIS* 2.8 15.3 + - - -
290G ILE 3.1 2.6 - - - -
291G LEU* 1.3 80.5 - - - +
293G GLY* 1.3 57.7 + - - +
294G ALA 3.2 8.1 + - - -
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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
------------------------------------------------------------
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