Contacts of the strand formed by residues 294 - 301 (chain B) in PDB entry 1G4C
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 LEU 294 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B ILE* 3.9 22.7 - - + -
208B GLY 3.5 12.3 - - - +
209B SER* 4.4 2.9 - - - -
217B GLN* 3.9 21.5 - - + +
218B VAL* 5.0 2.0 - - + -
221B ALA* 3.9 25.8 - - + -
276B ILE* 4.2 17.5 - - + +
277B GLU* 3.7 21.5 - - - +
280B GLN* 4.0 22.2 - - + -
281B GLY* 3.9 17.0 - - - -
292B ALA* 4.7 7.9 - - - +
293B THR* 1.3 78.7 + - - +
295B ASP* 1.3 60.5 + - - +
296B LEU* 4.1 12.6 - - + -
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Residues in contact with ASP 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LYS* 5.4 9.7 - - - +
206B ALA 3.5 1.0 - - - +
207B ILE* 3.5 5.7 - - - -
208B GLY* 2.9 40.4 + - - +
277B GLU* 3.4 3.8 - - - +
293B THR 3.9 1.3 + - - +
294B LEU* 1.3 73.6 - - - +
296B LEU* 1.3 64.4 + - - +
297B ASP* 3.0 7.8 - - - +
362B MG 2.1 27.9 - - - -
363B MG 2.0 29.5 - - - -
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B ILE* 4.5 6.5 - - + -
206B ALA 3.3 2.9 - - - +
207B ILE* 3.7 40.4 - - + -
221B ALA* 4.7 3.6 - - + -
225B LEU* 4.3 24.9 - - + -
270B LEU* 5.8 2.9 - - - +
273B THR* 3.6 37.0 + - - +
276B ILE* 3.6 27.6 - - + -
277B GLU* 2.8 32.5 + - + +
294B LEU* 4.3 10.5 - - + -
295B ASP* 1.3 75.6 + - - +
297B ASP* 1.3 65.5 + - - +
298B ILE 4.2 0.7 + - - -
362B MG 4.2 0.3 - - - -
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Residues in contact with ASP 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLU* 2.9 8.0 - - - +
205B ILE* 3.4 5.2 - - - +
206B ALA* 2.9 42.8 + - + +
295B ASP* 3.0 6.4 - - - +
296B LEU* 1.3 73.8 - - - +
298B ILE* 1.3 59.9 + - - +
299B MET* 3.2 4.1 + - + +
315B HIS* 3.6 24.7 - - + +
324B MET* 3.6 12.5 - - + +
362B MG 2.0 30.2 - - - -
363B MG 2.1 27.7 - - - -
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Residues in contact with ILE 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B ALA* 4.9 1.3 - - + -
204B TYR 3.9 3.6 - - - +
205B ILE* 4.5 8.7 - - + +
266B PRO 4.2 5.4 - - - +
269B LEU* 3.8 37.2 - - + -
270B LEU* 3.9 34.9 - - + +
273B THR* 4.3 11.9 - - + +
296B LEU 4.2 0.2 + - - -
297B ASP* 1.3 68.9 - - - +
299B MET* 1.3 66.6 + - - +
300B LEU 3.7 18.8 - - - +
301B PHE* 4.6 9.0 - - + -
311B LEU* 4.4 16.6 - - + +
312B THR 4.4 0.5 - - - +
313B VAL* 4.0 23.0 - - + +
315B HIS* 3.6 16.9 - - - +
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Residues in contact with MET 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B TYR* 2.7 25.5 + - + +
205B ILE 3.8 7.2 - - - +
206B ALA* 3.7 37.9 - - + +
257B ALA* 4.1 19.1 - - + -
297B ASP 3.2 1.5 + - - +
298B ILE* 1.3 73.1 - - - +
300B LEU* 1.3 62.8 + - + +
313B VAL* 3.7 1.2 - - - +
314B PRO* 3.3 9.4 - - - +
315B HIS* 3.0 30.1 + - + -
318B MET* 3.7 25.9 - - + +
324B MET* 3.8 42.0 - - + +
328B LEU* 4.2 17.0 - - + -
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B VAL 4.7 0.7 - - - -
203B ALA* 3.4 2.1 - - - -
204B TYR* 2.8 41.4 + - + +
298B ILE* 3.7 7.3 - - - +
299B MET* 1.3 85.9 - - + +
301B PHE* 1.3 59.0 + - - +
302B GLY 4.0 10.8 - - - +
304B GLU 5.8 0.4 - - - +
313B VAL* 3.7 6.5 - - + -
314B PRO* 3.6 31.0 - - + -
318B MET* 4.4 3.6 - - + -
328B LEU* 4.3 9.9 - - + -
335B LEU* 3.8 41.5 - - + -
336B VAL 5.6 0.9 - - - +
337B PHE* 3.8 19.7 - - + -
338B PRO* 4.2 9.6 - - + -
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Residues in contact with PHE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B THR* 3.9 19.3 - - + -
202B VAL 4.1 1.6 - - - -
203B ALA* 3.9 13.7 - - + +
262B THR* 3.8 24.7 - - + -
264B LEU 3.2 24.0 - - - -
265B ALA* 5.1 0.2 - - - -
266B PRO* 3.7 39.5 - - + -
269B LEU* 4.1 13.2 - - + -
298B ILE* 4.6 8.3 - - + -
300B LEU* 1.3 73.2 - - - +
302B GLY* 1.3 66.2 + - - +
304B GLU* 3.0 42.8 + - - +
306B ILE* 4.3 15.7 - - + -
313B VAL* 3.7 9.4 - - + +
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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