Contacts of the helix formed by residues 241 - 248 (chain B) in PDB entry 1Q6X
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 241 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B ASN* 4.0 26.5 - - + +
238B ARG* 6.5 0.2 - - - -
239B LEU 3.8 2.2 - - - +
240B PRO* 1.3 82.7 - - + +
242B ILE* 1.3 63.2 + - - +
243B GLY 3.1 3.4 - - - -
244B LEU* 3.0 29.7 + - + +
305B CYS* 6.3 0.7 - - + -
310B ALA* 3.8 24.5 - - + +
387B LEU* 3.7 18.9 - - + +
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Residues in contact with ILE 242 (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 PHE* 5.0 3.0 - - + -
240B PRO* 2.8 29.9 + - + +
241B PRO* 1.3 71.1 - - - +
243B GLY* 1.3 63.6 + - - +
245B LEU* 3.0 33.1 + - + +
246B THR 4.2 0.7 + - - -
253B TRP* 5.3 0.2 - - + -
260B LEU* 4.3 12.1 - - + -
313B TRP* 4.0 23.0 - - + -
377B TRP* 3.5 57.9 - - + +
379B CYS* 5.1 3.1 - - + -
383B THR* 4.4 22.2 - - + -
387B LEU* 4.5 7.4 - - + -
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Residues in contact with GLY 243 (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 PHE* 3.9 10.3 - - - -
241B PRO 3.0 2.2 + - - -
242B ILE* 1.3 78.0 - - - +
244B LEU* 1.3 61.0 + - - +
246B THR* 2.7 27.4 + - - -
247B SER* 3.8 1.7 + - - -
309B GLY 5.4 1.0 - - - +
310B ALA* 3.9 10.7 + - - -
312B ARG* 3.3 24.2 - - - +
313B TRP* 3.8 14.1 - - - -
314B TYR* 5.1 0.7 - - - -
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Residues in contact with LEU 244 (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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241B PRO* 3.0 21.9 + - + +
242B ILE 3.0 0.2 + - - -
243B GLY* 1.3 75.7 - - - +
245B LEU* 1.3 61.1 + - - +
247B SER* 2.6 38.5 + - - +
248B ASP 4.0 0.2 + - - -
305B CYS* 4.1 17.0 - - + -
309B GLY 5.0 2.2 - - - +
310B ALA* 4.2 17.2 + - + +
387B LEU* 3.7 34.1 - - + +
390B SER* 3.8 21.6 - - - +
391B ALA* 3.8 17.9 - - + +
394B LEU* 3.8 21.8 - - + -
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Residues in contact with LEU 245 (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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242B ILE* 3.0 28.5 + - + +
244B LEU* 1.3 77.4 - - - +
246B THR* 1.3 60.4 + - - +
247B SER 3.1 1.5 + - - -
248B ASP* 3.4 12.3 + - - +
253B TRP* 3.5 47.6 - - + +
256B ALA* 4.5 10.8 - - + -
260B LEU* 4.3 8.7 - - + -
383B THR* 4.5 15.9 - - + -
386B HIS* 3.8 23.1 - - + +
387B LEU* 3.6 26.0 - - + +
390B SER* 3.7 19.3 - - - +
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Residues in contact with THR 246 (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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102B LEU* 4.9 0.3 - - - +
103B PRO* 4.7 2.4 - - - +
242B ILE 4.8 0.4 - - - +
243B GLY 2.7 20.9 + - - +
245B LEU* 1.3 75.6 - - - +
247B SER* 1.3 58.9 + - - +
248B ASP 3.4 2.6 + - - +
250B ARG* 4.0 13.7 + - - -
253B TRP* 3.8 29.6 - - + +
312B ARG 4.1 0.2 + - - -
313B TRP* 3.6 44.9 - - + +
314B TYR* 3.1 43.4 + - - +
315B ASP* 4.5 2.7 - - - +
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Residues in contact with SER 247 (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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101B ALA* 3.1 21.3 - - - +
103B PRO* 3.7 23.4 - - - +
243B GLY 4.9 0.4 - - - -
244B LEU* 2.6 36.1 + - - +
246B THR* 1.3 79.6 + - - +
248B ASP* 1.3 58.8 + - - +
309B GLY 5.1 1.3 - - - -
314B TYR* 4.1 12.6 - - - -
390B SER* 4.6 2.8 + - - -
394B LEU* 4.1 24.9 - - - +
397B ILE* 4.8 4.5 - - - +
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Residues in contact with ASP 248 (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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101B ALA* 3.6 12.2 - - - -
102B LEU 4.6 0.3 + - - -
244B LEU 4.0 0.2 + - - -
245B LEU 3.4 12.2 + - - +
246B THR 3.4 6.7 - - - +
247B SER* 1.3 83.5 + - - +
249B GLY* 1.3 85.5 + - - +
250B ARG* 3.4 6.2 + - - -
252B GLU* 3.8 21.5 - - + +
253B TRP* 4.6 5.1 - - - +
389B SER* 4.3 5.5 - - - -
390B SER* 3.1 35.4 + - - +
393B LYS* 3.3 37.6 + - - +
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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