Contacts of the helix formed by residues 246 - 254 (chain A) in PDB entry 1A7A
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 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A ILE 3.8 2.7 - - - +
245A ASP* 1.3 87.9 - - - +
247A ILE* 1.3 51.3 + - - +
249A ALA* 3.1 7.5 + - + +
250A LEU* 2.6 37.6 + - - +
392B GLU* 3.7 28.0 - - + +
395B ALA* 4.0 3.1 - - - -
396B GLU* 3.7 33.9 - - + +
399B LEU* 4.1 4.6 - - + +
406B LEU* 3.6 21.1 - - + -
425B PHE* 3.8 22.4 - - + -
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Residues in contact with ILE 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ASP* 2.9 13.2 + - - +
246A PRO* 1.3 70.0 - - - +
248A ASN* 1.3 63.7 + - - +
250A LEU* 3.0 4.9 + - - +
251A GLN* 2.8 28.9 + - - +
184B VAL* 3.6 27.4 - - + -
185B THR* 4.2 5.2 - - + -
189B PHE* 3.7 16.4 - - + -
388B LYS* 5.4 0.4 - - + +
391B ASP* 4.5 3.1 - - + +
392B GLU* 4.1 29.2 - - + +
395B ALA* 3.9 21.1 - - + -
432B TYR* 3.5 47.6 - - + +
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Residues in contact with ASN 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A TYR* 3.0 30.3 - - - +
226A LYS* 3.5 2.6 + - - -
243A GLU* 3.4 24.2 - - + +
245A ASP* 3.0 19.9 + - - +
247A ILE* 1.3 78.2 - - - +
249A ALA* 1.3 62.0 + - - +
251A GLN* 3.2 18.8 + - - +
252A ALA* 3.0 20.1 + - - +
433A NAD 3.4 12.3 + - - -
426B LYS* 2.9 35.0 - - - +
430B TYR* 3.9 10.7 + - - -
432B TYR* 4.3 5.1 - - - -
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Residues in contact with ALA 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A GLU* 4.0 13.0 - - + +
245A ASP 2.8 18.6 + - - +
246A PRO* 3.2 5.8 - - + +
248A ASN* 1.3 74.8 - - - +
250A LEU* 1.3 65.6 + - - +
252A ALA* 3.2 8.5 + - - +
253A ALA* 3.1 19.1 + - - +
259A VAL* 3.7 18.5 - - + +
399B LEU* 4.6 3.1 - - + -
404B VAL* 4.5 9.5 - - + +
406B LEU* 3.6 22.4 - - + -
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Residues in contact with LEU 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A PRO 2.6 20.9 + - - +
247A ILE* 3.5 4.9 - - - +
249A ALA* 1.3 70.9 - - - +
251A GLN* 1.3 64.5 + - - +
253A ALA* 3.2 6.7 + - + +
254A MSE 2.8 40.9 + - + +
189B PHE* 3.7 23.1 - - + -
360B ASN* 3.8 25.4 - - - +
395B ALA* 4.1 19.3 - - + +
398B HIS* 4.4 9.4 - - + +
399B LEU* 4.0 19.7 - - + +
402B LEU* 3.8 27.6 - - + -
404B VAL* 5.6 1.1 - - + -
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Residues in contact with GLN 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A TYR* 3.9 10.3 - - + -
226A LYS* 2.9 30.5 - - - +
247A ILE* 2.8 18.9 + - - +
248A ASN* 3.2 28.1 + - - +
250A LEU* 1.3 73.6 - - - +
252A ALA* 1.3 70.1 + - - +
254A MSE 2.9 5.2 + - - +
255A GLU* 2.9 22.6 + - - +
188B LYS* 5.0 11.3 - - - +
189B PHE* 3.6 21.8 - - + -
193B TYR* 4.2 16.6 + - + +
432B TYR* 3.1 32.6 + - - +
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Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A TYR* 3.6 19.6 - - + -
241A ILE* 4.1 24.5 - - + -
248A ASN 3.0 12.2 + - - +
249A ALA* 3.4 9.4 - - - +
251A GLN* 1.3 74.4 - - - +
253A ALA* 1.3 55.8 + - - +
255A GLU* 2.6 26.3 + - - +
256A GLY 3.1 8.0 + - - -
257A TYR* 3.3 12.7 + - + -
259A VAL* 3.4 18.2 - - + -
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Residues in contact with ALA 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ALA 3.1 9.9 + - - +
250A LEU* 3.5 9.0 - - - +
252A ALA* 1.3 78.0 - - - +
254A MSE 1.3 62.7 + - - +
256A GLY* 3.0 14.2 + - - -
257A TYR 3.5 15.4 + - - +
259A VAL* 3.9 1.9 - - + +
402B LEU* 4.4 18.2 - - + -
404B VAL* 3.9 26.5 - - + -
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Residues in contact with MSE 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A LEU* 2.8 46.0 + - + +
251A GLN 2.9 4.7 + - - +
253A ALA* 1.3 74.0 - - - +
255A GLU* 1.3 59.3 + - - +
256A GLY 3.2 1.2 + - - -
189B PHE* 4.3 7.2 - - + -
193B TYR* 3.3 44.0 - - + -
196B ARG* 3.1 23.0 + - - -
356B PHE* 3.1 40.6 - - + -
357B VAL* 5.1 12.6 - - + -
360B ASN* 5.2 2.9 - - - +
402B LEU* 4.9 4.3 - - - -
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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