Contacts of the helix formed by residues 1216 - 1220 (chain G) in PDB entry 2BT4
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 ASN1216 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1215G PRO* 1.3 83.6 + - - +
1217G LEU* 1.3 55.0 + - - +
1218G ASN* 3.1 14.3 - - - +
1219G LEU* 3.0 21.3 + - - +
1257G ASN* 2.9 10.9 + - - -
1360G CA2 3.4 31.3 - - + -
1463H VAL* 3.7 3.1 - - - +
1467H HIS* 2.7 29.9 + - - +
1489H ALA* 3.0 26.3 + - - +
1492H ASP* 3.3 16.3 + - + +
1493H ALA* 3.2 20.9 - - - +
1496H THR* 4.6 4.8 - - + +
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Residues in contact with LEU1217 (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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1213G ASN* 3.8 15.3 - - + +
1214G GLY 3.5 32.6 + - - +
1215G PRO 3.1 1.4 - - - -
1216G ASN* 1.3 73.1 - - - +
1218G ASN* 1.3 63.8 + - - +
1219G LEU 3.1 0.7 - - - -
1220G LEU* 3.1 31.1 + - + +
1228G TYR* 6.0 0.2 - - + -
1233G LEU* 3.6 21.8 - - + +
1279G ASN* 3.7 36.6 - - - +
1281G ALA* 4.1 4.9 - - + -
1307G ILE* 4.2 18.2 - - + -
1338G TYR* 4.7 1.8 - - - +
1360G CA2 3.8 29.8 - - + +
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Residues in contact with ASN1218 (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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1216G ASN* 3.3 16.1 - - - -
1217G LEU* 1.3 77.3 - - - +
1219G LEU* 1.3 76.6 + - - +
1220G LEU 3.3 2.6 + - - +
1222G GLN* 4.6 3.3 - - - +
1233G LEU* 4.1 16.5 + - + +
1255G GLN* 3.5 30.2 + - - +
1257G ASN* 3.7 4.2 - - - +
1467H HIS* 3.4 32.6 + - - +
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Residues in contact with LEU1219 (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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1216G ASN 3.0 10.6 + - - +
1218G ASN* 1.3 95.3 - - - +
1220G LEU* 1.3 68.4 + - - +
1221G GLY 3.3 0.2 + - - -
1222G GLN* 3.1 45.5 + - + +
1223G ARG* 6.3 0.2 - - - -
1360G CA2 3.4 16.5 - - + -
1467H HIS* 3.6 36.1 - - + +
1470H ARG* 3.9 23.6 - - - +
1496H THR* 3.8 22.7 - - + +
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Residues in contact with LEU1220 (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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1217G LEU* 3.1 21.7 + - + +
1218G ASN 3.3 2.8 + - - +
1219G LEU* 1.3 80.1 - - - +
1221G GLY* 1.3 63.8 + - - +
1222G GLN* 3.5 4.7 + - - +
1228G TYR* 3.9 19.7 - - + +
1231G ASP 3.5 13.5 - - - +
1232G THR* 3.4 18.7 - - - +
1233G LEU* 4.0 20.2 + - + +
1236G VAL* 3.8 29.6 - - + -
1307G ILE* 3.9 24.9 - - + -
1335G VAL* 4.5 3.6 - - + -
1360G CA2 3.8 30.4 - - + -
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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