Contacts of the helix formed by residues 1232 - 1247 (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 THR1232 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1220G LEU* 3.4 17.7 - - - +
1221G GLY* 5.1 2.5 - - - -
1222G GLN* 6.3 1.6 - - + -
1230G SER 4.6 4.7 - - - +
1231G ASP* 1.3 77.4 - - - +
1233G LEU* 1.3 65.2 + - - +
1234G ALA* 3.5 9.5 + - - +
1235G ASP* 2.9 32.5 + - - +
1236G VAL* 3.0 20.1 + - - +
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Residues in contact with LEU1233 (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* 3.9 19.5 - - + +
1217G LEU* 3.6 36.6 - - + +
1218G ASN* 4.1 11.1 + - - +
1220G LEU* 4.0 19.7 + - + +
1232G THR* 1.3 75.5 - - - +
1234G ALA* 1.3 57.2 + - - +
1236G VAL* 3.2 11.6 + - + +
1237G GLU* 2.9 26.2 + - - +
1253G PHE* 3.9 19.4 - - + -
1255G GLN* 3.7 35.0 - - + -
1338G TYR* 4.5 4.0 - - - +
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Residues in contact with ALA1234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1232G THR* 3.1 9.0 + - - +
1233G LEU* 1.3 75.8 - - - +
1235G ASP* 1.3 65.8 + - - +
1237G GLU* 3.4 15.1 + - - +
1238G ALA* 3.0 22.2 + - - +
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Residues in contact with ASP1235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1230G SER 4.5 1.0 - - - +
1231G ASP* 3.4 27.2 - - + +
1232G THR* 2.9 40.9 + - - +
1234G ALA* 1.3 76.5 - - - +
1236G VAL* 1.3 63.2 + - - +
1238G ALA* 3.3 9.1 + - - +
1239G LEU* 3.1 25.7 + - + +
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Residues in contact with VAL1236 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1220G LEU* 3.8 17.3 - - + -
1231G ASP* 5.0 2.2 - - + -
1232G THR 3.0 16.5 + - - +
1233G LEU* 3.3 11.2 - - + +
1235G ASP* 1.3 75.3 - - - +
1237G GLU* 1.3 66.9 + - - +
1239G LEU* 3.0 12.1 + - + +
1240G CYS* 3.0 20.8 + - - -
1253G PHE* 3.9 17.5 - - + -
1335G VAL* 3.6 32.1 - - + -
1338G TYR* 3.8 37.9 - - + -
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Residues in contact with GLU1237 (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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1233G LEU 2.9 12.1 + - - +
1234G ALA* 3.5 16.9 - - - +
1236G VAL* 1.3 75.6 - - - +
1238G ALA* 1.3 59.0 + - - +
1240G CYS* 3.1 3.9 + - - +
1241G VAL* 2.9 43.0 + - + +
1251G VAL* 5.5 0.6 - - + +
1253G PHE* 3.7 53.5 - - + +
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Residues in contact with ALA1238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1234G ALA 3.0 14.4 + - - +
1235G ASP* 3.5 12.3 - - - +
1237G GLU* 1.3 77.6 - - - +
1239G LEU* 1.3 61.2 + - - +
1241G VAL* 3.4 9.3 + - - +
1242G LYS* 3.1 24.4 + - - +
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Residues in contact with LEU1239 (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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1231G ASP* 5.5 4.5 - - - +
1235G ASP 3.1 17.3 + - - +
1236G VAL* 3.0 13.2 + - + +
1238G ALA* 1.3 77.1 - - - +
1240G CYS* 1.3 59.1 + - - +
1242G LYS* 3.6 19.8 + - + +
1243G ALA* 3.0 28.2 + - - +
1335G VAL* 3.7 41.1 - - + +
1336G GLN* 5.1 1.1 - - - +
1338G TYR* 6.1 0.7 - - + -
1339G VAL* 4.4 20.6 - - + +
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Residues in contact with CYS1240 (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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1211G ILE* 3.9 30.5 - - + -
1236G VAL 3.0 16.1 + - - -
1237G GLU* 3.4 9.6 - - - +
1239G LEU* 1.3 76.8 - - - +
1241G VAL* 1.3 65.7 + - - +
1243G ALA* 3.8 5.1 - - - +
1244G ALA* 2.9 27.5 + - - +
1251G VAL* 3.5 10.1 - - + +
1253G PHE* 4.0 14.8 - - + -
1338G TYR* 3.8 31.0 - - - -
1339G VAL* 5.8 0.7 - - - -
1342G VAL* 4.5 6.9 - - + +
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Residues in contact with VAL1241 (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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1237G GLU* 2.9 29.9 + - + +
1238G ALA* 3.7 9.9 - - - +
1240G CYS* 1.3 76.1 - - - +
1242G LYS* 1.3 64.3 + - - +
1244G ALA* 3.9 1.2 - - - +
1245G ALA* 3.1 26.9 + - + +
1249G GLY 5.0 0.3 - - - +
1250G THR* 5.8 0.9 - - - +
1251G VAL* 4.0 22.0 - - + +
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Residues in contact with LYS1242 (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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1238G ALA 3.1 15.4 + - - +
1239G LEU* 3.6 19.0 - - + +
1241G VAL* 1.3 81.2 - - - +
1243G ALA* 1.3 63.2 + - - +
1245G ALA* 3.2 6.6 + - - +
1246G ALA* 3.1 22.6 + - + +
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Residues in contact with ALA1243 (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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1239G LEU 3.0 18.9 + - - +
1240G CYS* 3.8 4.7 - - - +
1242G LYS* 1.3 76.6 - - - +
1244G ALA* 1.3 65.9 + - - +
1246G ALA* 3.3 13.3 + - - +
1247G HIS* 3.3 22.1 - - + -
1339G VAL* 4.0 27.8 - - + +
1342G VAL* 3.7 20.9 - - + -
1343G GLU* 5.5 1.1 - - + -
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Residues in contact with ALA1244 (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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1204G LEU* 5.2 0.4 - - - -
1209G ILE* 4.4 5.8 - - + -
1240G CYS 2.9 16.6 + - - +
1241G VAL 3.9 2.5 - - - +
1243G ALA* 1.3 76.4 - - - +
1245G ALA* 1.3 63.7 + - - +
1247G HIS* 2.9 13.6 + - - +
1248G GLY 3.0 0.3 + - - -
1249G GLY* 2.8 39.7 + - - +
1250G THR* 3.9 3.8 - - - +
1251G VAL* 3.4 22.7 - - + -
1342G VAL* 3.6 13.8 - - + +
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Residues in contact with ALA1245 (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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1241G VAL* 3.1 22.1 + - + +
1242G LYS* 3.6 6.3 - - - +
1243G ALA 3.2 0.2 - - - -
1244G ALA* 1.3 78.9 - - - +
1246G ALA* 1.3 61.2 + - - +
1247G HIS 3.0 0.4 - - - -
1248G GLY* 3.1 13.0 + - - +
1249G GLY 3.5 11.4 + - - +
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Residues in contact with ALA1246 (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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1242G LYS* 3.1 13.1 + - + +
1243G ALA* 3.5 13.5 - - - +
1244G ALA 3.2 0.2 - - - -
1245G ALA* 1.3 76.6 - - - +
1247G HIS* 1.3 69.4 + - + +
1248G GLY 3.6 0.4 + - - -
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Residues in contact with HIS1247 (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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1204G LEU* 3.7 13.8 - - + +
1243G ALA* 3.3 22.0 - - - +
1244G ALA* 2.9 9.2 + - - +
1246G ALA* 1.3 88.9 + - + +
1248G GLY* 1.3 59.9 + - - +
1249G GLY 3.4 0.2 - - - -
1342G VAL* 5.1 2.0 - - + -
1343G GLU* 4.0 31.2 + - + +
1346G ALA* 3.8 31.8 - - + +
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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