Contacts of the helix formed by residues 1335 - 1349 (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 VAL1335 (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* 4.5 3.8 - - + -
1228G TYR 4.4 13.0 + - - +
1229G GLY* 6.1 0.4 - - - -
1231G ASP* 3.9 26.2 - - + +
1236G VAL* 3.6 31.2 - - + -
1239G LEU* 3.7 28.3 - - + +
1307G ILE* 4.3 16.6 - - + +
1334G GLY* 1.3 68.1 - - - -
1336G GLN* 1.3 66.3 + - - +
1337G GLY 3.1 1.3 - - - -
1338G TYR* 3.1 27.5 + - + +
1339G VAL* 4.0 1.6 + - - +
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Residues in contact with GLN1336 (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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343B GLU* 3.5 22.2 + - - +
344B ARG* 2.9 35.2 + - - +
347B ALA* 3.3 16.7 - - - +
1239G LEU* 5.4 1.3 - - - -
1333G CYS 3.4 9.9 - - - +
1334G GLY 3.1 0.4 - - - -
1335G VAL* 1.3 81.3 - - - +
1337G GLY* 1.3 61.2 + - - +
1339G VAL* 2.8 31.9 + - + +
1340G PHE* 3.0 40.9 + - + -
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Residues in contact with GLY1337 (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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1305G VAL* 3.4 20.6 - - - +
1306G HIS 5.9 0.2 - - - -
1330G VAL* 3.8 24.3 - - - +
1333G CYS* 3.3 8.4 + - - +
1334G GLY 3.1 12.2 + - - -
1335G VAL 3.1 2.4 - - - -
1336G GLN* 1.3 77.4 - - - +
1338G TYR* 1.3 55.9 + - - +
1340G PHE* 3.4 7.7 + - - +
1341G GLY 2.9 21.3 + - - -
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Residues in contact with TYR1338 (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* 4.1 22.7 - - + -
1213G ASN* 2.7 32.1 + - - -
1217G LEU* 4.3 3.1 - - - +
1233G LEU* 4.5 3.7 - - + +
1236G VAL* 3.8 31.0 - - + -
1239G LEU* 6.1 1.1 - - + -
1240G CYS* 3.8 16.2 - - - -
1277G VAL* 4.5 10.8 - - + +
1279G ASN* 3.3 32.4 + - + +
1305G VAL* 4.0 16.8 - - + -
1307G ILE* 4.0 28.2 - - + +
1335G VAL* 3.1 21.1 + - - +
1336G GLN 3.1 0.2 + - - -
1337G GLY* 1.3 76.4 - - - +
1339G VAL* 1.3 58.2 + - + +
1341G GLY* 3.1 1.9 + - - -
1342G VAL* 3.0 32.8 + - - +
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Residues in contact with VAL1339 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1239G LEU* 4.4 36.3 - - + +
1240G CYS* 6.0 0.2 - - - -
1243G ALA* 4.0 19.7 - - + -
1335G VAL 4.4 3.1 - - - +
1336G GLN* 2.8 29.0 + - + +
1338G TYR* 1.3 75.3 - - + +
1340G PHE* 1.3 61.9 + - + +
1342G VAL* 3.2 3.9 + - - +
1343G GLU* 2.9 50.5 + - - +
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Residues in contact with PHE1340 (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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330B VAL* 5.0 0.9 - - + -
340B PHE* 3.3 58.8 - + + -
343B GLU* 3.4 28.0 - - + -
344B ARG* 3.8 6.7 - - + -
1303G VAL* 5.3 0.9 - - - -
1330G VAL* 4.1 17.5 - - + -
1333G CYS* 3.7 26.9 - - + -
1336G GLN* 3.0 50.9 + - + -
1337G GLY* 3.5 14.1 - - - +
1339G VAL* 1.3 78.2 - - + +
1341G GLY* 1.3 55.7 + - - +
1343G GLU* 3.2 8.2 + - - -
1344G ARG* 2.8 28.8 + - - +
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Residues in contact with GLY1341 (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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1277G VAL* 3.9 15.9 - - - -
1303G VAL* 3.9 23.6 - - - +
1330G VAL* 5.3 0.2 - - - +
1337G GLY 2.9 15.0 + - - -
1338G TYR 3.1 6.4 + - - -
1340G PHE* 1.3 77.3 - - - +
1342G VAL* 1.3 61.6 + - - +
1344G ARG* 3.3 1.9 + - - +
1345G ILE* 3.1 27.9 + - - +
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Residues in contact with VAL1342 (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* 5.8 0.2 - - + -
1209G ILE* 4.1 12.8 - - + +
1211G ILE* 4.1 25.8 - - + -
1240G CYS* 4.5 11.4 - - - +
1243G ALA* 3.7 16.2 - - + +
1244G ALA* 3.6 38.1 - - + +
1247G HIS* 5.1 3.1 - - + -
1251G VAL* 5.0 0.4 - - + -
1277G VAL* 4.6 4.3 - - + -
1338G TYR 3.0 14.6 + - - +
1339G VAL 3.2 7.6 + - - +
1341G GLY* 1.3 75.8 - - - +
1343G GLU* 1.3 58.2 + - - +
1345G ILE* 3.4 6.3 + - - +
1346G ALA* 2.9 28.9 + - + +
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Residues in contact with GLU1343 (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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336B GLN* 3.5 14.3 + - - +
340B PHE* 3.2 19.7 - - + -
343B GLU* 2.5 38.1 - - - +
1243G ALA* 5.5 1.3 - - + -
1247G HIS* 4.0 27.8 + - + +
1339G VAL* 2.9 36.1 + - + +
1340G PHE* 3.2 6.6 + - - +
1342G VAL* 1.3 78.0 - - + +
1344G ARG* 1.3 56.7 + - - +
1346G ALA* 3.4 6.6 + - - +
1347G ALA* 3.0 22.5 + - - +
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Residues in contact with ARG1344 (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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332B GLY 4.3 5.6 + - - +
333B CYS* 3.1 52.0 + - - +
334B GLY* 3.8 6.7 - - - +
336B GLN* 2.8 43.3 + - - +
340B PHE* 3.8 7.1 - - + -
1303G VAL* 3.8 21.5 - - + -
1327G ASP* 6.2 0.6 - - + +
1328G GLY* 5.8 1.3 - - - +
1340G PHE 2.8 19.9 + - - +
1341G GLY* 3.6 4.3 - - - +
1343G GLU* 1.3 70.7 - - - +
1345G ILE* 1.3 66.6 + - - +
1347G ALA* 3.2 6.5 + - - +
1348G LEU* 3.0 64.1 + - + +
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Residues in contact with ILE1345 (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* 4.3 6.5 - - + -
1209G ILE* 4.0 28.7 - - + -
1274G CYS 4.2 7.2 - - - +
1275G GLY* 4.2 12.8 - - - -
1276G ILE 3.9 14.6 - - - +
1277G VAL* 4.0 15.0 - - + -
1301G PRO* 3.5 37.9 - - + +
1303G VAL* 3.9 11.4 - - + -
1341G GLY 3.1 16.9 + - - +
1342G VAL 3.8 4.7 - - - +
1344G ARG* 1.3 74.6 - - - +
1346G ALA* 1.3 58.4 + - - +
1348G LEU* 3.9 3.8 - - + +
1349G ALA* 2.7 37.0 + - + +
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Residues in contact with ALA1346 (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* 3.6 32.2 - - + +
1247G HIS* 3.8 28.5 - - + +
1342G VAL 2.9 18.2 + - - +
1343G GLU 3.7 4.3 - - - +
1345G ILE* 1.3 80.1 - - - +
1347G ALA* 1.3 60.0 + - - +
1349G ALA 3.8 5.5 + - - -
1350G GLY* 3.8 9.9 + - - -
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Residues in contact with ALA1347 (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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336B GLN* 3.5 29.8 - - - +
1343G GLU 3.0 10.2 + - - +
1344G ARG* 3.2 11.0 + - - +
1346G ALA* 1.3 78.4 - - - +
1348G LEU* 1.3 64.1 + - - +
1350G GLY 3.4 15.9 - - - +
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Residues in contact with LEU1348 (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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1301G PRO* 4.2 28.2 - - + +
1303G VAL* 5.6 2.2 - - + -
1327G ASP* 5.0 15.7 - - + -
1344G ARG* 3.0 62.6 + - + +
1345G ILE 3.9 2.2 - - - +
1347G ALA* 1.3 76.5 - - - +
1349G ALA* 1.3 59.0 + - - +
1350G GLY 2.9 15.5 + - - +
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Residues in contact with ALA1349 (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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1202G ARG 4.0 13.9 - - - +
1203G SER* 3.8 20.0 - - - -
1204G LEU* 3.8 23.6 + - + +
1274G CYS* 4.0 19.5 - - + +
1301G PRO* 4.6 5.4 - - + -
1345G ILE* 2.7 23.0 + - + +
1346G ALA 4.0 4.0 - - - +
1348G LEU* 1.3 71.0 - - - +
1350G GLY* 1.3 55.2 + - - +
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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