Contacts of the helix formed by residues 1307 - 1326 (chain B) in PDB entry 2ASD
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 SER1307 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PHE* 3.6 23.8 + - - -
67A ILE* 2.4 47.6 + - - +
68A LEU* 4.3 5.2 - - - +
1273B TYR* 3.3 2.5 + - - -
1305B GLY 3.6 2.2 + - - -
1306B ILE* 1.3 76.6 - - - +
1308B LYS* 1.3 66.7 + - - +
1309B GLU* 3.2 12.5 + - - +
1310B THR* 3.0 10.2 + - - -
1311B ALA 2.9 19.1 + - - -
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Residues in contact with LYS1308 (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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53A PHE* 5.4 0.2 - - - -
1269B ILE* 4.9 3.4 - - + -
1270B GLU* 2.7 41.9 + - - +
1273B TYR* 3.8 51.0 + - + -
1307B SER* 1.3 74.0 + - - +
1309B GLU* 1.3 73.5 + - - +
1311B ALA* 3.3 3.3 + - - +
1312B TYR* 3.1 40.6 + - + -
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Residues in contact with GLU1309 (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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66A LYS 3.3 21.1 - - - +
67A ILE 3.7 4.4 - - - +
68A LEU* 4.9 1.4 - - - +
69A PRO* 3.4 39.0 - - + +
70A ASN* 5.1 6.6 + - - -
1307B SER* 3.2 8.0 + - - -
1308B LYS* 1.3 90.2 - - - +
1310B THR* 1.3 60.6 + - - +
1311B ALA 3.4 0.2 + - - -
1312B TYR* 3.4 14.6 + - + +
1313B SER* 3.3 21.3 + - - -
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Residues in contact with THR1310 (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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53A PHE 5.3 0.2 + - - -
66A LYS 5.4 0.8 - - - -
67A ILE* 3.8 34.6 - - + +
1302B PHE* 4.3 26.5 - - + -
1304B HIS* 5.2 7.5 + - - +
1306B ILE* 4.1 12.6 - - + -
1307B SER* 3.0 17.5 + - - +
1309B GLU* 1.3 75.1 - - - +
1311B ALA* 1.3 64.9 + - - +
1313B SER* 3.5 7.1 + - - -
1314B GLU* 3.0 23.7 + - + +
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Residues in contact with ALA1311 (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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1269B ILE* 4.1 7.9 - - + -
1273B TYR* 3.7 33.0 - - + +
1284B ILE* 3.8 7.4 - - + +
1306B ILE* 3.7 6.9 - - + +
1307B SER 2.9 4.9 + - - -
1308B LYS 3.5 9.4 - - - +
1309B GLU 3.2 0.2 - - - -
1310B THR* 1.3 74.7 - - - +
1312B TYR* 1.3 65.7 + - - +
1314B GLU* 4.9 0.9 - - - -
1315B SER* 2.9 28.3 + - - -
1337B PHE* 3.9 18.4 - - + -
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Residues in contact with TYR1312 (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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1266B PHE* 3.6 56.7 + + + +
1269B ILE* 4.2 11.6 - - + +
1270B GLU* 2.4 44.4 + - + +
1308B LYS* 3.1 37.8 + - + -
1309B GLU* 3.5 13.9 - - + +
1311B ALA* 1.3 78.6 - - - +
1313B SER* 1.3 61.9 + - - +
1315B SER* 2.9 20.2 + - - -
1316B VAL* 3.3 16.0 + - - +
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Residues in contact with SER1313 (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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1309B GLU 3.3 12.8 + - - -
1310B THR* 3.8 7.2 - - - -
1311B ALA 3.2 0.6 - - - -
1312B TYR* 1.3 81.9 - - - +
1314B GLU* 1.3 63.6 + - - +
1315B SER 3.4 0.2 + - - -
1316B VAL* 3.4 13.4 + - - +
1317B LYS* 3.5 20.7 + - - +
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Residues in contact with GLU1314 (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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1284B ILE* 4.2 12.1 - - + -
1300B ARG* 3.5 30.5 + - - -
1302B PHE* 3.8 26.2 - - + -
1310B THR* 3.0 18.4 + - + +
1311B ALA* 4.2 2.0 - - - +
1313B SER* 1.3 77.5 + - - +
1315B SER* 1.3 57.6 + - - +
1317B LYS* 3.2 32.2 + - - +
1318B LEU* 3.0 60.3 + - + +
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Residues in contact with SER1315 (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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1265B LEU* 3.6 15.5 - - - +
1266B PHE* 3.8 4.5 - - - -
1269B ILE* 3.2 27.2 - - - +
1284B ILE* 4.4 5.3 - - - +
1286B VAL* 3.6 23.9 - - - +
1311B ALA 2.9 14.3 + - - -
1312B TYR* 2.9 16.1 + - - -
1314B GLU* 1.3 74.4 - - - +
1316B VAL* 1.3 59.6 + - - +
1318B LEU* 4.3 1.8 - - - -
1319B LEU* 2.9 29.5 + - - +
1335B VAL* 5.4 0.2 - - - -
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Residues in contact with VAL1316 (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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1258B LEU* 4.5 12.7 - - + +
1262B LYS* 4.0 17.9 - - + -
1265B LEU* 5.0 1.3 - - + -
1266B PHE* 3.5 29.2 - - + -
1312B TYR 3.3 14.5 + - - +
1313B SER* 3.6 10.1 - - - +
1314B GLU 3.3 0.4 - - - -
1315B SER* 1.3 82.1 + - - +
1317B LYS* 1.3 58.5 + - + +
1319B LEU* 3.3 7.9 + - - +
1320B GLN* 2.9 46.2 + - + +
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Residues in contact with LYS1317 (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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1300B ARG* 5.7 7.2 - - - +
1313B SER* 3.5 19.7 + - - +
1314B GLU* 3.2 37.7 + - - +
1316B VAL* 1.3 78.0 - - + +
1318B LEU* 1.3 59.9 + - + +
1320B GLN* 3.5 17.5 + - - +
1321B LYS* 3.1 25.3 + - - +
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Residues in contact with LEU1318 (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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1284B ILE* 3.9 24.7 - - + +
1286B VAL* 3.7 21.1 - - + +
1298B ARG* 3.4 35.3 - - + +
1299B GLY* 4.2 12.1 - - - +
1300B ARG* 4.7 3.6 - - + +
1314B GLU* 3.0 54.6 + - + +
1315B SER* 4.3 0.7 - - - -
1317B LYS* 1.3 77.4 - - + +
1319B LEU* 1.3 64.8 + - - +
1321B LYS* 3.3 12.4 + - + +
1322B ILE* 3.2 27.3 + - - +
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Residues in contact with LEU1319 (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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1258B LEU* 3.5 25.6 - - + +
1261B ILE* 3.7 28.3 - - + -
1262B LYS* 4.5 12.3 - - + +
1265B LEU* 3.9 19.1 - - + -
1286B VAL* 4.4 3.5 - - + +
1315B SER 2.9 18.4 + - - +
1316B VAL* 3.6 4.9 - - - +
1318B LEU* 1.3 74.9 - - - +
1320B GLN* 1.3 63.5 + - - +
1322B ILE* 3.1 21.9 + - + +
1323B LEU* 3.1 23.6 + - + +
1330B ILE* 4.3 11.0 - - + -
1333B ILE* 3.9 24.2 - - + -
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Residues in contact with GLN1320 (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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1258B LEU* 3.9 29.0 - - + +
1316B VAL* 2.9 30.2 + - - +
1317B LYS* 3.5 19.6 - - - +
1319B LEU* 1.3 76.9 - - - +
1321B LYS* 1.3 61.0 + - - +
1323B LEU* 3.4 9.8 + - + +
1324B GLU* 3.1 41.9 + - + +
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Residues in contact with LYS1321 (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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1298B ARG* 3.5 20.0 - - + +
1317B LYS 3.1 14.3 + - - +
1318B LEU* 3.5 15.9 - - + +
1319B LEU 3.2 0.4 - - - -
1320B GLN* 1.3 76.6 - - - +
1322B ILE* 1.3 59.7 + - - +
1324B GLU* 3.4 10.1 + - - +
1325B GLU* 3.1 57.9 + - - +
1807H A 3.4 24.7 - - - -
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Residues in contact with ILE1322 (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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1286B VAL* 3.6 44.0 - - + +
1288B ALA* 4.4 9.0 - - + -
1296B VAL* 3.8 34.3 - - + +
1297B SER 4.7 0.2 - - - -
1298B ARG* 4.0 25.1 - - + +
1318B LEU 3.2 12.0 + - - +
1319B LEU* 3.1 11.6 + - + +
1321B LYS* 1.3 74.3 - - - +
1323B LEU* 1.3 60.7 + - + +
1325B GLU 3.4 0.5 + - - -
1326B ASP* 3.0 34.7 + - + +
1330B ILE* 4.2 23.1 - - + -
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Residues in contact with LEU1323 (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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1256B ARG* 3.0 68.6 + - + +
1258B LEU* 3.9 28.5 - - + -
1261B ILE* 4.5 2.5 - - + -
1319B LEU* 3.1 34.7 + - + +
1320B GLN* 3.7 7.6 - - - +
1322B ILE* 1.3 77.7 - - + +
1324B GLU* 1.3 61.0 + - + +
1326B ASP 3.1 9.0 + - - +
1327B GLU* 5.6 0.5 - - - +
1330B ILE* 3.7 28.5 - - + -
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Residues in contact with GLU1324 (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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1320B GLN* 3.1 30.5 + - - +
1321B LYS* 3.9 11.5 - - - +
1322B ILE 3.2 0.4 - - - -
1323B LEU* 1.3 81.2 - - + +
1325B GLU* 1.3 63.5 + - + +
1326B ASP 3.5 0.2 - - - -
1327B GLU* 6.0 1.8 - - - +
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Residues in contact with GLU1325 (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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1298B ARG* 3.0 38.3 + - - +
1321B LYS* 3.1 50.8 + - - +
1324B GLU* 1.3 83.8 - - + +
1326B ASP* 1.3 62.3 + - - +
1327B GLU* 5.9 1.1 - - - -
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Residues in contact with ASP1326 (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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1256B ARG* 3.1 11.3 + - - -
1290B THR* 4.2 4.6 - - - +
1296B VAL* 4.6 23.9 - - + +
1298B ARG* 4.9 0.9 - - - +
1322B ILE* 3.0 19.3 + - + +
1323B LEU* 3.1 16.1 - - - +
1324B GLU 3.5 1.0 - - - -
1325B GLU* 1.3 82.5 - - - +
1327B GLU* 1.3 62.3 + - - +
1328B ARG* 3.2 61.9 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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