Contacts of the helix formed by residues 1301 - 1319 (chain B) in PDB entry 5JPM
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 SER1301 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004B LEU* 3.8 6.7 - - - -
1006B LEU* 4.0 19.3 - - - +
1126B ARG* 5.8 1.8 - - - -
1259B ALA* 5.2 3.1 - - - -
1300B ARG* 1.3 76.9 - - - +
1302B THR* 1.3 74.9 + - - +
1303B GLN* 3.5 2.2 + - - -
1304B ASP* 2.6 25.6 + - - +
1305B THR* 2.4 30.4 + - - -
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Residues in contact with THR1302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004B LEU* 4.0 25.1 - - + -
1006B LEU* 5.4 3.1 - - + -
1007B PRO 5.7 0.4 - - - +
1008B ARG* 4.9 5.6 - - + -
1012B GLU* 2.9 29.8 + - - -
1013B GLN* 4.0 29.4 - - + +
1016B ILE* 4.3 14.4 - - + -
1301B SER* 1.3 87.1 + - - +
1303B GLN* 1.3 68.6 + - - +
1305B THR* 3.1 1.9 + - - -
1306B VAL* 3.1 29.0 + - - +
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Residues in contact with GLN1303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012B GLU* 3.1 26.1 + - - +
1077B TRP* 3.3 27.9 - - + -
1081B PHE* 3.2 30.3 - - - -
1124B LEU* 3.6 21.8 - - + -
1126B ARG* 3.8 11.9 - - - +
1144B PHE* 4.9 3.3 - - - -
1263B GLU* 3.7 18.2 - - - +
1301B SER* 3.5 1.8 + - - -
1302B THR* 1.3 81.0 + - - +
1304B ASP* 1.3 63.2 + - - +
1306B VAL* 3.2 17.0 - - - +
1307B ILE* 3.3 38.7 - - - +
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Residues in contact with ASP1304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1126B ARG* 4.1 5.0 + - - -
1259B ALA* 3.4 36.6 - - - +
1262B ILE* 4.2 13.4 - - + +
1263B GLU* 3.9 15.9 + - + +
1299B PHE* 3.4 3.3 - - - +
1300B ARG* 2.7 17.5 + - - -
1301B SER* 2.6 48.5 + - - +
1303B GLN* 1.3 72.7 - - - +
1305B THR* 1.3 61.0 + - - +
1307B ILE* 4.3 0.8 - - - +
1308B ALA* 2.9 34.6 + - - +
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Residues in contact with THR1305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000B VAL* 4.5 3.8 - - + -
1004B LEU* 3.3 12.0 - - + +
1016B ILE* 3.9 15.9 - - + -
1298B GLY* 4.0 17.9 - - - -
1299B PHE* 3.1 26.3 + - + +
1301B SER 2.4 26.2 + - - -
1302B THR 3.1 4.2 + - - -
1304B ASP* 1.3 75.6 + - - +
1306B VAL* 1.3 60.0 + - - +
1309B LEU* 2.9 58.0 + - + +
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Residues in contact with VAL1306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012B GLU* 5.1 1.3 - - - +
1015B MET* 4.1 7.9 - - + +
1016B ILE* 3.6 22.7 - - + -
1019B ALA* 3.8 22.5 - - + +
1020B PRO* 3.7 22.7 - - + -
1081B PHE* 3.8 25.4 - - + -
1084B LYS* 5.2 2.8 + - - +
1302B THR* 3.1 14.3 + - - +
1303B GLN* 3.2 22.0 - - - +
1305B THR* 1.3 76.3 - - - +
1307B ILE* 1.3 63.9 + - + +
1309B LEU* 4.2 1.5 - - - +
1310B ASP* 3.1 26.2 + - - +
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Residues in contact with ILE1307 (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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1081B PHE* 5.9 2.5 - - + -
1084B LYS* 5.6 6.5 - - - +
1144B PHE* 5.2 2.5 - - + -
1263B GLU* 3.5 27.1 - - + +
1266B ALA* 3.7 17.9 - - + -
1267B TYR* 3.3 50.0 - - + +
1270B LEU* 4.5 5.5 - - + +
1303B GLN* 3.3 32.6 + - - +
1304B ASP 4.3 1.8 - - - +
1305B THR 3.2 0.4 - - - -
1306B VAL* 1.3 83.6 - - + +
1308B ALA* 1.3 59.6 + - - +
1310B ASP* 3.3 6.2 + - + +
1311B ALA* 2.9 27.9 + - - +
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Residues in contact with ALA1308 (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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1262B ILE* 4.1 11.9 - - + -
1266B ALA* 3.8 11.8 - - + +
1289B LEU* 4.4 7.9 - - + -
1299B PHE* 3.6 33.9 - - + -
1304B ASP 2.9 20.6 + - - +
1307B ILE* 1.3 75.6 - - - +
1309B LEU* 1.3 53.6 + - - +
1311B ALA* 3.1 2.1 + - - +
1312B LEU* 2.7 40.0 + - - +
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Residues in contact with LEU1309 (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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988B THR* 3.7 30.3 - - + -
989B LEU* 4.5 16.3 - - + +
994B ALA* 5.2 2.9 - - + -
1000B VAL* 4.4 11.4 - - + -
1020B PRO* 3.7 33.9 - - + -
1023B ALA* 3.9 5.4 - - + +
1298B GLY* 5.6 2.7 - - - -
1299B PHE* 4.0 17.9 - - + -
1305B THR* 2.9 35.7 + - + +
1306B VAL* 4.4 3.1 - - - +
1308B ALA* 1.3 76.3 - - - +
1310B ASP* 1.3 57.5 + - - +
1312B LEU* 4.4 8.7 - - + +
1313B SER* 2.9 32.4 + - - -
1316B TRP* 5.4 1.1 - - + -
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Residues in contact with ASP1310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019B ALA* 5.8 2.0 - - + +
1023B ALA* 4.2 8.9 - - + +
1026B ARG* 2.6 44.9 + - - -
1084B LYS* 3.2 28.2 + - - +
1151B HIS* 5.8 0.5 + - - -
1198B TYR* 5.6 2.1 + - - -
1270B LEU* 3.9 16.2 - - + +
1306B VAL 3.1 22.3 + - - +
1307B ILE* 3.5 8.1 - - + +
1308B ALA 3.2 0.2 - - - -
1309B LEU* 1.3 78.1 - - - +
1311B ALA* 1.3 60.2 + - - +
1313B SER* 4.0 0.2 - - - -
1314B ALA* 3.3 21.0 + - - +
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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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1266B ALA* 3.4 35.2 - - + +
1269B LEU* 3.3 22.6 - - + +
1270B LEU* 3.7 15.7 - - + +
1289B LEU* 5.7 2.9 - - + -
1307B ILE 2.9 15.9 + - - +
1308B ALA* 3.6 4.0 - - - +
1310B ASP* 1.3 75.2 - - - +
1312B LEU* 1.3 65.7 + - + +
1314B ALA* 3.2 3.6 + - - +
1315B TYR 3.0 17.0 + - - -
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Residues in contact with LEU1312 (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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988B THR* 5.8 0.7 - - + -
1269B LEU* 5.9 0.9 - - + -
1286B SER* 3.8 25.4 - - - +
1289B LEU* 3.7 32.8 - - + +
1290B THR* 3.8 10.5 - - - +
1299B PHE* 3.7 31.9 - - + -
1308B ALA 2.7 19.9 + - - +
1309B LEU* 4.2 7.0 - - + +
1311B ALA* 1.3 72.7 - - + +
1313B SER* 1.3 57.5 + - - +
1315B TYR* 3.2 4.1 + - + +
1316B TRP* 2.8 70.9 + - + +
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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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989B LEU* 4.3 7.6 - - - -
1023B ALA* 2.8 37.4 + - - +
1026B ARG* 4.4 5.7 + - - +
1027B TYR* 3.7 11.7 + - - +
1309B LEU 2.9 20.6 + - - -
1310B ASP 4.0 2.7 - - - -
1312B LEU* 1.3 75.0 - - - +
1314B ALA* 1.3 63.0 + - - +
1316B TRP* 3.5 12.9 + - - +
1317B ILE* 3.1 30.5 + - - +
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Residues in contact with ALA1314 (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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1026B ARG* 4.6 8.0 - - - +
1270B LEU* 4.0 13.0 - - + -
1273B LEU* 3.6 19.3 - - + +
1274B LEU* 6.5 1.1 - - + -
1310B ASP 3.3 11.8 + - - +
1311B ALA 3.2 9.9 + - - +
1313B SER* 1.3 79.1 - - - +
1315B TYR* 1.3 61.3 + - - +
1317B ILE* 3.5 11.3 + - - +
1318B ALA* 3.3 19.9 + - - +
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Residues in contact with TYR1315 (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 LEU* 4.0 4.9 - - + -
1273B LEU* 3.5 21.0 - - + +
1278B LYS* 4.4 8.3 - - + -
1282B ALA* 3.8 11.7 - - + -
1283B ASP* 2.6 36.7 + - - +
1286B SER* 3.1 40.2 - - - +
1287B ALA 5.6 0.2 - - - -
1290B THR* 5.8 0.4 - - - -
1311B ALA 3.0 13.1 + - - +
1312B LEU* 3.2 7.4 + - + +
1314B ALA* 1.3 75.0 - - - +
1316B TRP* 1.3 81.6 + + - +
1318B ALA* 2.9 4.8 + - - +
1319B SER* 2.8 58.5 + - - -
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Residues in contact with TRP1316 (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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984B ASP* 4.3 8.8 - - + +
985B PRO* 3.6 45.6 - - + +
988B THR* 3.8 24.7 - - + -
989B LEU* 3.8 34.5 - - + -
1027B TYR* 3.5 22.7 - - + -
1290B THR* 4.3 16.7 + - + +
1309B LEU* 5.4 1.8 - - + -
1312B LEU* 2.8 59.7 + - + +
1313B SER* 4.0 1.6 - - - +
1315B TYR* 1.3 94.9 - + - +
1317B ILE* 1.3 60.5 + - - +
1319B SER* 3.8 5.2 - - - -
1320B HIS* 3.2 26.0 + - - +
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Residues in contact with ILE1317 (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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1026B ARG* 3.5 35.0 - - + +
1027B TYR* 3.8 20.2 - - + +
1030B LYS* 4.0 27.1 - - + +
1031B THR* 4.6 7.7 - - + +
1313B SER* 3.1 23.3 + - - +
1314B ALA* 3.7 9.0 - - - +
1315B TYR 3.1 0.4 - - - -
1316B TRP* 1.3 79.1 - - - +
1318B ALA* 1.3 61.3 - - - +
1320B HIS* 3.8 10.0 + - - +
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Residues in contact with ALA1318 (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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1273B LEU* 4.6 11.2 - - + -
1278B LYS* 4.4 25.6 - - + +
1314B ALA 3.3 10.8 + - - +
1315B TYR* 2.9 10.8 + - + +
1317B ILE* 1.3 82.0 - - - +
1319B SER* 1.3 57.8 + - - +
1320B HIS 3.4 4.2 + - - +
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Residues in contact with SER1319 (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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1278B LYS* 3.9 22.2 - - - +
1315B TYR* 2.8 57.1 + - - -
1316B TRP* 3.8 7.4 - - - -
1318B ALA* 1.3 72.0 - - - +
1320B HIS* 1.3 61.6 + - - +
1321B THR* 3.5 12.2 + - - +
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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
------------------------------------------------------------
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