Contacts of the strand formed by residues 1352 - 1366 (chain B) in PDB entry 4BHW
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 SER1352 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1332B THR* 4.2 15.0 + - - +
1333B VAL 3.3 14.8 - - - -
1334B GLU* 4.0 20.0 - - - -
1335B VAL 4.5 0.2 - - - +
1350B ALA* 3.2 12.5 - - - +
1351B GLU* 1.3 92.9 + - - +
1353B PHE* 1.3 69.0 + - - +
1354B PRO* 4.1 4.9 - - - +
1386B PRO* 4.6 2.3 - - - +
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Residues in contact with PHE1353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1332B THR* 3.1 5.8 - - - -
1333B VAL* 3.0 40.9 + - + +
1335B VAL* 4.1 19.5 - - + -
1349B MET* 3.9 11.9 - - + -
1350B ALA* 4.1 20.6 - - + -
1352B SER* 1.3 75.3 - - - +
1354B PRO* 1.3 66.8 - - + +
1355B TYR* 3.8 0.9 + - - -
1381B TYR* 4.1 6.3 - - + -
1385B CYS* 3.9 7.2 - - - -
1386B PRO* 3.6 23.3 - - + -
1387B PRO 3.1 29.8 - - - -
1388B PRO* 3.9 13.2 - - + -
1389B ASN* 3.1 26.9 - - - +
1503B TYR* 3.8 24.2 - + + -
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Residues in contact with PRO1354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1331B LYS 3.4 9.6 - - - +
1332B THR* 4.2 8.7 - - + -
1352B SER* 4.1 4.3 - - - +
1353B PHE* 1.3 84.9 - - - +
1355B TYR* 1.3 61.3 + - - +
1381B TYR* 3.5 3.7 - - - -
1382B GLY 4.8 1.0 + - - -
1384B ASP* 4.4 8.3 - - + +
1385B CYS* 3.5 43.2 - - + +
1386B PRO* 3.8 10.8 - - + -
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Residues in contact with TYR1355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1330B ASP* 3.7 6.3 - - - +
1331B LYS* 2.8 59.1 + - + +
1332B THR* 3.8 6.9 + - - -
1333B VAL* 3.5 32.3 - - + -
1353B PHE 4.0 1.1 - - - -
1354B PRO* 1.3 70.9 - - - +
1356B ARG* 1.3 70.7 + - - +
1357B THR* 3.9 16.2 - - - -
1379B GLN* 3.9 24.0 - - + -
1380B GLU 3.4 10.5 - - - +
1381B TYR* 3.3 45.3 - + + -
1382B GLY 5.5 0.2 - - - +
1505B GLU* 3.4 27.4 + - + +
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Residues in contact with ARG1356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1328B ALA* 4.9 3.8 - - - +
1329B SER 3.6 12.6 - - - +
1330B ASP* 2.9 33.5 + - - +
1355B TYR* 1.3 74.8 - - - +
1357B THR* 1.3 68.5 + - - +
1358B LYS* 4.5 7.6 - - + +
1378B VAL 3.9 0.2 - - - +
1379B GLN* 3.5 1.9 - - - -
1380B GLU* 2.7 59.8 + - + +
1430B TYR* 5.8 0.9 - - - +
1614B ASP* 2.9 43.2 + - - +
1616B ASP 3.9 9.7 + - - -
1617B PRO 4.9 2.2 + - - -
1618B LEU* 3.5 23.2 - - - +
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Residues in contact with THR1357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1327B HIS* 3.7 13.3 - - - +
1328B ALA* 3.3 4.7 - - - -
1329B SER* 2.8 59.9 + - - +
1331B LYS* 3.7 20.2 - - + +
1355B TYR* 3.9 16.3 + - - -
1356B ARG* 1.3 74.0 - - - +
1358B LYS* 1.3 67.6 + - - +
1377B HIS* 5.2 6.6 + - - +
1378B VAL 3.2 12.5 + - - -
1379B GLN* 5.0 2.0 - - - +
1396B SER* 5.5 0.7 + - - -
1625B ASP* 5.3 1.1 - - - +
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Residues in contact with LYS1358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1298B LEU* 4.2 26.6 - - + +
1325B VAL* 4.5 11.0 - - + -
1327B HIS* 3.0 14.1 - - - +
1328B ALA* 3.9 12.8 - - + -
1356B ARG* 4.5 7.0 - - + +
1357B THR* 1.3 82.0 + - - +
1359B ALA* 1.3 60.8 + - - +
1360B LEU* 5.4 3.4 - - + -
1376B MET 4.0 0.2 - - - +
1377B HIS* 3.2 6.9 + - - +
1378B VAL* 2.9 41.5 + - + +
1380B GLU* 2.9 41.5 + - - +
1424B TYR* 5.2 4.9 - - - -
1428B LEU* 5.9 1.4 - - - +
1614B ASP* 2.9 35.2 + - - -
1616B ASP* 5.2 6.9 + - - -
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Residues in contact with ALA1359 (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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1325B VAL* 3.4 3.6 - - - +
1326B VAL* 2.7 32.2 + - + +
1327B HIS* 3.0 25.3 + - + -
1358B LYS* 1.3 73.5 - - - +
1360B LEU* 1.3 62.6 + - - +
1361B PHE* 4.8 4.0 - - + -
1376B MET 3.5 5.4 - - - +
1377B HIS* 3.4 31.6 - - + +
1624B MET* 3.8 11.2 - - + +
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Residues in contact with LEU1360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1298B LEU* 4.1 24.5 - - + -
1302B LEU* 4.0 14.1 - - + -
1323B VAL* 4.0 20.9 - - + -
1324B ARG 3.3 12.6 - - - +
1325B VAL* 3.7 11.4 - - + -
1358B LYS* 5.4 3.1 - - + -
1359B ALA* 1.3 76.1 - - - +
1361B PHE* 1.3 64.6 + - - +
1362B ALA* 6.2 0.2 - - + -
1374B PHE* 4.8 3.6 - - + -
1375B GLY* 3.6 1.7 - - - -
1376B MET* 2.9 66.7 + - + +
1378B VAL* 5.3 9.6 - - + -
1417B ILE* 4.6 4.9 - - + -
1421B TYR* 4.9 8.5 - - + -
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Residues in contact with PHE1361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1323B VAL* 3.5 4.5 - - - -
1324B ARG 2.9 31.2 + - - +
1326B VAL* 3.9 20.0 - - + -
1359B ALA* 4.8 6.5 - - + -
1360B LEU* 1.3 78.2 - - - +
1362B ALA* 1.3 59.5 + - - +
1363B PHE* 3.6 17.3 - - + -
1372B CYS* 3.5 22.0 - - - -
1374B PHE 3.4 14.8 - - - -
1375B GLY* 3.6 8.7 - - - -
1376B MET 5.4 1.6 - - - -
1377B HIS* 5.0 6.5 - - - -
1447B ILE* 3.7 23.8 - - + -
1448B PHE* 3.7 20.2 - + - -
1624B MET* 3.4 39.3 - - + -
1630B PHE* 4.2 3.4 - + - -
1654B MET* 3.5 13.2 - - + -
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Residues in contact with ALA1362 (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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1321B VAL* 4.3 2.0 - - + -
1322B THR 3.2 7.6 - - - +
1323B VAL* 4.2 11.0 - - + +
1360B LEU* 4.5 0.6 + - + -
1361B PHE* 1.3 74.3 - - - +
1363B PHE* 1.3 60.9 + - - +
1372B CYS* 3.6 4.0 - - - -
1373B PHE* 3.0 41.9 + - + -
1374B PHE* 3.1 17.6 + - + -
1417B ILE* 3.8 28.9 - - + -
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Residues in contact with PHE1363 (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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1290B ALA* 3.4 29.6 - - + -
1293B LEU* 4.3 14.6 - - + -
1320B GLU 4.1 0.2 - - - +
1321B VAL* 3.5 5.7 - - - -
1322B THR* 2.7 50.5 + - + +
1324B ARG* 4.6 5.2 - - + -
1326B VAL* 5.7 0.9 - - + -
1361B PHE* 3.6 31.4 - + + -
1362B ALA* 1.3 74.3 - - - +
1364B GLU* 1.3 61.1 + - - +
1370B ASP* 4.9 2.7 - - + +
1371B LEU 3.3 9.2 - - - +
1372B CYS* 3.6 33.4 - - + -
1373B PHE* 3.6 5.4 - - - -
1651B THR* 4.1 7.6 - - + -
1654B MET* 4.1 13.2 - - + -
1655B LEU* 3.9 29.4 - - + -
1658B LEU* 5.3 1.1 - - + -
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Residues in contact with GLU1364 (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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1319B GLY* 3.3 21.3 + - - +
1320B GLU 3.7 15.0 - - - +
1321B VAL* 4.9 0.2 - - + -
1363B PHE* 1.3 75.8 - - - +
1365B GLU* 1.3 71.7 + - - +
1366B ILE* 3.5 18.6 + - + +
1370B ASP* 3.7 4.4 - - - -
1371B LEU* 2.9 35.2 + - + +
1373B PHE* 3.9 14.8 - - + -
1404B PHE* 3.2 20.4 - - + -
1405B ARG* 2.7 49.7 + - - +
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Residues in contact with GLU1365 (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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1319B GLY* 4.9 6.7 - - - -
1320B GLU* 4.0 16.4 + - + +
1364B GLU* 1.3 80.7 - - - +
1366B ILE* 1.3 65.2 + - - +
1367B ASP 4.3 0.2 - - - -
1368B GLY* 3.2 37.0 - - - +
1369B VAL 3.5 6.1 - - - +
1370B ASP* 4.8 6.9 + - - +
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Residues in contact with ILE1366 (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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1364B GLU* 3.5 25.3 + - + +
1365B GLU* 1.3 79.6 - - - +
1367B ASP* 1.3 78.7 + - - +
1369B VAL* 2.9 18.2 + - - +
1371B LEU* 3.5 24.2 - - + -
1403B PHE 3.1 28.5 - - - +
1405B ARG* 3.8 37.5 - - + +
1644B LEU* 4.2 12.3 - - + -
1648B GLN* 3.2 21.5 + - - +
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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