Contacts of the helix formed by residues 1459 - 1477 (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 LYS1459 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1147A GLU* 3.4 32.7 + - - +
1151A GLN* 3.2 39.7 - - - +
700B 01K 3.8 17.1 + - + +
1439B PRO* 4.4 0.9 - - - -
1442B GLU* 6.4 0.4 - - - +
1457B ILE 3.6 1.8 + - - +
1458B PRO* 1.3 79.2 - - - +
1460B PRO* 1.3 80.2 - - + +
1461B LYS* 3.4 4.0 - - + +
1462B ARG* 3.0 19.2 + - + +
1463B LEU* 3.2 8.5 + - - +
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Residues in contact with PRO1460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1151A GLN* 4.3 8.1 - - - +
1437B ALA 6.0 0.4 - - - +
1439B PRO* 4.1 28.7 - - + -
1459B LYS* 1.3 91.4 - - + +
1461B LYS* 1.3 59.1 + - - +
1462B ARG 3.1 0.2 + - - -
1463B LEU* 3.2 3.8 + - + +
1464B GLN* 2.8 51.6 + - - +
1594B VAL* 5.6 2.5 - - + -
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Residues in contact with LYS1461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1151A GLN* 5.2 8.4 - - - +
1155A PRO* 3.3 36.1 - - + +
1158A GLN* 5.6 2.2 + - - -
1459B LYS* 3.4 3.6 - - + +
1460B PRO* 1.3 78.8 - - - +
1462B ARG* 1.3 60.6 + - - +
1464B GLN* 3.9 14.0 - - + +
1465B GLU* 3.2 43.3 + - + +
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Residues in contact with ARG1462 (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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700B 01K 3.3 95.2 + - - +
1458B PRO* 3.7 5.8 - - + -
1459B LYS* 3.0 15.7 + - + +
1461B LYS* 1.3 75.2 - - - +
1463B LEU* 1.3 62.8 + - - +
1465B GLU* 3.1 11.8 + - - +
1466B TRP* 2.8 28.2 + - + +
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Residues in contact with LEU1463 (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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700B 01K 3.8 40.4 - - + +
1437B ALA* 4.1 3.1 - - + -
1438B CYS 3.6 17.5 - - - +
1439B PRO* 3.5 39.0 - - + -
1458B PRO* 4.2 13.4 - - + +
1459B LYS 3.2 8.6 + - - +
1460B PRO* 3.7 7.4 - - + +
1462B ARG* 1.3 79.8 - - - +
1464B GLN* 1.3 62.8 + - + +
1466B TRP* 3.1 13.4 + - + +
1467B PHE* 3.1 54.0 + - + -
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Residues in contact with GLN1464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1437B ALA* 4.5 9.8 + - + -
1460B PRO* 2.8 41.3 + - - +
1461B LYS* 3.9 14.3 - - + +
1463B LEU* 1.3 77.3 - - + +
1465B GLU* 1.3 63.4 + - + +
1466B TRP 3.1 0.2 + - - -
1467B PHE* 3.2 2.9 + - - -
1468B LYS* 3.0 32.4 + - - +
1593B GLU* 3.3 45.6 - - - +
1594B VAL* 3.7 21.6 - - - +
1596B PHE* 3.7 18.1 - - + -
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Residues in contact with GLU1465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1461B LYS* 3.2 40.3 + - + +
1462B ARG* 3.1 12.7 + - + +
1464B GLN* 1.3 78.8 - - + +
1466B TRP* 1.3 56.0 + - - +
1468B LYS* 3.4 18.6 + - + +
1469B LYS* 3.0 28.6 + - - +
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Residues in contact with TRP1466 (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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700B 01K 3.0 65.7 + - + +
1374B PHE* 5.3 0.9 - + - -
1398B LEU* 4.5 8.7 - - + -
1411B THR* 3.3 15.1 - - + +
1414B TYR* 3.7 28.5 - + + -
1415B HIS* 3.4 30.6 + + - -
1418B LEU* 3.7 23.8 - - + -
1462B ARG* 2.8 13.2 + - + +
1463B LEU* 3.2 19.1 - - + +
1464B GLN 3.0 0.2 - - - -
1465B GLU* 1.3 75.8 - - - +
1467B PHE* 1.3 106.1 + + - +
1469B LYS* 3.6 4.2 + - - -
1470B MET* 3.2 17.4 + - + +
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Residues in contact with PHE1467 (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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700B 01K 3.6 36.8 - - + -
1398B LEU* 4.2 11.4 - - + -
1418B LEU* 4.2 3.8 - - + -
1435B ILE* 3.8 33.0 - - + -
1437B ALA* 3.7 20.2 - - + -
1463B LEU* 3.1 45.2 + - + -
1464B GLN 3.2 5.1 + - - +
1466B TRP* 1.3 101.2 - + - +
1468B LYS* 1.3 58.7 + - - +
1470B MET* 3.3 11.3 + - + +
1471B LEU* 2.9 40.0 + - + +
1596B PHE* 4.1 16.8 - - + -
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Residues in contact with LYS1468 (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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1464B GLN* 3.0 23.2 + - - +
1465B GLU* 3.7 20.7 - - + +
1466B TRP 3.3 0.2 - - - -
1467B PHE* 1.3 73.5 - - - +
1469B LYS* 1.3 59.8 + - - +
1471B LEU* 4.5 0.7 - - - -
1472B ASP* 2.8 42.4 + - - +
1483B TYR* 3.7 24.0 + - + +
1593B GLU 6.1 0.7 - - - -
1596B PHE* 4.0 20.9 - - + -
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Residues in contact with LYS1469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1411B THR* 4.8 11.1 - - + +
1412B ALA* 5.5 7.5 - - - +
1415B HIS* 3.9 23.1 + - + +
1465B GLU 3.0 16.5 + - - +
1466B TRP* 3.9 6.5 - - + +
1467B PHE 3.3 0.2 - - - -
1468B LYS* 1.3 76.0 - - - +
1470B MET* 1.3 63.5 + - - +
1472B ASP* 3.5 7.1 + - - +
1473B LYS* 3.3 22.9 + - - +
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Residues in contact with MET1470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1415B HIS* 3.6 43.5 - - + -
1418B LEU* 3.9 23.8 - - + -
1419B ILE* 3.4 28.3 - - + +
1422B LEU* 4.3 10.5 - - + -
1435B ILE* 4.3 9.6 - - + -
1466B TRP* 3.2 16.6 + - + +
1467B PHE* 3.6 23.6 - - + +
1468B LYS 3.2 0.6 - - - -
1469B LYS* 1.3 80.2 - - - +
1471B LEU* 1.3 92.7 + - + +
1473B LYS* 3.5 1.0 + - - -
1474B ALA* 3.3 14.8 + - - -
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Residues in contact with LEU1471 (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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1422B LEU* 4.1 7.0 - - + -
1435B ILE* 5.5 0.7 - - + -
1467B PHE* 2.9 24.4 + - + +
1468B LYS 3.9 0.9 - - - +
1470B MET* 1.3 90.6 - - + +
1472B ASP* 1.3 59.5 + - - +
1473B LYS 3.1 1.8 - - - -
1474B ALA* 2.9 6.7 + - - +
1475B VAL* 2.8 32.6 + - - +
1480B VAL* 4.5 4.9 - - + +
1483B TYR* 3.6 44.4 - - + -
1596B PHE* 3.6 22.0 - - + -
1598B ILE* 3.5 42.8 - - + -
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Residues in contact with ASP1472 (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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1468B LYS* 2.8 34.0 + - - +
1469B LYS* 3.9 8.3 + - - +
1471B LEU* 1.3 72.7 - - - +
1473B LYS* 1.3 57.7 + - - +
1475B VAL* 3.3 8.0 + - - +
1476B SER* 2.8 27.0 + - - -
1483B TYR* 2.7 28.9 + - - -
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Residues in contact with LYS1473 (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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1305B ARG* 4.5 0.8 - - - +
1309B PHE* 5.3 8.4 - - - -
1312B ARG* 5.5 4.8 - - - +
1415B HIS* 5.5 6.3 - - + +
1416B GLU* 2.9 31.8 + - - +
1419B ILE* 3.7 12.5 - - + +
1469B LYS 3.3 10.2 + - - +
1470B MET* 3.7 10.1 - - - +
1472B ASP* 1.3 80.8 - - - +
1474B ALA* 1.3 57.7 + - - +
1476B SER* 3.2 9.0 + - - -
1477B GLU* 3.0 46.7 + - - +
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Residues in contact with ALA1474 (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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1419B ILE* 3.8 26.5 - - + -
1422B LEU* 5.4 1.3 - - + -
1470B MET* 3.3 12.3 + - - +
1471B LEU* 2.9 11.0 + - - +
1473B LYS* 1.3 78.5 - - - +
1475B VAL* 1.3 59.8 + - - +
1477B GLU* 3.4 7.7 + - - -
1479B ILE* 2.8 32.3 + - + +
1480B VAL* 3.1 28.8 + - + +
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Residues in contact with VAL1475 (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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1471B LEU 2.8 16.8 + - - +
1472B ASP* 3.6 9.6 - - - +
1474B ALA* 1.3 74.1 - - - +
1476B SER* 1.3 64.9 + - - +
1477B GLU 3.0 2.0 + - - -
1478B ARG* 3.2 15.9 + - - -
1480B VAL* 3.4 34.0 - - + +
1481B HIS 3.8 16.4 - - - +
1482B ASP* 4.6 1.8 - - - -
1483B TYR* 4.3 16.8 - - + -
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Residues in contact with SER1476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1472B ASP 2.8 14.9 + - - -
1473B LYS* 3.3 15.5 - - - -
1475B VAL* 1.3 77.5 - - - +
1477B GLU* 1.3 56.3 + - - +
1478B ARG* 3.2 10.0 + - - +
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Residues in contact with GLU1477 (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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1305B ARG* 2.5 41.9 + - - -
1419B ILE* 4.4 1.6 - - - +
1473B LYS* 3.0 37.7 + - - +
1474B ALA 3.8 5.8 - - - +
1475B VAL 3.0 1.0 - - - -
1476B SER* 1.3 75.2 - - - +
1478B ARG* 1.3 70.5 + - - +
1479B ILE* 3.2 21.0 + - + +
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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
------------------------------------------------------------
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