Contacts of the helix formed by residues 1483 - 1499 (chain H) in PDB entry 5YWB
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 SER1483 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715H VAL* 4.6 8.6 - - - +
716H GLY 5.1 0.2 - - - -
775H GLN* 4.2 2.1 + - - -
1480H GLU* 5.0 0.8 + - - +
1482H PHE* 1.3 74.9 - - - +
1484H GLN* 1.3 78.4 + - - +
1485H GLY 3.3 7.2 + - - -
1486H GLN* 2.9 18.6 + - - -
1487H ARG* 3.1 22.0 + - - +
2501H ADP 2.4 55.9 + - - -
2503H MG 3.9 0.9 - - - -
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Residues in contact with GLN1484 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775H GLN* 3.9 44.3 + - + +
776H LYS* 4.7 15.9 - - - +
1429H PRO* 4.6 10.8 - - + +
1483H SER* 1.3 80.2 + - - +
1485H GLY* 1.3 61.5 + - - +
1487H ARG* 3.2 47.8 + - - +
1488H GLN* 2.9 25.2 + - - +
1511H SER* 3.3 22.2 - - - +
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Residues in contact with GLY1485 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715H VAL* 4.0 14.5 - - - +
1483H SER* 3.3 5.1 + - - -
1484H GLN* 1.3 78.2 - - - +
1486H GLN* 1.3 57.2 + - - +
1488H GLN* 3.2 7.6 + - - +
1489H LEU* 2.9 36.4 + - - +
1511H SER* 3.4 25.8 + - - -
1512H ILE* 4.7 3.4 - - - -
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Residues in contact with GLN1486 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715H VAL* 4.1 17.0 - - + +
716H GLY* 5.1 2.5 - - - -
1460H LEU* 4.7 9.6 - - + -
1463H VAL* 3.3 36.2 - - - +
1481H ASN 4.9 1.0 + - - -
1482H PHE* 3.4 34.7 - - + -
1483H SER* 2.9 31.2 + - - +
1485H GLY* 1.3 72.8 - - - +
1487H ARG* 1.3 61.1 + - - +
1489H LEU* 3.2 9.1 + - + +
1490H PHE* 2.9 35.8 + - - -
2501H ADP 3.7 21.1 + - - -
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Residues in contact with ARG1487 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776H LYS* 4.7 17.2 - - - +
1429H PRO* 3.8 29.2 + - + +
1431H LEU* 3.6 33.7 - - + +
1478H GLY* 3.8 24.1 + - - -
1479H GLY 2.5 32.0 + - - +
1482H PHE* 3.1 20.9 + - + +
1483H SER* 3.1 11.0 + - - +
1484H GLN* 3.2 41.1 + - - +
1486H GLN* 1.3 74.1 - - - +
1488H GLN* 1.3 65.7 + - - +
1490H PHE* 3.2 3.3 + - - +
1491H CYS* 3.0 26.9 + - - -
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Residues in contact with GLN1488 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1425H ILE* 4.8 3.4 - - - +
1426H LEU 2.9 28.4 + - - -
1427H GLN* 4.0 7.5 + - - +
1429H PRO* 3.2 31.4 - - - +
1484H GLN* 2.9 13.0 + - - +
1485H GLY* 3.4 12.1 - - - +
1487H ARG* 1.3 77.4 - - - +
1489H LEU* 1.3 56.9 + - - +
1491H CYS* 3.2 6.6 + - - +
1492H LEU* 2.9 37.7 + - + +
1507H GLU 3.4 18.3 + - - -
1508H ALA* 4.1 24.0 - - - +
1510H ALA* 4.6 7.7 - - - +
1511H SER* 5.2 8.1 - - - +
1512H ILE* 4.5 10.5 - - + -
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Residues in contact with LEU1489 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715H VAL* 6.3 2.2 - - + -
1458H ALA* 3.5 18.6 - - - +
1459H GLN* 3.2 29.6 - - + +
1460H LEU* 3.6 25.5 - - + +
1485H GLY 2.9 23.1 + - - +
1486H GLN* 3.2 11.0 + - + +
1488H GLN* 1.3 76.0 - - - +
1490H PHE* 1.3 58.2 + - - +
1492H LEU* 3.2 10.7 + - + +
1493H ALA* 2.9 26.5 + - - +
1512H ILE* 3.6 31.2 - - + -
1520H LEU* 4.3 11.0 - - + -
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Residues in contact with PHE1490 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1431H LEU* 4.2 28.5 - - + -
1436H ILE* 3.6 31.2 - - + -
1439H ASN* 5.1 4.3 - - + -
1440H LEU* 3.8 23.6 - - + +
1455H LEU* 4.9 1.3 - - + -
1460H LEU* 3.5 27.1 - - + -
1464H VAL* 4.6 8.3 - - + -
1475H ILE* 6.0 1.1 - - + -
1482H PHE* 3.4 45.3 - + - -
1486H GLN 2.9 27.5 + - - -
1487H ARG* 3.2 9.4 + - - +
1489H LEU* 1.3 75.2 - - - +
1491H CYS* 1.3 59.6 + - - +
1493H ALA* 3.1 6.5 + - - +
1494H ARG* 2.9 32.8 + - - +
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Residues in contact with CYS1491 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508H LEU* 5.0 8.3 - - - -
1424H ILE 5.6 0.3 - - - +
1425H ILE* 3.9 22.9 - - + +
1426H LEU* 5.5 5.6 - - - +
1429H PRO* 4.1 27.1 - - - -
1430H VAL 4.3 9.2 - - - -
1431H LEU* 5.7 0.2 - - - -
1487H ARG 3.0 18.2 + - - -
1488H GLN* 3.5 9.2 - - - +
1490H PHE* 1.3 76.8 - - - +
1492H LEU* 1.3 62.6 + - - +
1494H ARG* 3.2 28.3 + - - +
1495H ALA* 3.0 20.8 + - - +
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Residues in contact with LEU1492 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1425H ILE* 3.6 38.1 - - + -
1458H ALA* 5.0 3.8 - - + +
1488H GLN* 2.9 27.7 + - + +
1489H LEU* 3.2 18.6 + - + +
1491H CYS* 1.3 76.0 - - - +
1493H ALA* 1.3 56.8 + - - +
1495H ALA* 3.2 2.6 + - - +
1496H PHE* 2.8 49.7 + - + -
1505H MET* 5.9 3.4 - - + -
1508H ALA* 3.9 21.8 - - + -
1512H ILE* 5.0 1.1 - - + -
1520H LEU* 3.8 38.6 - - + -
1524H VAL* 5.6 4.5 - - + -
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Residues in contact with ALA1493 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1440H LEU* 3.6 22.2 - - + -
1454H ALA* 4.8 6.1 - - + +
1455H LEU* 4.3 17.3 - - + -
1458H ALA* 4.6 8.3 - - + -
1460H LEU* 5.3 0.2 - - + -
1489H LEU 2.9 13.5 + - - +
1490H PHE* 3.1 10.9 + - - +
1492H LEU* 1.3 73.8 - - - +
1494H ARG* 1.3 65.9 + - - +
1496H PHE* 3.1 10.5 + - - +
1497H VAL* 3.0 28.9 + - + +
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Residues in contact with ARG1494 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508H LEU* 4.0 8.8 - - - +
512H TYR* 3.4 24.4 + - + +
514H TRP* 3.2 40.5 - - + -
1430H VAL* 2.7 31.7 + - - +
1431H LEU* 3.3 23.5 - - - +
1432H PHE* 3.7 11.5 - - - -
1439H ASN* 3.5 25.2 + - - +
1440H LEU* 4.5 5.9 - - + +
1490H PHE 2.9 13.0 + - - +
1491H CYS* 3.3 29.1 - - - +
1493H ALA* 1.3 75.3 - - - +
1495H ALA* 1.3 62.1 + - - +
1497H VAL* 3.2 10.9 - - - +
1498H ARG* 3.0 32.6 + - + +
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Residues in contact with ALA1495 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1423H SER* 3.7 22.1 + - - +
1424H ILE 5.4 1.3 - - - +
1425H ILE* 3.6 32.5 - - + -
1491H CYS 3.0 6.4 + - - +
1492H LEU 3.2 9.2 + - - +
1494H ARG* 1.3 77.1 - - - +
1496H PHE* 1.3 67.5 + - + +
1498H ARG* 3.5 12.7 + - - +
1499H LYS 4.0 0.9 + - - -
1503H PHE* 3.6 28.2 - - + -
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Residues in contact with PHE1496 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1425H ILE* 5.9 1.1 - - + -
1454H ALA* 3.7 27.4 - - + -
1457H ILE* 3.5 26.9 - - + -
1458H ALA* 3.5 33.4 - - + -
1492H LEU* 2.8 42.9 + - + -
1493H ALA* 3.1 9.4 + - - +
1495H ALA* 1.3 83.5 - - + +
1497H VAL* 1.3 60.9 + - - +
1498H ARG 3.4 0.2 + - - -
1499H LYS* 3.7 16.1 + - - +
1520H LEU* 5.2 2.5 - - + -
1524H VAL* 3.5 27.1 - - + -
1528H PHE* 3.3 41.0 - + + -
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Residues in contact with VAL1497 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514H TRP* 6.4 0.7 - - + -
1440H LEU* 3.6 27.1 - - + +
1441H ASP* 5.3 5.8 - - + +
1446H CYS* 5.1 11.0 - - - -
1450H THR* 5.2 7.6 - - + +
1451H LEU* 4.1 22.0 - - + -
1454H ALA* 3.6 26.5 - - + -
1493H ALA* 3.0 18.4 + - + +
1494H ARG* 3.2 14.4 - - - +
1496H PHE* 1.3 75.2 - - - +
1498H ARG* 1.3 68.2 + - + +
1499H LYS* 3.3 16.1 + - - +
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Residues in contact with ARG1498 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512H TYR* 3.3 56.0 + - - +
514H TRP* 4.0 19.6 - - + +
1419H ARG 3.8 9.3 + - - -
1420H SER* 4.3 9.1 + - - +
1422H LEU 3.3 25.9 + - - -
1423H SER* 4.0 17.4 - - - +
1443H GLU* 5.6 1.6 + - - -
1494H ARG* 3.0 29.9 + - + +
1495H ALA* 3.8 6.5 - - - +
1496H PHE 3.3 1.2 - - - -
1497H VAL* 1.3 81.2 - - + +
1499H LYS* 1.3 69.7 + - - +
1500H THR* 4.0 17.2 - - + +
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Residues in contact with LYS1499 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1450H THR* 5.0 17.1 - - - +
1495H ALA 4.0 3.8 + - - -
1496H PHE 3.7 16.2 + - - +
1497H VAL* 3.3 14.3 - - - +
1498H ARG* 1.3 81.7 - - - +
1500H THR* 1.3 61.5 + - - +
1503H PHE* 5.5 0.9 - - - -
1531H ARG* 4.3 17.5 - - - +
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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
------------------------------------------------------------
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