Contacts of the helix formed by residues 1482 - 1496 (chain H) in PDB entry 6C3P
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 SER1482 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716H GLY* 3.8 3.8 - - - -
774H GLN* 5.2 1.8 - - - -
1481H PHE* 1.3 78.4 - - - +
1483H GLN* 1.3 67.8 + - - +
1484H GLY 3.3 0.2 - - - -
1485H GLN* 3.1 15.5 + - - +
1486H ARG* 2.9 23.8 + - - +
2004H ATP 2.3 71.8 + - - -
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Residues in contact with GLN1483 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774H GLN* 3.4 41.8 + - + +
775H LYS* 3.1 42.3 - - - +
854H ASP* 5.4 0.4 - - - +
888H HIS* 6.0 1.3 - - - +
1428H PRO* 4.0 18.1 - - - +
1482H SER* 1.3 74.3 - - - +
1484H GLY* 1.3 59.2 + - - +
1486H ARG* 2.9 34.9 + - - +
1487H GLN* 2.9 27.1 + - - +
1510H SER* 4.7 13.0 + - - +
2004H ATP 4.0 1.5 + - - +
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Residues in contact with GLY1484 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715H VAL* 3.5 23.1 - - - +
1482H SER 3.3 0.4 - - - -
1483H GLN* 1.3 76.7 - - - +
1485H GLN* 1.3 59.5 + - - +
1487H GLN* 3.3 7.6 + - - +
1488H LEU* 2.9 36.8 + - - +
1510H SER* 4.2 16.3 - - - -
1511H ILE* 5.2 0.2 - - - -
2004H ATP 3.6 7.5 + - - -
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Residues in contact with GLN1485 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715H VAL* 3.3 34.7 + - - +
716H GLY* 3.4 9.5 - - - -
1459H LEU* 4.4 15.3 - - - +
1462H VAL* 4.4 21.3 - - - +
1481H PHE* 3.5 23.6 - - + -
1482H SER* 3.1 36.5 + - - +
1484H GLY* 1.3 75.2 - - - +
1486H ARG* 1.3 57.8 + - - +
1488H LEU* 3.1 9.6 + - - +
1489H PHE* 2.9 37.6 + - + -
2004H ATP 5.1 6.2 + - - +
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Residues in contact with ARG1486 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775H LYS* 5.0 6.0 - - - +
1428H PRO* 3.6 15.5 + - + +
1430H LEU* 3.5 25.4 - - + +
1477H GLY 3.5 19.9 + - - -
1478H GLY* 2.5 33.2 + - - +
1479H GLU* 4.5 6.3 + - - +
1481H PHE* 2.3 39.5 + - + +
1482H SER* 2.9 12.2 + - - +
1483H GLN* 2.9 50.3 + - - +
1485H GLN* 1.3 73.3 - - - +
1487H GLN* 1.3 65.7 + - - +
1489H PHE* 3.2 11.0 + - - +
1490H CYS* 3.0 26.3 + - - -
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Residues in contact with GLN1487 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1424H ILE* 3.6 6.3 - - - +
1425H LEU 3.3 21.0 + - - -
1426H GLN 2.9 19.7 - - - +
1428H PRO* 3.2 26.0 - - + +
1483H GLN 2.9 13.3 + - - +
1484H GLY* 3.6 7.4 - - - +
1486H ARG* 1.3 75.0 - - - +
1488H LEU* 1.3 59.0 + - - +
1490H CYS* 3.1 6.2 + - - +
1491H LEU* 2.9 55.0 + - + +
1507H ALA* 3.3 28.2 + - - +
1510H SER* 4.2 16.7 + - - -
1511H ILE* 3.6 11.9 - - + -
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Residues in contact with LEU1488 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715H VAL* 5.1 8.1 - - + -
1457H ALA* 2.9 32.5 - - + +
1458H GLN* 5.3 1.1 - - + +
1459H LEU* 3.4 21.3 - - + +
1484H GLY 2.9 26.8 + - - +
1485H GLN* 3.3 11.4 - - - +
1487H GLN* 1.3 77.6 - - - +
1489H PHE* 1.3 63.1 + - - +
1491H LEU* 3.2 7.3 + - + +
1492H ALA* 2.9 24.1 + - - +
1511H ILE* 3.5 31.4 - - + -
1515H THR* 4.9 10.1 - - + -
1519H LEU* 3.4 22.7 - - + -
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Residues in contact with PHE1489 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1430H LEU* 4.3 20.4 - - + -
1435H ILE* 4.1 25.8 - - + -
1438H ASN* 6.5 0.2 - - + -
1439H LEU* 4.3 7.8 - - + +
1454H LEU* 5.3 7.0 - - + -
1459H LEU* 4.1 24.5 - - + -
1462H VAL* 6.4 1.1 - - + -
1463H VAL* 5.2 9.4 - - + -
1466H LEU* 6.0 1.3 - - + -
1474H ILE* 4.9 4.9 - - + -
1481H PHE* 3.8 45.5 - + + -
1485H GLN* 2.9 41.2 + - + -
1486H ARG* 3.2 12.3 + - - +
1488H LEU* 1.3 75.1 - - - +
1490H CYS* 1.3 57.3 + - - +
1492H ALA* 3.3 6.5 + - + +
1493H ARG* 2.9 32.5 + - - +
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Residues in contact with CYS1490 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512H TYR* 4.7 2.7 + - - +
1424H ILE* 4.5 8.2 - - + +
1425H LEU* 5.7 3.4 - - + +
1427H ASP 4.8 1.8 - - - +
1428H PRO* 3.6 9.6 - - + -
1429H VAL 3.4 40.4 - - - -
1430H LEU* 4.1 3.1 - - - -
1486H ARG 3.0 18.9 + - - -
1487H GLN* 3.4 15.5 - - - +
1489H PHE* 1.3 73.7 - - - +
1491H LEU* 1.3 66.3 + - - +
1493H ARG* 3.2 27.1 + - - +
1494H ALA* 3.0 23.2 + - - +
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Residues in contact with LEU1491 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1424H ILE* 3.6 23.3 - - + -
1457H ALA* 5.1 0.2 - - + -
1487H GLN* 2.9 56.1 + - + +
1488H LEU* 3.2 13.2 + - + +
1490H CYS* 1.3 77.5 - - - +
1492H ALA* 1.3 58.0 + - - +
1494H ALA* 3.2 2.8 + - - +
1495H PHE* 2.9 46.3 + - + -
1504H MET* 5.7 2.2 - - - -
1507H ALA* 3.6 19.1 - - + +
1508H THR* 6.3 0.2 - - - -
1511H ILE* 4.9 6.1 - - + -
1519H LEU* 3.6 42.8 - - + -
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Residues in contact with ALA1492 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1439H LEU* 4.2 8.7 - - + -
1453H ALA* 3.9 23.9 - - + +
1454H LEU* 4.7 9.6 - - + +
1457H ALA* 3.9 7.2 - - + +
1459H LEU* 5.0 3.1 - - + -
1488H LEU 2.9 15.9 + - - +
1489H PHE* 3.6 7.0 - - + +
1491H LEU* 1.3 75.1 - - - +
1493H ARG* 1.3 58.6 + - - +
1495H PHE* 2.8 30.6 + - - +
1496H VAL* 2.8 18.8 + - - +
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Residues in contact with ARG1493 (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* 3.2 31.0 - - - +
512H TYR* 3.9 21.8 + - + -
514H TRP* 3.4 37.7 - - + -
1425H LEU* 6.4 0.4 - - - +
1429H VAL 3.6 14.1 + - - -
1430H LEU* 4.9 4.4 - - - +
1431H PHE* 4.4 9.5 - - - -
1438H ASN* 3.4 25.0 + - - +
1439H LEU* 3.5 23.2 - - + +
1489H PHE* 2.9 19.5 + - - +
1490H CYS* 3.2 34.2 + - - +
1492H ALA* 1.3 76.8 - - - +
1494H ALA* 1.3 62.7 + - - +
1496H VAL* 3.1 18.8 + - - +
1497H ARG* 4.2 5.0 + - - +
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Residues in contact with ALA1494 (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* 4.4 10.7 - - + +
1422H SER* 4.2 14.4 + - - -
1423H ILE 3.9 13.7 - - - +
1424H ILE* 3.5 29.6 - - + -
1490H CYS 3.0 8.8 + - - +
1491H LEU 3.4 8.3 - - - +
1493H ARG* 1.3 76.9 - - - +
1495H PHE* 1.3 65.0 + - + +
1496H VAL 3.1 1.2 + - - -
1497H ARG* 3.1 23.3 + - - +
1499H THR* 5.1 0.5 + - - -
1502H PHE* 5.6 4.7 - - + -
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Residues in contact with PHE1495 (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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1424H ILE* 3.8 7.4 - - + -
1453H ALA* 4.4 7.0 - - + +
1456H ILE* 3.4 35.2 - - + -
1457H ALA* 4.2 9.4 - - + -
1491H LEU* 2.9 54.0 + - + -
1492H ALA* 2.8 17.6 + - - +
1494H ALA* 1.3 73.0 - - + +
1496H VAL* 1.3 65.1 + - - +
1497H ARG 3.1 10.0 + - - +
1502H PHE* 4.3 5.6 - + - -
1504H MET* 3.6 33.9 - - + -
1519H LEU* 5.0 5.2 - - + -
1523H VAL* 4.3 11.2 - - + -
1527H PHE* 3.9 31.1 - + + -
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Residues in contact with VAL1496 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1439H LEU* 4.0 28.0 - - + +
1440H ASP* 3.8 20.4 - - - +
1445H CYS* 4.1 15.8 - - - -
1449H THR* 5.7 7.4 - - - +
1450H LEU* 4.7 7.4 - - + -
1453H ALA* 4.2 14.4 - - + -
1492H ALA 2.8 17.9 + - - +
1493H ARG* 3.3 18.8 - - - +
1494H ALA 3.1 0.6 - - - -
1495H PHE* 1.3 77.8 - - - +
1497H ARG* 1.3 63.8 + - + +
1498H LYS* 3.5 3.1 + - - +
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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