Contacts of the helix formed by residues 1441 - 1462 (chain C) in PDB entry 5Y3R
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 ALA1441 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1434C VAL* 4.3 4.3 - - + -
1437C TYR* 3.4 16.6 - - + -
1438C GLY 3.6 15.0 + - - +
1439C PRO* 3.4 3.0 - - - +
1440C ASP* 1.3 74.9 - - - +
1442C GLN* 1.3 55.9 + - - +
1443C VAL 3.6 0.4 - - - -
1445C ARG* 2.5 56.5 + - - +
1495C ASP* 4.8 5.3 + - + +
1496C GLU* 4.3 4.7 - - - +
1499C CYS* 3.9 21.1 - - - -
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Residues in contact with GLN1442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700C LYS* 3.3 41.4 - - + +
701C TYR* 3.9 18.9 + - - -
1440C ASP* 2.7 15.7 + - - +
1441C ALA* 1.3 73.0 - - - +
1443C VAL* 1.3 76.6 + - + +
1445C ARG* 3.1 27.3 + - - +
1446C SER* 2.9 28.0 + - - -
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Residues in contact with VAL1443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1437C TYR* 5.4 4.0 - - + +
1440C ASP 3.9 5.3 + - - +
1441C ALA 3.6 0.6 - - - -
1442C GLN* 1.3 91.9 - - + +
1444C ASP* 1.3 64.2 + - - +
1446C SER* 3.3 17.0 - - - -
1447C ARG* 3.1 40.5 + - - +
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Residues in contact with ASP1444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1430C GLU* 2.6 54.2 - - - +
1433C ALA* 3.3 2.9 - - + +
1434C VAL* 2.8 21.1 + - + +
1437C TYR* 3.4 28.9 + - + +
1441C ALA 4.0 0.4 + - - -
1442C GLN 3.4 0.2 - - - -
1443C VAL* 1.3 74.4 - - - +
1445C ARG* 1.3 57.1 + - - +
1446C SER 3.0 2.0 - - - -
1447C ARG* 2.4 42.2 + - - +
1448C LEU* 2.8 17.5 + - - +
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Residues in contact with ARG1445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640C GLU* 4.3 15.1 + - - -
1434C VAL* 4.2 1.7 - - + +
1441C ALA* 2.5 33.3 + - - +
1442C GLN* 3.1 40.2 + - - +
1444C ASP* 1.3 72.3 - - - +
1446C SER* 1.3 64.7 + - - +
1448C LEU* 2.9 29.8 - - + +
1449C ALA* 3.0 6.4 + - - +
1495C ASP* 3.1 47.5 + - - +
1498C GLN* 4.9 6.3 - - + +
1499C CYS* 3.3 39.0 - - - +
1502C SER* 4.8 0.8 + - - +
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Residues in contact with SER1446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1442C GLN 2.9 16.2 + - - -
1443C VAL* 3.3 14.4 + - - -
1445C ARG* 1.3 74.5 + - - +
1447C ARG* 1.3 58.9 + - - -
1449C ALA* 2.6 32.9 + - - +
1450C ALA* 2.8 11.3 + - - +
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Residues in contact with ARG1447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1376C LEU* 5.1 22.8 - - + +
1426C GLN* 4.5 15.5 + - - +
1430C GLU* 3.3 14.3 - - + +
1437C TYR* 5.6 1.6 + - - -
1443C VAL* 3.1 45.7 + - - +
1444C ASP* 2.4 25.4 + - - +
1446C SER* 1.3 72.7 - - - +
1448C LEU* 1.3 58.9 + - - -
1450C ALA* 3.7 15.0 - - + -
1451C VAL* 2.9 37.6 + - + +
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Residues in contact with LEU1448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1430C GLU* 4.2 17.0 - - + +
1431C LEU* 5.2 0.4 - - - +
1434C VAL* 3.5 39.0 - - + -
1444C ASP* 2.8 22.7 + - - +
1445C ARG* 2.9 27.1 - - + +
1447C ARG* 1.3 77.1 - - - +
1449C ALA* 1.3 63.0 + - - +
1451C VAL* 4.1 1.4 - - - +
1452C VAL* 2.9 28.7 + - - +
1499C CYS* 4.3 11.2 - - + +
1502C SER* 3.5 16.6 - - - +
1503C LEU* 3.6 32.5 - - + -
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Residues in contact with ALA1449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1445C ARG 3.0 5.4 + - - +
1446C SER* 2.6 19.0 + - - +
1448C LEU* 1.3 74.6 - - - +
1450C ALA* 1.3 53.9 + - - +
1452C VAL* 3.5 4.7 + - - +
1453C SER* 2.8 32.8 + - - +
1502C SER* 3.6 10.6 + - - +
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Residues in contact with ALA1450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1375C THR* 4.8 23.3 - - + +
1376C LEU* 5.2 7.4 - - + -
1446C SER 2.8 11.1 + - - +
1447C ARG* 3.8 22.0 - - + -
1449C ALA* 1.3 70.2 - - - +
1451C VAL* 1.3 60.7 + - + +
1453C SER* 2.7 29.2 + - - -
1454C ALA* 2.8 11.7 + - - +
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Residues in contact with VAL1451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1375C THR* 6.2 0.2 - - - -
1376C LEU* 6.4 2.2 - - + -
1422C LYS* 4.4 16.8 - - - +
1426C GLN* 4.0 15.5 - - + +
1427C SER* 4.6 5.2 - - - +
1430C GLU* 3.5 28.3 - - - +
1447C ARG* 2.9 28.1 + - + +
1448C LEU* 4.1 1.6 - - - +
1450C ALA* 1.3 74.7 - - + +
1452C VAL* 1.3 57.6 + - + +
1454C ALA* 3.2 12.4 + - + +
1455C CYS* 2.8 40.7 + - - -
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Residues in contact with VAL1452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1448C LEU* 2.9 22.9 + - - +
1449C ALA* 3.6 7.0 - - - +
1451C VAL* 1.3 78.3 - - + +
1453C SER* 1.3 56.0 + - - +
1455C CYS* 2.7 25.8 + - + +
1456C LYS* 2.8 18.6 + - + +
1502C SER* 3.8 29.2 - - - +
1503C LEU* 5.8 2.0 - - + -
1505C LEU* 4.7 18.8 - - + -
1506C SER* 3.1 31.9 - - - +
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Residues in contact with SER1453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1375C THR* 6.0 3.1 - - - -
1396C PRO* 5.8 2.2 - - - -
1449C ALA* 2.8 19.5 + - - +
1450C ALA* 2.7 20.1 + - - -
1452C VAL* 1.3 71.4 - - - +
1454C ALA* 1.3 59.9 + - - -
1456C LYS* 3.0 52.5 + - - +
1457C GLN* 3.0 12.6 + - - +
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Residues in contact with ALA1454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1375C THR* 4.7 13.5 - - + +
1450C ALA 2.8 9.8 + - - +
1451C VAL* 3.2 18.6 - - + +
1453C SER* 1.3 75.0 - - - +
1455C CYS* 1.3 55.9 + - - +
1457C GLN* 3.1 21.2 + - - +
1458C LEU* 2.8 34.0 + - + +
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Residues in contact with CYS1455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1451C VAL* 2.8 34.4 + - - -
1452C VAL* 2.7 24.1 + - - +
1454C ALA* 1.3 70.0 - - - +
1456C LYS* 1.3 57.6 + - - +
1458C LEU* 3.1 16.5 + - + +
1459C HIS* 2.8 50.1 + - + +
1468C LEU* 5.8 8.7 - - - -
1506C SER* 4.0 20.0 - - - +
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Residues in contact with LYS1456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1396C PRO* 3.9 22.4 - - - +
1452C VAL* 2.8 25.0 + - + +
1453C SER* 3.3 33.4 + - - +
1455C CYS* 1.3 75.9 - - - +
1457C GLN* 1.3 58.1 + - - +
1459C HIS* 2.9 28.3 + - + +
1460C ARG* 2.9 38.6 + - - +
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Residues in contact with GLN1457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1375C THR* 4.8 10.0 + - - +
1395C LEU* 4.1 9.7 + - - +
1396C PRO* 3.2 31.3 - - + +
1399C CYS* 2.9 47.0 - - + +
1400C VAL* 3.2 7.1 - - + +
1453C SER* 3.0 12.4 + - - +
1454C ALA* 3.1 22.3 + - - +
1456C LYS* 1.3 76.4 - - - +
1458C LEU* 1.3 50.3 + - - +
1460C ARG* 2.8 21.3 - - - +
1461C ALA* 2.5 40.9 + - - +
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Residues in contact with LEU1458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1419C LEU* 4.5 11.7 - - + -
1454C ALA* 2.8 18.7 + - + +
1455C CYS* 3.1 19.7 + - + +
1457C GLN* 1.3 75.4 - - - +
1459C HIS* 1.3 54.9 + - - +
1461C ALA* 3.9 3.1 - - + -
1462C GLY* 2.2 56.4 + - - +
1463C LEU* 3.4 16.4 - - + +
1464C LEU* 3.4 28.3 - - + +
1467C ILE* 3.5 33.2 - - + -
1468C LEU* 6.3 1.1 - - + -
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Residues in contact with HIS1459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1455C CYS* 2.8 41.8 + - + +
1456C LYS* 2.9 11.0 + - - +
1458C LEU* 1.3 79.3 - - - +
1460C ARG* 1.3 65.1 + - + +
1462C GLY* 3.1 8.1 + - - -
1464C LEU* 3.2 36.6 - - + +
1506C SER* 5.3 0.7 - - - -
1509C GLN* 3.2 52.1 + - + +
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Residues in contact with ARG1460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1396C PRO* 3.6 26.0 - - - +
1397C ASP* 4.7 7.5 + - - +
1400C VAL* 3.4 23.7 - - + +
1404C LYS* 2.3 36.8 + - - +
1456C LYS* 2.9 33.1 + - - +
1457C GLN* 2.8 43.7 - - - +
1459C HIS* 1.3 76.0 - - + +
1461C ALA* 1.3 52.9 + - - +
1462C GLY 3.9 0.2 + - - -
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Residues in contact with ALA1461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1400C VAL* 3.9 17.0 - - + +
1403C MET* 4.8 11.9 - - + -
1404C LYS* 3.7 17.4 - - + +
1407C LYS* 3.2 24.7 - - - -
1457C GLN 2.5 26.0 + - - +
1458C LEU* 2.9 5.6 - - + +
1460C ARG* 1.3 78.9 - - - +
1462C GLY* 1.3 62.7 + - - +
1463C LEU* 4.5 0.2 - - - +
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Residues in contact with GLY1462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1458C LEU* 2.2 37.1 + - - +
1459C HIS 3.1 9.2 + - - -
1460C ARG 3.5 0.6 - - - -
1461C ALA* 1.3 77.6 - - - +
1463C LEU* 1.3 63.4 + - - +
1464C LEU* 2.8 16.7 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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