Contacts of the helix formed by residues 1446 - 1457 (chain B) in PDB entry 1FP7
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 SER1446 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1444B ASP 3.6 1.1 + - - -
1445B LEU* 1.3 74.2 - - - +
1447B ILE* 1.3 69.5 + - - +
1448B LYS* 2.7 13.3 + - - +
1449B ASP* 2.8 36.9 + - - -
1450B LYS* 3.0 9.9 + - - +
1474B ILE* 5.8 0.3 - - - +
1478B GLU* 3.5 14.1 + - - -
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Residues in contact with ILE1447 (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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1445B LEU 3.5 1.6 + - - -
1446B SER* 1.3 73.5 + - - +
1448B LYS* 1.3 60.9 + - - +
1450B LYS* 3.6 12.0 - - - +
1451B ILE* 3.5 28.1 + - + +
1474B ILE* 4.0 27.4 - - + -
1477B TYR* 4.6 5.4 - - + -
1478B GLU* 3.0 41.1 + - + +
1482B TYR 3.6 9.9 - - - +
1483B GLY* 3.4 29.6 - - - +
1487B VAL* 4.4 2.9 - - + +
1516B VAL* 6.0 3.1 - - + -
1524B LEU* 3.8 30.3 - - + -
1526B VAL* 5.6 2.2 - - + -
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Residues in contact with LYS1448 (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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1446B SER* 2.7 13.1 + - - +
1447B ILE* 1.3 72.1 - - - +
1449B ASP* 1.3 53.7 + - - +
1450B LYS 2.9 5.3 + - - -
1451B ILE 3.0 2.1 + - - -
1452B ALA* 2.7 34.8 + - - +
1466B TYR* 3.4 64.3 + - + +
1471B ASP* 3.3 23.6 + - - +
1474B ILE* 3.7 19.7 - - + -
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Residues in contact with ASP1449 (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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1445B LEU* 4.2 15.8 - - + +
1446B SER* 2.8 40.1 + - - +
1448B LYS* 1.3 74.8 - - - +
1450B LYS* 1.3 58.7 + - - +
1452B ALA* 3.1 23.4 - - + +
1453B LYS* 3.2 17.2 + - - +
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Residues in contact with LYS1450 (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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1441B TYR* 4.0 16.5 - - + -
1442B ASN 2.9 27.1 - - - +
1443B LEU* 2.7 28.8 + - - +
1445B LEU* 3.0 30.5 - - + +
1446B SER 3.0 12.3 + - - +
1447B ILE* 3.6 11.9 - - - +
1448B LYS 2.9 0.6 - - - -
1449B ASP* 1.3 76.3 - - - +
1451B ILE* 1.3 63.7 + - - +
1452B ALA 3.1 1.1 + - - -
1453B LYS* 3.8 2.6 + - - +
1454B ILE* 3.0 28.6 + - - +
1483B GLY 3.3 13.1 + - - -
1485B LEU 2.5 32.1 + - - +
1487B VAL* 3.7 18.6 - - + -
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Residues in contact with ILE1451 (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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1447B ILE* 3.5 17.2 + - + +
1448B LYS 3.0 1.2 + - - -
1450B LYS* 1.3 73.8 - - - +
1452B ALA* 1.3 72.4 + - - +
1454B ILE* 2.8 12.3 + - - +
1455B ALA* 2.9 11.1 + - + +
1464B VAL* 4.2 17.5 - - + -
1466B TYR* 3.5 34.8 - - + +
1474B ILE* 5.9 0.4 - - + -
1487B VAL* 3.6 7.9 - - + -
1489B MET* 3.2 37.7 - - + -
1511B ILE* 6.1 1.1 - - + -
1513B VAL* 4.8 4.3 - - + -
1516B VAL* 5.3 0.7 - - + -
1526B VAL* 3.3 35.4 - - + -
1528B ILE* 5.7 2.0 - - + -
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Residues in contact with ALA1452 (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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1448B LYS 2.7 13.6 + - - +
1449B ASP* 3.1 22.2 - - + +
1451B ILE* 1.3 74.3 - - - +
1453B LYS* 1.3 56.7 + - + +
1454B ILE 2.6 1.2 + - - -
1455B ALA* 2.6 29.5 + - - +
1456B THR* 3.1 15.3 + - - +
1464B VAL* 4.4 13.9 - - + -
1466B TYR* 4.6 0.4 + - - -
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Residues in contact with LYS1453 (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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1440B LEU* 3.4 34.1 - - + +
1441B TYR* 5.0 7.2 - - + +
1445B LEU* 4.5 18.6 - - + -
1449B ASP 3.2 13.9 + - - +
1450B LYS 4.3 3.6 - - - +
1452B ALA* 1.3 78.8 - - + +
1454B ILE* 1.3 61.3 + - - +
1456B THR* 3.9 10.2 - - - -
1457B GLU* 2.5 57.9 + - - +
1458B ILE 4.4 0.5 + - - -
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Residues in contact with ILE1454 (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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1311B GLU* 4.0 26.5 - - + +
1440B LEU* 5.6 3.6 - - + -
1441B TYR* 3.8 34.3 - - + -
1450B LYS 3.0 19.3 - - - +
1451B ILE* 2.8 12.0 + - - +
1452B ALA 2.6 5.1 + - - -
1453B LYS* 1.3 74.9 - - + +
1455B ALA* 1.3 59.4 + - - -
1458B ILE* 3.3 24.0 - - + +
1459B TYR* 2.9 44.7 - - + +
1487B VAL* 4.1 13.2 - - + +
1489B MET* 3.7 15.0 - - + -
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Residues in contact with ALA1455 (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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1451B ILE* 2.9 6.6 + - + +
1452B ALA 2.6 10.7 + - - +
1454B ILE* 1.3 71.1 - - - +
1456B THR* 1.3 67.8 + - - +
1459B TYR* 3.2 18.1 - - + +
1460B GLY 2.7 18.9 + - - -
1461B ALA* 2.9 21.9 + - + -
1463B GLY 5.2 0.9 - - - +
1464B VAL* 3.3 34.3 - - + -
1511B ILE* 4.4 6.5 - - + -
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Residues in contact with THR1456 (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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1452B ALA* 3.1 18.5 + - - +
1453B LYS* 3.9 10.3 + - - +
1454B ILE 3.4 0.2 - - - -
1455B ALA* 1.3 83.6 - - - +
1457B GLU* 1.3 70.0 + - + +
1460B GLY* 2.9 23.7 + - - -
1461B ALA 3.5 16.5 + - - +
1462B ASP* 6.1 0.6 - - - -
1463B GLY 5.9 1.2 + - - +
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Residues in contact with GLU1457 (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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1365B LYS* 2.6 22.2 + - - +
1369B ASN* 2.5 18.0 - - - +
1372B LYS* 2.9 41.8 + - + +
1440B LEU* 3.8 21.8 - - + +
1453B LYS* 2.5 47.0 + - - +
1456B THR* 1.3 88.6 - - + +
1458B ILE* 1.3 56.7 + - - +
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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
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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