Contacts of the helix formed by residues 1483 - 1499 (chain E) in PDB entry 6BAA
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1481E ASN 4.2 0.6 + - - -
1482E PHE* 1.3 77.7 - - - +
1484E GLN* 1.3 56.9 + - - +
1485E GLY* 3.2 6.2 + - - -
1486E GLN* 2.6 33.8 + - - +
1487E ARG* 2.7 34.7 + - - +
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Residues in contact with GLN1484 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1427E GLN 5.1 0.3 - - - +
1429E PRO* 4.5 6.1 - - + +
1483E SER* 1.3 73.2 - - - +
1485E GLY* 1.3 57.5 + - - +
1487E ARG* 3.6 7.5 - - - +
1488E GLN* 2.9 27.5 + - - +
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Residues in contact with GLY1485 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1483E SER* 3.2 7.3 + - - -
1484E GLN* 1.3 77.4 - - - +
1486E GLN* 1.3 58.1 + - - +
1488E GLN* 3.1 9.0 + - - +
1489E LEU* 2.8 27.4 + - - +
1512E ILE* 5.4 12.0 - - - +
1516E THR* 5.6 8.1 - - - -
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Residues in contact with GLN1486 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1482E PHE* 3.7 12.6 - - + -
1483E SER* 2.6 34.9 + - - +
1485E GLY* 1.3 67.7 - - - +
1487E ARG* 1.3 60.4 + - - +
1489E LEU* 3.3 10.1 + - - +
1490E PHE* 2.9 26.4 + - - +
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Residues in contact with ARG1487 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1429E PRO* 3.3 26.6 - - + +
1431E LEU* 5.5 9.9 - - + -
1479E GLY* 5.3 4.9 - - - +
1482E PHE* 4.1 8.8 - - + +
1483E SER 2.7 21.8 + - - +
1484E GLN* 3.6 9.0 - - - +
1486E GLN* 1.3 71.0 - - - +
1488E GLN* 1.3 59.0 + - - +
1490E PHE* 3.2 9.9 + - - +
1491E CYS* 2.9 23.6 + - - +
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Residues in contact with GLN1488 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1426E LEU 5.5 0.4 - - - -
1427E GLN* 4.1 18.6 - - - +
1429E PRO* 3.5 10.2 - - - +
1484E GLN 2.9 14.1 + - - +
1485E GLY* 3.1 13.2 + - - +
1487E ARG* 1.3 72.5 - - - +
1489E LEU* 1.3 61.6 + - - +
1491E CYS* 3.3 5.0 + - - +
1492E LEU* 2.8 27.9 + - - +
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Residues in contact with LEU1489 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1458E ALA* 3.4 27.8 - - - +
1459E GLN 5.6 0.7 - - - +
1460E LEU* 4.5 10.7 - - + +
1485E GLY 2.8 13.5 + - - +
1486E GLN* 3.4 13.0 - - - +
1488E GLN* 1.3 72.5 - - - +
1490E PHE* 1.3 60.1 + - - +
1492E LEU* 3.2 6.4 + - - -
1493E ALA* 2.9 25.5 + - - +
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Residues in contact with PHE1490 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1439E ASN* 5.7 5.7 - - + +
1460E LEU* 5.3 0.4 - - - +
1486E GLN 2.9 13.3 + - - +
1487E ARG* 3.2 13.7 + - - +
1489E LEU* 1.3 76.0 - - - +
1491E CYS* 1.3 57.2 + - - +
1493E ALA* 3.3 7.7 + - - +
1494E ARG* 2.9 27.9 + - - +
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Residues in contact with CYS1491 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1425E ILE* 3.7 16.8 - - + +
1426E LEU 4.6 7.0 - - - +
1429E PRO* 3.7 22.7 - - + -
1487E ARG 2.9 13.4 + - - +
1488E GLN* 3.5 9.2 - - - +
1489E LEU 3.3 0.2 - - - -
1490E PHE* 1.3 72.1 - - - +
1492E LEU* 1.3 61.5 + - - +
1494E ARG* 3.3 8.7 + - - +
1495E ALA* 2.9 28.6 + - - +
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Residues in contact with LEU1492 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1425E ILE* 4.7 4.2 - - - +
1458E ALA* 3.7 13.2 - - + -
1488E GLN 2.8 14.2 + - - +
1489E LEU* 3.2 11.4 + - - +
1491E CYS* 1.3 77.1 - - - +
1493E ALA* 1.3 55.9 + - - +
1495E ALA* 3.3 7.4 + - - +
1496E PHE* 2.8 28.9 + - - +
1523E VAL* 5.7 9.4 - - + -
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Residues in contact with ALA1493 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1440E LEU* 6.3 3.6 - - + -
1451E LEU 5.3 0.9 - - - +
1454E ALA* 3.3 42.0 - - + +
1455E LEU* 3.8 10.1 - - + +
1458E ALA* 3.4 6.0 - - + +
1460E LEU* 5.7 1.6 - - + -
1489E LEU 2.9 13.5 + - - +
1490E PHE* 3.6 10.8 - - - +
1492E LEU* 1.3 76.9 - - - +
1494E ARG* 1.3 56.0 + - - +
1496E PHE* 4.3 1.3 - - - -
1497E VAL* 2.8 27.9 + - - +
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Residues in contact with ARG1494 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1439E ASN 5.2 4.0 - - - +
1440E LEU* 5.8 5.6 - - - +
1442E PRO* 4.3 27.6 - - + -
1490E PHE 2.9 14.5 + - - +
1491E CYS* 3.3 12.5 + - - +
1493E ALA* 1.3 75.2 - - - +
1495E ALA* 1.3 57.3 + - - +
1497E VAL* 3.9 5.8 - - - +
1498E ARG* 3.0 28.6 + - - +
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Residues in contact with ALA1495 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1423E SER* 4.8 9.2 - - - -
1424E ILE 5.3 1.8 - - - -
1425E ILE* 3.7 23.6 - - + +
1491E CYS 2.9 14.0 + - - +
1492E LEU* 3.5 9.2 - - - +
1493E ALA 3.3 0.2 - - - -
1494E ARG* 1.3 74.4 - - - +
1496E PHE* 1.3 59.5 + - - +
1498E ARG* 3.1 7.7 + - - +
1499E LYS* 2.9 24.8 + - - -
1500E THR* 4.0 7.1 + - - -
1531E ARG* 5.6 0.7 + - - -
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Residues in contact with PHE1496 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1453E GLU* 4.5 6.5 - - + -
1454E ALA* 3.6 24.9 - - + -
1457E ILE* 3.6 29.6 - - + -
1458E ALA* 5.7 0.9 - - + +
1492E LEU 2.8 20.3 + - - +
1493E ALA* 3.3 7.8 + - - +
1495E ALA* 1.3 72.7 - - - +
1497E VAL* 1.3 62.4 + - - +
1499E LYS* 3.1 18.6 + - - +
1531E ARG* 4.7 19.9 + - - +
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Residues in contact with VAL1497 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1440E LEU* 5.4 7.6 - - + +
1443E GLU* 6.0 4.3 - - + +
1450E THR* 4.7 11.4 - - - +
1451E LEU* 5.3 3.4 - - - -
1454E ALA* 3.7 15.7 - - + +
1493E ALA 2.8 17.9 + - - +
1494E ARG* 3.9 5.8 - - - +
1496E PHE* 1.3 78.2 - - - +
1498E ARG* 1.3 60.8 + - - +
1499E LYS* 3.4 4.2 + - - +
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Residues in contact with ARG1498 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1423E SER* 3.7 24.3 - - - -
1443E GLU* 5.7 10.3 - - + -
1494E ARG 3.0 19.0 + - - +
1495E ALA 3.1 5.1 + - - +
1497E VAL* 1.3 77.2 - - - +
1499E LYS* 1.3 67.8 + - - +
1500E THR* 3.3 2.9 + - - -
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Residues in contact with LYS1499 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1495E ALA 2.9 7.2 + - - -
1496E PHE 3.1 15.4 + - - +
1497E VAL 4.3 3.8 - - - +
1498E ARG* 1.3 77.3 - - - +
1500E THR* 1.3 67.0 + - - +
1501E SER 3.7 0.2 + - - -
1531E ARG* 3.5 20.6 + - - +
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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