Contacts of the helix formed by residues 1484 - 1495 (chain A) in PDB entry 4C6C
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 ASP1484 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1474A LEU* 3.4 11.4 - - - +
1476A GLU* 3.3 15.3 - - - +
1480A THR* 3.9 16.9 - - + -
1483A GLU* 1.3 76.1 - - - +
1485A PHE* 1.3 68.5 + - - +
1486A ALA* 3.2 10.6 + - - +
1487A SER* 2.9 38.8 + - - -
1488A GLY* 2.8 21.1 + - - -
1768A LYS* 3.1 21.6 + - - +
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Residues in contact with PHE1485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1474A LEU* 3.6 34.1 - - + -
1476A GLU* 2.9 61.4 + - + +
1484A ASP* 1.3 71.0 - - - +
1486A ALA* 1.3 60.3 + - - +
1489A THR* 2.7 32.6 + - + +
1502A ALA* 4.5 3.8 - - + -
1519A ALA* 3.9 9.9 - - + -
1522A LEU* 3.7 8.7 - - + -
1523A ALA* 3.6 44.6 - - + -
1526A GLY* 3.8 6.7 - - - -
1527A ALA* 3.8 22.4 - - + +
1531A PHE* 5.7 3.1 - + + -
1533A LEU* 4.2 19.7 - - + -
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Residues in contact with ALA1486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1476A GLU* 4.6 0.4 + - - -
1484A ASP* 3.2 11.0 + - - +
1485A PHE* 1.3 80.6 - - - +
1487A SER* 1.3 57.5 + - - +
1489A THR* 4.0 0.7 - - - -
1490A ALA* 3.1 15.2 + - - +
1526A GLY* 3.2 21.9 + - - +
1528A ARG* 2.9 29.3 + - - +
1803A PRO* 4.0 23.8 - - + -
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Residues in contact with SER1487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1483A GLU* 2.6 26.1 + - - +
1484A ASP* 2.9 37.5 + - - -
1486A ALA* 1.3 72.4 - - - +
1488A GLY* 1.3 58.8 + - - +
1490A ALA* 3.3 7.3 + - - +
1491A ALA* 3.0 27.5 + - - +
1528A ARG* 5.7 0.7 - - - +
1766A PHE 4.0 14.2 - - - +
1768A LYS* 3.5 21.8 - - - -
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Residues in contact with GLY1488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1474A LEU* 4.0 15.0 - - - -
1483A GLU* 3.7 20.4 - - - -
1484A ASP 2.8 15.8 + - - -
1487A SER* 1.3 79.3 + - - +
1489A THR* 1.3 59.6 + - - +
1491A ALA* 3.3 6.6 + - - +
1492A ALA* 2.9 21.0 + - - +
1707A LEU* 3.4 11.6 - - - +
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Residues in contact with THR1489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1474A LEU* 4.2 18.4 - - + -
1485A PHE* 2.7 26.1 + - + +
1486A ALA 3.5 0.2 + - - -
1488A GLY* 1.3 74.6 - - - +
1490A ALA* 1.3 61.0 + - - +
1492A ALA* 3.5 6.5 - - - +
1493A LEU* 3.0 32.2 + - - +
1500A VAL* 4.5 7.2 - - + -
1527A ALA* 4.0 17.5 - - + -
1528A ARG* 2.7 33.0 + - - +
1529A CYS* 3.8 22.2 - - - +
1531A PHE* 5.9 0.7 - - + -
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Residues in contact with ALA1490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1486A ALA 3.1 20.1 + - - +
1487A SER* 3.5 7.9 - - - +
1489A THR* 1.3 77.3 + - - +
1491A ALA* 1.3 61.9 + - - +
1493A LEU* 3.3 4.6 + - - +
1494A ALA* 3.0 24.1 + - - +
1528A ARG* 3.8 20.8 - - - +
1766A PHE* 3.8 25.4 - - + -
1799A VAL* 3.9 16.0 - - + +
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Residues in contact with ALA1491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1487A SER 3.0 13.8 + - - +
1488A GLY* 3.3 12.8 - - - +
1490A ALA* 1.3 76.3 - - - +
1492A ALA* 1.3 62.8 + - - +
1494A ALA 3.4 0.9 + - - -
1495A GLY* 3.1 18.2 + - - -
1687A HIS* 4.7 1.1 - - + -
1707A LEU* 3.9 16.1 - - + +
1708A GLU* 3.4 37.9 - - + +
1766A PHE* 3.7 7.5 - - + +
1767A SER* 4.1 10.8 - - - +
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Residues in contact with ALA1492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1488A GLY 2.9 13.8 + - - +
1489A THR* 3.5 11.9 - - - +
1490A ALA 3.3 0.4 - - - -
1491A ALA* 1.3 76.3 - - - +
1493A LEU* 1.3 64.8 + - - +
1495A GLY 2.9 8.8 + - - -
1497A ILE* 2.9 36.1 + - + +
1500A VAL* 3.9 27.4 - - + -
1529A CYS* 4.0 3.8 - - - -
1707A LEU* 4.0 15.9 - - + +
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Residues in contact with LEU1493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1489A THR 3.0 20.0 + - - +
1490A ALA 3.3 4.2 + - - +
1492A ALA* 1.3 75.3 - - - +
1494A ALA* 1.3 58.7 + - - +
1496A GLY 2.9 16.1 + - - -
1497A ILE 3.5 14.8 - - - +
1498A THR* 4.5 5.2 - - + -
1528A ARG* 3.9 16.8 - - + +
1529A CYS* 3.9 15.5 - - + -
1786A VAL* 3.4 32.7 - - + +
1788A LEU* 4.6 5.2 - - + -
1793A ALA* 4.0 23.3 - - + +
1794A TYR* 4.1 13.1 - - + -
1799A VAL* 4.2 9.0 - - + -
1801A VAL* 3.7 28.9 - - + -
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Residues in contact with ALA1494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1490A ALA 3.0 16.5 + - - +
1491A ALA 3.8 4.5 - - - +
1492A ALA 3.2 0.2 - - - -
1493A LEU* 1.3 76.0 - - - +
1495A GLY* 1.3 55.8 + - - +
1496A GLY 3.3 0.9 - - - -
1708A GLU* 4.3 10.9 - - + +
1712A PRO* 6.0 0.7 - - - +
1766A PHE* 3.7 20.0 - - + -
1783A VAL* 3.6 20.1 - - - +
1794A TYR* 3.5 36.9 + - + +
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Residues in contact with GLY1495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1491A ALA 3.1 5.9 + - - -
1492A ALA 2.9 7.7 + - - -
1494A ALA* 1.3 76.8 - - - +
1496A GLY* 1.3 61.5 + - - +
1497A ILE* 3.3 11.1 + - - +
1707A LEU 3.5 21.9 - - - +
1708A GLU* 4.3 9.4 - - - +
1711A LEU* 3.4 26.3 - - - +
1712A PRO* 5.3 1.1 - - - -
1783A VAL* 3.8 7.2 - - - -
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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