Contacts of the helix formed by residues 1540 - 1553 (chain A) in PDB entry 2H7C
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 LYS1540 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1350A ILE* 3.8 21.8 - - + -
1352A LYS 5.1 7.7 + - - -
1419A ASP* 6.2 1.2 - - - +
1423A ASP* 2.9 31.1 + - - +
1427A GLY* 4.3 20.4 - - - +
1428A VAL 5.1 0.4 - - - +
1431A VAL* 3.9 9.4 - - + -
1448A GLU* 4.2 14.6 + - - -
1538A LYS 3.3 2.2 + - - -
1539A LEU* 1.3 85.5 - - + +
1541A ASP* 1.3 63.8 + - - +
1543A GLU* 3.1 36.4 + - + +
1544A VAL* 2.9 27.4 + - + +
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Residues in contact with ASP1541 (chain A).
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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1435A ARG* 2.9 33.5 + - - +
1524A GLU* 4.3 1.6 - - - +
1538A LYS* 3.3 39.8 + - + +
1539A LEU 2.9 2.8 + - - -
1540A LYS* 1.3 77.0 - - - +
1542A LYS* 1.3 70.3 + - + +
1544A VAL* 3.3 2.6 + - - +
1545A ALA* 3.2 22.8 + - - +
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Residues in contact with LYS1542 (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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1402A LYS* 5.1 12.8 - - - +
1540A LYS 3.3 0.4 - - - -
1541A ASP* 1.3 82.7 - - + +
1543A GLU* 1.3 78.8 + - - +
1545A ALA* 3.4 8.2 + - - +
1546A PHE* 3.1 22.2 + - - +
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Residues in contact with GLU1543 (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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1403A TYR* 3.5 15.4 - - + +
1423A ASP* 3.3 26.0 - - - +
1428A VAL* 4.0 13.7 - - + -
1540A LYS* 3.1 39.9 + - + +
1542A LYS* 1.3 90.5 + - - +
1544A VAL* 1.3 66.1 + - - +
1546A PHE* 3.2 5.1 + - - +
1547A TRP* 3.0 30.6 + - - -
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Residues in contact with VAL1544 (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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1428A VAL* 4.0 24.9 - - + +
1431A VAL* 3.8 32.1 - - + -
1432A ILE* 4.1 17.3 - - + -
1435A ARG* 3.4 22.9 - - - +
1540A LYS* 2.9 22.4 + - + +
1541A ASP 3.3 4.9 + - - +
1543A GLU* 1.3 75.4 - - - +
1545A ALA* 1.3 57.0 + - - +
1547A TRP* 4.3 0.3 - - - +
1548A THR* 2.7 48.1 + - - +
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Residues in contact with ALA1545 (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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1541A ASP* 3.2 11.2 + - - +
1542A LYS* 3.5 11.0 - - - +
1543A GLU 3.2 0.2 - - - -
1544A VAL* 1.3 80.1 - - - +
1546A PHE* 1.3 61.4 + - - +
1548A THR* 3.9 2.9 - - - -
1549A ASN* 2.7 42.0 + - - +
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Residues in contact with PHE1546 (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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1398A GLU* 4.2 14.4 - - + -
1399A ALA* 4.0 8.7 - - - -
1402A LYS* 3.4 59.9 - - + +
1403A TYR* 4.3 3.6 - + - -
1542A LYS 3.1 14.4 + - - +
1543A GLU* 3.2 8.9 + - - +
1545A ALA* 1.3 75.9 - - - +
1547A TRP* 1.3 90.5 + + - +
1549A ASN* 3.8 4.9 - - - +
1550A LEU* 2.9 62.8 + - + +
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Residues in contact with TRP1547 (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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1391A ILE* 3.6 27.8 - - + -
1399A ALA* 3.6 15.9 - - + -
1403A TYR* 2.9 44.2 + + - -
1420A LEU* 3.8 11.0 - - + -
1423A ASP* 4.3 1.6 - - - +
1424A VAL* 3.5 29.9 - - + +
1428A VAL* 3.7 29.2 - - + -
1543A GLU* 3.0 29.0 + - + +
1544A VAL 4.3 1.1 - - - +
1546A PHE* 1.3 84.8 - + - +
1548A THR* 1.3 66.1 + - - +
1550A LEU* 3.6 24.2 - - + +
1551A PHE* 2.9 61.6 + + + -
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Residues in contact with THR1548 (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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1428A VAL* 5.2 0.9 - - - +
1432A ILE* 4.5 11.6 - - - +
1544A VAL* 2.7 37.9 + - - +
1545A ALA* 3.9 4.3 - - - -
1547A TRP* 1.3 76.9 - - - +
1549A ASN* 1.3 63.6 + - - +
1551A PHE* 4.0 3.7 - - - +
1552A ALA* 3.1 33.2 + - + +
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Residues in contact with ASN1549 (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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1545A ALA* 2.7 31.5 + - - +
1546A PHE* 3.9 3.6 - - - +
1548A THR* 1.3 80.4 - - - +
1550A LEU* 1.3 67.0 + - - +
1552A ALA* 3.4 14.2 + - - +
1553A LYS* 3.4 16.2 + - - +
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Residues in contact with LEU1550 (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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1391A ILE* 5.4 0.7 - - + -
1395A LEU* 3.8 29.6 - - + +
1398A GLU* 3.0 40.4 - - + +
1399A ALA* 4.1 12.3 - - + -
1546A PHE* 2.9 39.0 + - + +
1547A TRP* 3.2 37.2 + - + +
1549A ASN* 1.3 77.9 - - - +
1551A PHE* 1.3 61.3 + - + +
1553A LYS* 3.3 33.7 - - - +
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Residues in contact with PHE1551 (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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1389A VAL 4.4 8.3 - - - -
1390A CYS 4.2 9.9 - - - -
1391A ILE* 4.0 26.5 - - + -
1392A ALA 5.5 0.2 - - - -
1395A LEU* 4.3 17.5 - - + -
1424A VAL* 4.5 10.3 - - + -
1547A TRP* 2.9 59.7 + + + +
1548A THR* 4.3 3.4 - - - +
1550A LEU* 1.3 79.5 - - + +
1552A ALA* 1.3 63.2 + - - +
1553A LYS* 3.3 3.4 + - - +
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Residues in contact with ALA1552 (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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1548A THR* 3.1 24.0 + - + +
1549A ASN* 3.4 7.8 + - - +
1551A PHE* 1.3 78.5 - - - +
1553A LYS* 1.3 65.4 + - - +
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Residues in contact with LYS1553 (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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1395A LEU* 3.8 17.5 - - + +
1398A GLU* 2.6 45.9 + - - -
1549A ASN 3.4 9.6 + - - +
1550A LEU* 3.3 31.1 - - - +
1551A PHE 3.3 3.7 - - - +
1552A ALA* 1.3 83.4 - - - +
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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