Contacts of the helix formed by residues 1544 - 1554 (chain A) in PDB entry 5ZCS
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 ALA1544 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1538A ARG* 5.3 9.4 - - + +
1540A THR 3.5 11.1 + - - +
1541A HIS* 4.1 9.4 - - - +
1542A ASP 3.3 0.6 - - - -
1543A GLY* 1.3 75.1 - - - +
1545A PHE* 1.3 63.2 + - - +
1546A TYR 3.5 0.2 - - - -
1547A ARG* 3.8 19.2 + - + +
1548A ALA* 4.4 2.1 + - - +
1563A CYS 4.0 14.8 - - - +
1566A LYS* 5.2 6.7 - - + +
1567A ALA* 4.7 26.3 - - + +
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Residues in contact with PHE1545 (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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1521A TRP* 5.6 1.8 - + - -
1541A HIS 3.9 6.6 + - - +
1542A ASP* 3.5 16.5 + - - +
1543A GLY 3.2 0.6 - - - -
1544A ALA* 1.3 80.1 - - - +
1546A TYR* 1.3 85.3 + + + +
1547A ARG 3.4 1.0 + - - -
1548A ALA* 3.8 1.7 + - - +
1549A VAL* 3.4 24.9 + - + +
1567A ALA* 6.0 1.6 - - - -
1595A MET* 3.5 62.4 - - + -
1596A LEU* 4.7 13.0 - - + -
1599A LEU* 3.7 38.6 - - + +
1639A VAL* 4.1 22.4 - - + -
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Residues in contact with TYR1546 (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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1514A ARG* 3.6 44.3 + - + -
1517A ALA* 5.4 5.6 - - + -
1518A ALA* 3.7 25.1 - - + +
1521A TRP* 4.3 23.6 - + - -
1529A MET* 3.7 25.4 - - + -
1533A THR* 4.3 17.3 - - + +
1536A ILE* 6.1 1.1 - - + -
1542A ASP 3.5 18.8 - - - -
1543A GLY* 3.8 5.2 + - - +
1544A ALA 3.5 0.2 - - - -
1545A PHE* 1.3 97.3 - + + +
1547A ARG* 1.3 59.3 + - - +
1548A ALA 3.5 0.2 - - - -
1549A VAL* 3.5 11.5 - - + +
1550A LEU* 2.9 32.7 + - - +
1595A MET* 5.3 4.0 - - + +
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Residues in contact with ARG1547 (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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1533A THR* 3.9 28.3 + - - +
1534A CYS* 4.7 10.1 + - - +
1536A ILE* 2.9 28.3 + - - +
1537A PRO* 4.4 9.9 + - - +
1538A ARG* 3.9 31.9 - - - +
1543A GLY 3.5 17.4 + - - +
1544A ALA* 4.0 15.0 - - - +
1545A PHE 3.3 1.2 - - - -
1546A TYR* 1.3 77.0 - - - +
1548A ALA* 1.3 57.2 + - - +
1550A LEU* 3.3 10.5 + - - +
1551A ALA* 2.9 26.3 + - - +
1559A LEU* 5.0 1.0 - - - +
1563A CYS* 3.7 24.7 - - + -
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Residues in contact with ALA1548 (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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1544A ALA 4.4 1.7 + - - +
1545A PHE 3.8 2.7 + - - +
1546A TYR 3.5 0.2 - - - -
1547A ARG* 1.3 76.0 - - - +
1549A VAL* 1.3 60.5 + - - +
1551A ALA* 3.7 8.1 - - - +
1552A LEU* 2.9 35.7 + - + +
1560A ALA* 4.0 12.8 - - + +
1563A CYS* 3.7 10.5 - - + +
1564A ILE* 3.8 25.8 - - + +
1599A LEU* 3.8 21.8 - - + -
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Residues in contact with VAL1549 (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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1521A TRP* 3.4 37.2 - - + +
1526A TRP* 3.5 19.8 - - + -
1529A MET* 3.9 9.9 - - + -
1545A PHE* 3.4 31.4 - - + +
1546A TYR* 3.3 17.2 + - + +
1547A ARG 3.2 0.4 - - - -
1548A ALA* 1.3 77.0 - - - +
1550A LEU* 1.3 60.8 + - - +
1552A LEU* 3.4 22.0 - - + +
1553A HIS 3.6 2.6 + - - -
1599A LEU* 3.9 15.5 - - + -
1639A VAL* 5.9 1.8 - - + -
1642A LEU* 4.3 7.0 - - + -
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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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1526A TRP* 3.7 29.8 - - + +
1529A MET* 3.8 23.3 - - + -
1530A GLU* 4.3 23.3 - - + +
1533A THR* 3.7 35.0 - - + +
1534A CYS* 5.9 2.5 - - - -
1546A TYR 2.9 16.9 + - - +
1547A ARG* 3.3 10.1 + - - +
1549A VAL* 1.3 75.8 - - - +
1551A ALA* 1.3 61.1 + - - +
1553A HIS* 3.6 2.8 + - - +
1554A GLN* 3.5 35.7 + - - +
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Residues in contact with ALA1551 (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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1547A ARG 2.9 16.4 + - - +
1548A ALA* 3.2 6.0 + - - +
1550A LEU* 1.3 76.7 - - - +
1552A LEU* 1.3 62.4 + - - +
1554A GLN* 3.5 5.6 + - - +
1555A ASP 3.4 4.2 + - - -
1556A LEU* 3.1 46.7 + - + +
1559A LEU* 3.8 23.8 - - + -
1560A ALA* 3.8 13.9 - - + -
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Residues in contact with LEU1552 (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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1526A TRP* 5.2 0.9 - - + -
1548A ALA* 2.9 23.3 + - + +
1549A VAL* 3.4 22.7 - - + +
1551A ALA* 1.3 77.2 - - - +
1553A HIS* 1.3 65.4 + - + +
1555A ASP* 3.7 16.2 + - - +
1556A LEU 5.1 1.3 - - - +
1557A PHE* 5.2 12.2 - - + -
1560A ALA* 4.7 6.9 - - + +
1599A LEU* 4.1 15.9 - - + +
1602A VAL* 3.8 40.6 - - + +
1606A LYS* 3.9 10.6 + - - +
1642A LEU* 4.1 26.7 - - + -
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Residues in contact with HIS1553 (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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1526A TRP* 3.4 70.3 + + + +
1549A VAL 3.6 4.8 + - - +
1550A LEU 3.6 5.5 + - - +
1551A ALA 3.3 0.6 - - - -
1552A LEU* 1.3 83.9 - - + +
1554A GLN* 1.3 65.1 + - + +
1555A ASP* 3.3 9.0 + - - +
1606A LYS* 5.6 1.0 + - - +
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Residues in contact with GLN1554 (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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1530A GLU* 4.1 27.9 + - - +
1550A LEU* 3.5 26.3 + - - +
1551A ALA* 3.5 4.8 + - - +
1552A LEU 3.4 0.2 - - - -
1553A HIS* 1.3 82.9 - - - +
1555A ASP* 1.3 69.5 + - - +
1556A LEU* 3.5 27.3 + - + +
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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