Contacts of the helix formed by residues 1567 - 1577 (chain E) in PDB entry 3SUA
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 ASP1567 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1565E PHE 4.3 5.4 - - - +
1566E LEU* 1.3 75.1 - - - +
1568E TYR* 1.3 67.3 + - - +
1569E LYS* 3.3 6.3 - - + +
1570E VAL* 3.2 16.3 + - + +
1571E TYR* 3.0 19.1 + - - +
1696E TYR* 3.5 4.9 - - - -
1700E ARG* 4.0 19.2 + - - +
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Residues in contact with TYR1568 (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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1567E ASP* 1.3 72.6 - - - +
1569E LYS* 1.4 63.3 + - - +
1571E TYR* 3.8 23.6 - + - -
1572E ALA* 2.9 43.1 + - + +
1576E PHE* 4.7 0.3 - - - -
1646E HIS* 2.7 40.7 + + - -
1693E ILE* 3.1 34.7 - - + +
1696E TYR* 3.3 37.1 + + + -
1700E ARG* 5.0 0.6 - - - +
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Residues in contact with LYS1569 (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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1567E ASP* 3.3 5.8 - - + +
1568E TYR* 1.4 77.1 - - - +
1570E VAL* 1.4 64.7 + - + +
1572E ALA* 3.8 3.1 - - - +
1573E GLU* 3.1 52.0 + - + +
1586E HIS* 3.9 20.5 - - - -
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Residues in contact with VAL1570 (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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1566E LEU* 3.2 28.0 - - + -
1567E ASP* 3.2 17.6 + - + +
1569E LYS* 1.4 75.0 - - + +
1571E TYR* 1.3 67.0 + - - +
1573E GLU* 3.2 12.6 + - - +
1574E ARG* 2.9 59.2 + - + +
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Residues in contact with TYR1571 (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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1566E LEU* 4.1 18.7 - - + +
1567E ASP 3.0 15.6 + - - +
1568E TYR* 3.7 14.4 - + - +
1570E VAL* 1.3 74.9 - - - +
1572E ALA* 1.4 62.7 + - - +
1574E ARG* 3.7 4.0 - - - +
1575E ILE* 3.0 57.1 + - + +
1692E SER* 2.9 46.6 + - - -
1695E LEU* 4.5 0.7 - - - +
1696E TYR* 3.5 45.4 + + + -
1699E VAL* 4.5 21.9 - - + +
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Residues in contact with ALA1572 (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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1568E TYR* 2.9 38.9 + - + +
1569E LYS* 3.8 4.3 - - - +
1571E TYR* 1.4 74.9 - - - +
1573E GLU* 1.4 56.4 + - - +
1575E ILE* 3.0 4.9 + - - +
1576E PHE* 2.8 67.5 + - + -
1646E HIS* 5.6 0.4 - - + +
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Residues in contact with GLU1573 (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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1569E LYS* 3.1 41.9 + - + +
1570E VAL* 3.5 12.0 - - - +
1572E ALA* 1.4 76.6 - - + +
1574E ARG* 1.3 57.5 + - + +
1576E PHE* 4.8 2.2 - - - -
1577E PHE* 2.9 47.3 + - + +
1581E ARG 5.1 2.6 - - - +
1582E GLU* 5.5 1.6 - - - +
1583E SER* 3.7 28.8 + - - +
1586E HIS* 2.8 31.4 + - - +
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Residues in contact with ARG1574 (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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1566E LEU* 3.4 39.4 - - - +
1570E VAL* 2.9 35.8 + - + +
1571E TYR* 3.7 4.7 - - - +
1573E GLU* 1.3 77.4 - - + +
1575E ILE* 1.3 62.6 + - + +
1577E PHE 5.0 0.4 - - - -
1578E PRO* 3.5 25.0 - - - +
1581E ARG 4.2 18.8 + - - +
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Residues in contact with ILE1575 (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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1571E TYR* 3.0 61.4 + - + +
1572E ALA* 3.0 6.9 + - - +
1574E ARG* 1.3 79.0 - - + +
1576E PHE* 1.4 72.6 + - + +
1578E PRO* 3.6 8.7 - - - +
1685E LYS* 3.3 17.8 + - - +
1688E THR* 4.9 6.7 - - + +
1689E ASN* 4.4 6.1 - - - +
1692E SER* 3.4 26.9 - - - +
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Residues in contact with PHE1576 (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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1568E TYR* 5.4 0.2 - + - -
1572E ALA* 2.8 49.2 + - + +
1573E GLU* 4.4 1.1 - - - -
1575E ILE* 1.4 78.4 - - + +
1577E PHE* 1.4 72.5 + + + +
1578E PRO* 3.5 8.1 - - - +
1635E ALA* 5.0 2.3 - - - +
1636E TYR* 5.9 0.2 - - - -
1639E SER* 2.6 34.2 + - - +
1642E THR* 3.6 27.8 - - + -
1643E VAL* 4.0 23.8 - - + -
1646E HIS* 4.6 11.2 - + - -
1685E LYS* 4.1 4.7 - - - +
1689E ASN* 3.1 43.7 - - + -
1692E SER* 4.9 2.7 - - - -
1693E ILE* 3.9 15.7 - - + -
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Residues in contact with PHE1577 (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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1573E GLU* 2.9 29.2 + - + +
1576E PHE* 1.4 82.6 - + + +
1578E PRO* 1.3 66.0 - - - +
1579E GLY 3.7 0.8 + - - -
1580E HIS* 4.1 11.7 + + + +
1581E ARG 4.0 16.3 + - - +
1582E GLU 4.4 0.5 - - - +
1583E SER* 3.8 17.7 - - - -
1584E PRO* 3.6 21.5 - - + -
1585E LEU* 3.7 25.6 - - + -
1636E TYR* 3.5 38.1 - + - -
1639E SER* 3.6 34.8 - - - -
1640E LEU* 4.0 2.5 - - + -
1643E VAL* 3.7 20.4 - - + -
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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