Contacts of the helix formed by residues 1552 - 1559 (chain A) in PDB entry 3B13
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 THR1552 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1547A GLU 4.9 0.7 - - - +
1548A LYS* 3.7 25.6 - - - +
1549A ALA 4.3 4.4 + - - +
1550A PHE 3.4 0.9 - - - +
1551A PHE* 1.3 84.7 - - - +
1553A GLU* 1.3 63.7 + - - +
1554A GLU* 3.8 12.6 + - - +
1555A TYR* 3.6 19.6 + - - +
1556A VAL* 3.4 20.6 + - - +
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Residues in contact with GLU1553 (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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1552A THR* 1.3 73.8 - - - +
1554A GLU* 1.3 70.2 + - + +
1555A TYR 3.4 0.2 + - - -
1556A VAL* 3.4 7.5 + - - +
1557A ARG* 2.9 38.1 + - - +
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Residues in contact with GLU1554 (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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1552A THR* 4.2 12.1 - - - +
1553A GLU* 1.3 82.1 - - + +
1555A TYR* 1.3 55.5 + - - +
1557A ARG* 3.5 28.5 + - - +
1558A ASP* 2.9 41.1 + - - +
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Residues in contact with TYR1555 (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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1493A SER* 5.2 1.9 + - - -
1494A PRO* 6.6 0.2 - - + -
1495A LEU* 3.5 21.7 - - + +
1549A ALA 4.2 8.7 - - - +
1550A PHE* 3.2 48.7 - + + +
1552A THR* 3.6 12.2 + - - +
1553A GLU 3.3 1.0 - - - -
1554A GLU* 1.3 78.9 - - - +
1556A VAL* 1.3 54.0 + - - +
1558A ASP* 3.1 2.3 + - - -
1559A HIS* 2.8 70.0 + + - +
1562A ASP* 3.0 26.9 + - + -
1566A LEU* 3.8 29.6 - - + -
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Residues in contact with VAL1556 (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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1550A PHE 4.0 8.7 - - - +
1551A PHE* 5.0 4.0 - - + +
1552A THR 3.4 16.6 - - - +
1553A GLU* 3.4 10.9 + - - +
1555A TYR* 1.3 76.4 - - - +
1557A ARG* 1.3 62.5 + - - +
1559A HIS 3.3 22.7 - - - +
1560A PRO* 3.4 7.9 - - + +
1563A GLN* 3.4 26.5 - - - +
1566A LEU* 3.8 22.0 - - + -
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Residues in contact with ARG1557 (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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1553A GLU* 2.9 23.5 + - - +
1554A GLU* 3.7 39.4 + - - +
1556A VAL* 1.3 78.7 - - - +
1558A ASP* 1.3 76.8 + - - +
1559A HIS 3.5 0.7 + - - -
1560A PRO* 3.7 12.5 - - - +
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Residues in contact with ASP1558 (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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1554A GLU* 2.9 31.0 + - - +
1555A TYR* 3.1 1.2 + - - -
1557A ARG* 1.3 96.0 + - - +
1559A HIS* 1.3 86.1 + - + +
1560A PRO* 3.6 4.4 - - - +
1561A GLU* 4.4 1.7 - - - +
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Residues in contact with HIS1559 (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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1555A TYR* 2.8 51.8 + + + +
1556A VAL* 3.3 14.1 - - - +
1558A ASP* 1.3 98.7 + - + +
1560A PRO* 1.3 66.6 - - - +
1561A GLU* 3.3 19.3 - - - +
1562A ASP* 3.1 37.2 + - + +
1563A GLN 4.4 1.4 + - - -
1566A LEU* 4.8 1.0 - - - +
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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