Contacts of the strand formed by residues 1556 - 1561 (chain H) in PDB entry 5TWV
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 ALA1556 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1363H LYS* 3.3 20.4 - - + +
1364H HIS* 5.2 2.9 - - + +
1365H VAL* 4.4 0.9 - - - -
1552H LEU* 3.3 6.1 - - - -
1553H LYS* 2.8 34.8 + - - +
1554H ARG 3.4 2.6 - - - +
1555H GLY* 1.3 78.7 - - - +
1557H ILE* 1.3 66.8 + - - +
1558H LEU* 3.4 4.3 + - + +
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Residues in contact with ILE1557 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1364H HIS 5.5 1.7 - - - +
1365H VAL* 4.2 22.4 - - + +
1366H ASN 4.3 18.3 + - - +
1367H THR* 5.6 2.9 - - - -
1550H MET* 5.7 5.4 - - + -
1551H VAL 3.7 10.1 - - - +
1552H LEU* 3.7 18.6 - - + +
1556H ALA* 1.3 74.5 - - - +
1558H LEU* 1.3 60.8 + - - +
1559H GLU 5.0 4.5 - - - +
1560H PHE* 5.4 6.7 - - + -
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Residues in contact with LEU1558 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1551H VAL 3.4 7.3 + - - +
1553H LYS* 5.3 10.8 - - + +
1556H ALA* 3.4 7.7 + - + +
1557H ILE* 1.3 74.4 - - - +
1559H GLU* 1.3 62.5 + - + +
1560H PHE* 5.7 1.3 - - - -
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Residues in contact with GLU1559 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1550H MET* 4.8 0.2 - - - +
1551H VAL* 3.0 38.8 + - + +
1557H ILE* 3.6 2.4 - - - +
1558H LEU* 1.3 81.2 + - + +
1560H PHE* 1.3 69.3 + - - +
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Residues in contact with PHE1560 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1366H ASN 3.9 20.4 - - - -
1367H THR* 4.4 21.1 - - - -
1368H LEU 5.1 9.2 - - - -
1548H LEU* 6.0 6.1 - - + -
1549H VAL 3.3 13.7 - - - +
1550H MET* 3.8 15.5 - - + -
1557H ILE* 5.4 5.6 - - + -
1558H LEU 5.7 0.4 - - - -
1559H GLU* 1.3 82.4 - - - +
1561H ASP* 1.3 66.5 + - - +
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Residues in contact with ASP1561 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1548H LEU* 4.2 8.7 - - - +
1549H VAL* 2.6 41.2 + - - +
1560H PHE* 1.3 76.3 - - - +
1562H LYS* 1.3 66.4 + - - +
1565H THR* 4.4 15.3 - - - -
1566H LEU* 4.8 9.4 - - + +
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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