Contacts of the helix formed by residues 1562 - 1570 (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 LYS1562 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1546H ALA 4.8 3.4 - - - +
1547H ASP 3.9 21.1 + - - +
1548H LEU* 4.6 1.8 - - - +
1549H VAL* 4.6 1.1 - - - +
1561H ASP* 1.3 79.1 - - - +
1563H PRO* 1.3 61.3 - - - +
1564H GLU* 3.4 4.3 - - + +
1565H THR* 3.4 9.2 + - - +
1566H LEU* 2.9 27.7 + - - +
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Residues in contact with PRO1563 (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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1543H ILE 3.9 8.1 - - - +
1544H LEU* 3.6 39.9 - - + +
1546H ALA 4.9 4.5 - - - +
1548H LEU 6.0 0.2 - - - -
1549H VAL* 5.2 7.3 - - + -
1562H LYS* 1.3 74.6 - - - +
1564H GLU* 1.3 57.8 + - - +
1566H LEU* 3.4 6.5 + - + +
1567H LEU* 2.9 30.5 + - - +
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Residues in contact with GLU1564 (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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1562H LYS* 3.4 2.6 - - + +
1563H PRO* 1.3 77.6 - - - +
1565H THR* 1.3 57.9 - - - +
1567H LEU* 3.4 6.8 + - - +
1568H SER* 2.9 27.8 + - - -
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Residues in contact with THR1565 (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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1561H ASP* 4.4 14.4 - - - -
1562H LYS* 3.4 13.0 + - - +
1563H PRO 3.3 0.4 - - - -
1564H GLU* 1.3 77.5 - - - +
1566H LEU* 1.3 59.4 + - - +
1568H SER* 3.1 9.7 + - - -
1569H GLN* 2.9 27.2 + - - +
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Residues in contact with LEU1566 (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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1549H VAL* 5.8 5.2 - - + +
1561H ASP* 4.8 11.6 - - + +
1562H LYS 2.9 18.3 + - - +
1563H PRO* 3.8 7.9 - - + +
1565H THR* 1.3 73.5 - - - +
1567H LEU* 1.3 66.0 + - - +
1569H GLN* 3.3 21.1 - - - +
1570H LYS 3.6 4.0 + - - -
1571H ASP* 4.4 1.0 + - - +
1573H VAL* 4.7 18.1 - - + +
1574H PHE* 3.6 11.5 + - - +
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Residues in contact with LEU1567 (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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1563H PRO 2.9 18.5 + - - +
1564H GLU* 3.6 7.4 - - - +
1566H LEU* 1.3 75.5 - - - +
1568H SER* 1.3 62.1 + - - +
1570H LYS* 3.2 15.6 + - - +
1574H PHE* 3.7 17.1 - - + +
1577H PHE* 5.4 9.2 - - + +
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Residues in contact with SER1568 (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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1564H GLU 2.9 14.3 + - - -
1565H THR* 3.1 13.4 + - - -
1567H LEU* 1.3 73.1 - - - +
1569H GLN* 1.3 64.7 + - - +
1570H LYS* 3.3 4.7 + - - +
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Residues in contact with GLN1569 (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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1565H THR 2.9 12.7 + - - +
1566H LEU* 3.3 15.7 - - - +
1568H SER* 1.3 77.4 - - - +
1570H LYS* 1.3 66.1 + - - +
1571H ASP* 3.4 13.6 + - + +
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Residues in contact with LYS1570 (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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1566H LEU 3.6 1.6 + - - -
1567H LEU 3.2 8.1 + - - +
1568H SER 3.2 7.4 - - - +
1569H GLN* 1.3 79.6 - - - +
1571H ASP* 1.3 63.8 + - - +
1574H PHE* 3.6 12.8 - - - -
1575H ALA 5.3 0.2 - - - -
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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