Contacts of the helix formed by residues 1535 - 1542 (chain B) in PDB entry 1N0W
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 ALA1535 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A GLU* 2.9 21.5 + - - +
1533B LYS 4.2 0.4 - - - -
1534B ILE* 1.3 74.0 - - - +
1536B LYS* 1.3 67.1 + - - +
1537B GLU* 3.7 17.5 - - + +
1538B SER* 2.9 25.1 + - - +
1539B LEU* 3.3 4.9 + - - +
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Residues in contact with LYS1536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1534B ILE 3.5 3.7 + - - -
1535B ALA* 1.3 72.1 - - - +
1537B GLU* 1.3 92.2 + - + +
1539B LEU* 3.3 14.4 + - - +
1540B ASP* 3.0 21.9 + - - +
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Residues in contact with GLU1537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1535B ALA* 3.7 16.1 - - + +
1536B LYS* 1.3 104.5 - - - +
1538B SER* 1.3 58.5 + - - +
1540B ASP* 3.2 8.3 + - - +
1541B LYS* 2.8 53.1 + - + +
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Residues in contact with SER1538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ALA* 3.9 22.9 - - - +
212A VAL* 4.8 7.9 - - - +
213A GLU* 2.6 39.5 + - - +
1534B ILE* 4.2 0.2 - - - -
1535B ALA* 2.9 12.8 + - - +
1537B GLU* 1.3 79.6 - - - +
1539B LEU* 1.3 60.7 + - - +
1541B LYS* 3.3 22.6 + - - +
1542B VAL* 3.4 18.9 + - - +
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Residues in contact with LEU1539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A TYR* 4.1 16.4 - - + +
206A GLN* 4.3 12.1 - - + -
209A ALA* 3.5 20.9 - - + -
1534B ILE* 3.7 27.1 - - + +
1535B ALA 4.2 4.3 - - - +
1536B LYS* 3.3 13.8 + - - +
1537B GLU 3.3 0.4 - - - -
1538B SER* 1.3 76.2 - - - +
1540B ASP* 1.3 63.6 + - - +
1542B VAL* 3.3 8.3 + - + +
1543B LYS* 3.2 21.1 + - - +
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Residues in contact with ASP1540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1536B LYS 3.0 14.3 + - - +
1537B GLU* 3.5 11.9 - - - +
1539B LEU* 1.3 78.5 - - - +
1541B LYS* 1.3 58.9 + - + +
1543B LYS* 2.9 59.0 + - - +
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Residues in contact with LYS1541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A VAL* 4.6 18.8 - - + +
1537B GLU* 2.8 41.7 + - - +
1538B SER* 3.6 13.5 + - - +
1539B LEU 3.3 0.2 - - - -
1540B ASP* 1.3 78.8 - - + +
1542B VAL* 1.3 62.9 + - + +
1543B LYS* 3.8 1.6 + - - +
1544B ASN 5.0 0.9 + - - -
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Residues in contact with VAL1542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A TYR* 4.2 15.8 - - + +
208A SER* 3.1 37.8 + - - +
209A ALA* 4.0 5.6 - - - +
212A VAL* 3.5 31.6 - - + -
259A PHE* 4.8 4.5 - - + -
1538B SER 3.5 10.8 - - - +
1539B LEU* 3.4 17.5 - - + +
1541B LYS* 1.3 78.4 - - + +
1543B LYS* 1.3 64.3 + - - +
1544B ASN 3.1 3.4 - - - -
1545B LEU* 3.0 26.4 + - + +
1546B PHE* 5.1 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