Contacts of the helix formed by residues 1747 - 1755 (chain X) in PDB entry 1N5O
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 GLN1747 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1736X VAL 5.2 0.9 - - - +
1737X ARG* 5.0 4.7 - - + +
1745X ASN 3.7 6.3 - - - +
1746X HIS* 1.3 74.4 - - - +
1748X GLY* 1.3 66.7 + - - +
1749X PRO* 3.5 3.4 - - - -
1750X LYS* 2.9 22.4 + - + -
1751X ARG* 2.9 19.5 + - + +
1844X LEU 5.3 0.9 - - - -
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Residues in contact with GLY1748 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1707X ILE* 4.3 3.6 - - - -
1742X ASN* 3.8 6.5 - - - +
1746X HIS* 3.2 6.7 + - - +
1747X GLN* 1.3 77.1 - - - +
1749X PRO* 1.3 69.7 - - - +
1750X LYS 3.2 0.2 + - - -
1751X ARG 3.3 0.9 + - - -
1752X ALA* 3.3 14.7 + - - +
1843X ALA 3.3 24.0 - - - -
1844X LEU* 4.1 12.4 + - - +
1845X TYR* 3.6 11.8 - - - +
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Residues in contact with PRO1749 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1703X TYR* 4.5 7.4 - - + +
1707X ILE* 3.9 25.3 - - + -
1711X LYS 4.7 4.9 - - - +
1713X VAL* 4.0 37.2 - - + +
1735X GLU* 5.7 3.6 - - + -
1736X VAL* 3.4 35.7 - - + +
1737X ARG* 5.1 2.0 - - - -
1742X ASN* 5.3 0.2 - - - +
1748X GLY* 1.3 87.7 - - - +
1750X LYS* 1.3 56.4 + - - +
1752X ALA* 3.2 4.6 + - + +
1753X ARG* 2.9 35.5 + - + +
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Residues in contact with LYS1750 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1735X GLU* 6.3 3.1 - - + +
1736X VAL 5.1 1.9 + - - +
1747X GLN* 2.9 25.7 + - + +
1749X PRO* 1.3 74.7 - - - +
1751X ARG* 1.3 67.5 + - - +
1752X ALA 3.0 1.8 + - - -
1753X ARG* 3.4 17.1 + - - +
1754X GLU* 3.4 21.0 + - - +
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Residues in contact with ARG1751 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1747X GLN* 2.9 15.3 + - + +
1748X GLY 3.8 7.4 - - - +
1750X LYS* 1.3 72.4 - - - +
1752X ALA* 1.3 52.8 - - - +
1754X GLU* 3.5 2.9 + - - +
1755X SER* 2.8 43.8 + - - +
1844X LEU 4.8 3.6 - - - +
1845X TYR* 3.8 22.9 - - + +
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Residues in contact with ALA1752 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1707X ILE* 3.4 31.6 - - + +
1710X GLY* 3.8 11.2 - - - -
1711X LYS 5.5 0.2 - - - +
1748X GLY 3.3 6.8 + - - +
1749X PRO* 3.2 9.8 + - + +
1750X LYS 3.0 1.8 - - - -
1751X ARG* 1.3 75.6 - - - +
1753X ARG* 1.3 66.5 + - - +
1754X GLU 3.1 1.8 - - - -
1755X SER 2.8 19.8 - - - +
1756X GLN* 5.2 0.3 - - - +
1845X TYR* 3.7 29.3 - - + -
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Residues in contact with ARG1753 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1710X GLY* 4.0 20.8 - - - +
1711X LYS 4.1 11.2 - - - +
1712X TRP* 3.3 52.9 - - - +
1713X VAL 5.9 0.2 - - - +
1732X HIS* 3.4 29.7 + - - -
1735X GLU* 5.5 3.7 - - - +
1749X PRO* 2.9 21.8 + - - +
1750X LYS* 3.7 17.9 + - - +
1752X ALA* 1.3 73.8 - - - +
1754X GLU* 1.3 62.7 + - - +
1755X SER 4.5 0.9 - - - +
1756X GLN* 5.0 4.0 - - - +
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Residues in contact with GLU1754 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1750X LYS 3.4 9.6 + - - +
1751X ARG* 3.7 7.4 - - - +
1752X ALA 3.1 1.2 - - - -
1753X ARG* 1.3 82.4 - - - +
1755X SER* 1.3 66.3 + - - +
1756X GLN* 3.3 7.1 + - - +
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Residues in contact with SER1755 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1751X ARG* 2.8 26.1 + - - +
1752X ALA 2.8 19.4 - - - +
1754X GLU* 1.3 70.1 - - - +
1756X GLN* 1.3 59.7 + - - +
1757X ASP* 4.4 1.8 - - - +
1758X ARG* 3.5 25.8 - - - +
1845X TYR* 3.9 22.6 + - - -
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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