Contacts of the helix formed by residues 1716 - 1726 (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 TYR1716 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1657X LEU* 3.7 24.2 - - + -
1661X GLU* 3.5 55.8 - - + +
1664X LEU* 3.5 22.8 - - + +
1665X VAL* 3.7 20.9 - - + -
1688X VAL* 3.8 11.7 - - + -
1689X MET 2.7 18.2 + - - +
1690X LYS* 4.2 18.2 - - + -
1691X THR 5.1 0.7 - - - +
1715X SER* 1.3 73.0 + - - +
1717X PHE* 1.3 62.9 + + - +
1719X VAL* 2.9 28.7 + - + +
1720X THR* 3.4 27.8 + - + +
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Residues in contact with PHE1717 (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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1690X LYS* 5.9 4.3 - - - -
1691X THR* 4.0 10.1 - - - -
1692X ASP 3.8 22.0 - - - -
1693X ALA* 3.9 19.3 - - + -
1695X PHE* 4.3 16.2 - + + -
1715X SER* 3.0 17.4 + - - +
1716X TYR* 1.3 82.9 - + - +
1718X TRP* 1.3 63.3 + - - +
1720X THR* 4.0 13.5 - - + -
1721X GLN* 3.1 34.6 + - + +
1734X PHE* 3.6 17.1 - - + -
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Residues in contact with TRP1718 (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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1650X MET* 4.6 5.8 - - - -
1652X MET* 3.8 18.8 - - - -
1668X PHE* 3.5 39.0 - + - -
1674X ILE* 4.8 0.2 - - + -
1686X HIS* 3.7 24.2 - + - -
1688X VAL* 4.7 3.6 - - + -
1714X VAL* 3.4 24.9 - - + -
1715X SER 2.9 16.6 + - - +
1717X PHE* 1.3 76.8 - - - +
1719X VAL* 1.3 71.5 + - + +
1721X GLN* 4.4 0.7 - - - +
1722X SER* 3.2 27.9 + - - -
1728X MET* 4.0 18.6 - - - -
1729X LEU* 2.9 32.2 + - + +
1731X GLU* 3.9 28.5 - - + +
1734X PHE* 3.6 35.4 - + + -
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Residues in contact with VAL1719 (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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1664X LEU 3.8 13.0 - - - +
1665X VAL* 4.0 24.5 - - + +
1668X PHE* 3.6 47.1 - - + -
1688X VAL* 4.2 16.4 - - + -
1716X TYR* 2.9 20.7 + - + +
1718X TRP* 1.3 81.6 - - + +
1720X THR* 1.3 62.0 + - + +
1722X SER* 2.9 8.7 + - - -
1723X ILE* 2.8 32.8 + - + +
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Residues in contact with THR1720 (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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1664X LEU* 5.2 9.0 - - + -
1716X TYR* 3.4 44.1 + - + +
1717X PHE* 3.9 18.9 + - + -
1719X VAL* 1.3 75.6 - - + +
1721X GLN* 1.3 68.1 + - - +
1723X ILE* 3.3 11.9 + - - +
1724X LYS* 2.9 30.5 + - - +
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Residues in contact with GLN1721 (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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1717X PHE* 3.1 23.6 + - + +
1720X THR* 1.3 87.9 + - - +
1722X SER* 1.3 52.4 + - - +
1724X LYS* 3.1 32.2 + - - +
1725X GLU* 2.7 62.7 + - - +
1729X LEU* 3.8 11.2 - - + -
1734X PHE* 3.9 17.5 - - + -
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Residues in contact with SER1722 (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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1668X PHE* 3.5 23.4 - - - -
1672X HIS* 5.2 1.8 + - - -
1718X TRP* 3.2 21.7 + - - -
1719X VAL 2.9 4.6 + - - -
1721X GLN* 1.3 78.3 - - - +
1723X ILE* 1.3 56.5 + - - +
1725X GLU* 4.3 0.7 - - - +
1726X ARG* 2.8 25.5 + - - -
1727X LYS 2.9 21.5 + - - -
1728X MET* 3.6 1.4 - - - -
1729X LEU* 2.8 37.6 + - - +
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Residues in contact with ILE1723 (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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1664X LEU* 3.3 52.3 - - + +
1667X LYS* 4.6 19.3 - - + -
1668X PHE* 4.1 20.6 - - + +
1719X VAL* 2.8 25.1 + - + +
1720X THR* 3.4 13.9 - - - +
1722X SER* 1.3 74.0 - - - +
1724X LYS* 1.3 62.2 + - + +
1726X ARG* 3.6 10.7 + - - +
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Residues in contact with LYS1724 (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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1720X THR 2.9 16.5 + - - +
1721X GLN* 3.4 32.5 - - - +
1723X ILE* 1.3 78.4 - - + +
1725X GLU* 1.3 64.0 + - + +
1726X ARG* 3.3 4.0 + - - +
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Residues in contact with GLU1725 (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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1721X GLN* 2.7 46.5 + - - +
1722X SER* 4.5 1.1 - - - +
1724X LYS* 1.3 80.5 - - + +
1726X ARG* 1.3 68.9 + - - +
1727X LYS* 3.4 5.1 + - - +
1729X LEU* 3.9 28.3 - - + +
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Residues in contact with ARG1726 (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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1672X HIS* 5.5 1.1 - - - -
1722X SER 2.8 11.0 + - - -
1723X ILE* 3.6 7.5 + - - +
1724X LYS 3.3 4.4 - - - +
1725X GLU* 1.3 81.0 - - - +
1727X LYS* 1.3 71.7 + - - +
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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