Contacts of the helix formed by residues 1658 - 1672 (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 THR1658 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1656X GLY 5.6 0.7 - - - +
1657X LEU* 1.3 77.2 - - - +
1659X PRO* 1.3 64.5 - - - +
1660X GLU* 3.8 14.7 - - - +
1661X GLU* 3.0 36.8 + - - +
1662X PHE* 2.7 34.0 + - - +
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Residues in contact with PRO1659 (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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1657X LEU 4.9 0.4 - - - +
1658X THR* 1.3 88.8 - - - +
1660X GLU* 1.3 70.1 + - - +
1662X PHE* 3.0 10.0 + - + +
1663X MET* 2.8 35.3 + - + +
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Residues in contact with GLU1660 (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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1658X THR* 3.8 14.2 - - - +
1659X PRO* 1.3 95.1 - - - +
1661X GLU* 1.3 61.1 + - + +
1663X MET* 3.6 10.1 - - - +
1664X LEU* 3.5 27.9 + - + +
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Residues in contact with GLU1661 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1656X GLY 4.3 0.7 - - - +
1657X LEU* 3.3 21.2 - - + +
1658X THR* 3.0 43.1 + - - +
1660X GLU* 1.3 78.0 - - + +
1662X PHE* 1.3 61.5 + - - +
1663X MET 3.1 0.7 - - - -
1664X LEU* 3.3 2.3 + - + -
1665X VAL* 3.3 24.3 + - - +
1690X LYS* 3.1 32.4 + - - +
1716X TYR* 3.5 36.5 + - + +
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Residues in contact with PHE1662 (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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1654X VAL* 4.0 30.5 - - + -
1657X LEU* 4.4 5.8 - - + +
1658X THR 2.7 16.9 + - - +
1659X PRO* 3.0 13.0 + - + +
1661X GLU* 1.3 72.3 - - - +
1663X MET* 1.3 71.6 - - - +
1665X VAL* 3.2 8.9 + - + +
1666X TYR* 2.8 34.9 + + + -
1676X LEU* 4.0 31.6 - - + -
1677X THR 5.2 4.7 - - - -
1678X ASN* 4.9 14.4 - - - -
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Residues in contact with MET1663 (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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1659X PRO* 2.8 22.2 - - + +
1660X GLU* 3.6 11.4 - - - +
1662X PHE* 1.3 91.4 - - - +
1664X LEU* 1.3 61.0 + - + +
1666X TYR* 3.3 18.4 + - + +
1667X LYS* 2.9 26.3 + - - +
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Residues in contact with LEU1664 (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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1660X GLU* 3.5 14.5 + - + +
1661X GLU* 3.3 2.3 + - + +
1662X PHE 3.3 0.6 - - - -
1663X MET* 1.3 75.1 - - + +
1665X VAL* 1.3 59.8 + - - +
1667X LYS* 3.3 13.4 + - + +
1668X PHE* 3.0 24.1 + - - +
1716X TYR* 3.5 28.3 - - + +
1719X VAL* 4.1 2.0 - - + -
1720X THR* 5.2 7.0 - - + -
1723X ILE* 3.3 40.3 - - + +
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Residues in contact with VAL1665 (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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1652X MET* 3.7 27.1 - - + -
1654X VAL* 3.8 20.4 - - + -
1657X LEU* 3.8 17.7 - - + -
1661X GLU 3.5 13.9 - - - +
1662X PHE* 3.2 8.6 + - + +
1664X LEU* 1.3 74.7 - - - +
1666X TYR* 1.3 52.8 + - - +
1668X PHE* 3.2 4.4 + - - +
1669X ALA* 2.7 32.7 + - - +
1676X LEU* 3.9 11.2 - - + -
1688X VAL* 4.7 1.8 - - + -
1716X TYR* 3.7 21.8 - - + -
1719X VAL* 4.0 17.5 - - + -
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Residues in contact with TYR1666 (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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1662X PHE* 2.8 24.5 + + + +
1663X MET* 3.3 24.9 - - + +
1664X LEU 3.2 0.2 - - - -
1665X VAL* 1.3 76.7 - - - +
1667X LYS* 1.3 65.3 + - - +
1669X ALA* 3.1 5.1 + - + +
1670X ARG* 3.0 30.5 + - + +
1676X LEU* 3.7 24.4 - - + +
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Residues in contact with LYS1667 (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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1663X MET 2.9 13.5 + - - +
1664X LEU* 3.3 23.0 + - + +
1666X TYR* 1.3 77.4 - - - +
1668X PHE* 1.3 65.1 + - - +
1670X ARG* 3.1 16.2 + - - +
1671X LYS* 3.1 15.9 + - + +
1723X ILE* 4.6 22.0 - - + -
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Residues in contact with PHE1668 (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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1652X MET* 4.1 12.8 - - + -
1664X LEU 3.0 10.8 + - - +
1665X VAL 3.4 6.3 - - - +
1667X LYS* 1.3 79.4 - - - +
1669X ALA* 1.3 63.3 + - - +
1671X LYS* 3.6 2.8 + - - -
1672X HIS* 3.2 55.4 + + - +
1674X ILE* 3.7 12.6 - - + -
1718X TRP* 3.5 52.7 - + - -
1719X VAL* 3.6 29.6 - - + -
1722X SER* 3.5 31.0 - - - -
1723X ILE* 4.1 12.5 - - + +
1728X MET* 4.0 11.2 - - + -
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Residues in contact with ALA1669 (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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1652X MET* 4.1 10.1 - - + -
1665X VAL 2.7 19.5 + - - +
1666X TYR* 3.1 8.2 + - + +
1668X PHE* 1.3 73.7 - - - +
1670X ARG* 1.3 57.4 + - - +
1672X HIS 3.6 0.2 + - - -
1673X HIS* 3.0 10.6 + - - -
1674X ILE* 3.0 52.4 + - - +
1676X LEU* 4.0 21.5 - - + -
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Residues in contact with ARG1670 (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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1666X TYR* 3.0 25.0 + - + +
1667X LYS* 3.1 10.1 + - - +
1669X ALA* 1.3 76.7 - - - +
1671X LYS* 1.3 63.8 - - - +
1672X HIS 3.2 0.7 + - - -
1673X HIS* 3.5 17.9 + - - +
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Residues in contact with LYS1671 (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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1667X LYS* 3.1 16.2 + - + +
1668X PHE* 4.0 7.2 - - - +
1670X ARG* 1.3 78.0 - - - +
1672X HIS* 1.3 74.0 + - + +
1673X HIS* 3.7 10.4 + - - -
1727X LYS* 4.9 7.0 + - - +
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Residues in contact with HIS1672 (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* 3.2 49.0 + + - -
1670X ARG 3.2 0.4 - - - -
1671X LYS* 1.3 89.0 + - + +
1673X HIS* 1.3 76.8 + - - +
1674X ILE* 3.3 23.7 + - + +
1722X SER* 5.2 1.8 + - - -
1726X ARG 5.5 0.6 - - - -
1727X LYS* 3.8 32.5 + - + +
1728X MET* 3.5 48.0 + - + +
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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