Contacts of the strand formed by residues 1764 - 1768 (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 LEU1764 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1760X ILE 4.5 2.0 - - - +
1761X PHE* 3.5 52.8 + - + +
1762X ARG* 3.9 1.5 + - + +
1763X GLY* 1.3 85.0 - - - +
1765X GLU* 1.3 55.9 + - - +
1766X ILE* 3.9 11.2 - - + -
1788X GLY 4.6 0.4 + - - -
1789X ALA* 4.2 2.6 - - + +
1790X SER* 2.7 36.6 + - - -
1804X VAL* 3.9 4.6 - - - +
1805X HIS* 4.0 29.2 - - + +
1807X ILE* 4.0 22.4 - - + -
1837X TRP* 4.1 6.1 - - + -
1847X CYS* 4.9 4.7 - - - -
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Residues in contact with GLU1765 (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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1764X LEU* 1.3 74.1 - - - +
1766X ILE* 1.3 62.7 + - - +
1790X SER* 3.4 16.8 + - - -
1792X VAL* 3.8 15.7 - - + -
1797X SER 4.9 1.5 - - - +
1798X PHE* 3.4 22.4 - - + +
1799X THR* 2.7 46.8 + - - -
1804X VAL* 3.6 28.9 - - + +
1805X HIS 3.1 10.3 + - - +
1806X PRO* 3.4 1.2 - - - +
1807X ILE 2.9 25.8 + - - -
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Residues in contact with ILE1766 (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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1761X PHE* 4.1 7.4 - - + -
1764X LEU* 4.2 9.0 - - + -
1765X GLU* 1.3 79.2 - - - +
1767X CYS* 1.3 64.2 + - - +
1768X CYS* 4.1 8.6 + - - -
1784X VAL* 3.8 35.0 - - + -
1789X ALA* 3.7 25.1 - - + -
1790X SER 2.9 8.6 + - - +
1791X VAL* 3.6 5.0 - - - +
1792X VAL* 2.9 25.8 + - - +
1807X ILE* 3.6 9.6 - - + +
1809X VAL* 3.8 24.5 - - + -
1837X TRP* 3.8 30.5 - - + -
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Residues in contact with CYS1767 (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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1766X ILE* 1.3 76.1 - - - +
1768X CYS* 1.3 64.2 + - - +
1769X TYR* 3.2 16.1 + - - -
1792X VAL* 3.6 18.8 - - + +
1793X LYS 3.9 18.4 - - - -
1794X GLU 4.6 0.9 - - - -
1795X LEU* 3.8 27.6 - - + -
1798X PHE* 3.6 23.3 - - + -
1807X ILE 3.0 10.1 + - - +
1808X VAL* 3.6 3.2 - - - +
1809X VAL 2.9 26.3 + - - +
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Residues in contact with CYS1768 (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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1766X ILE* 4.1 12.7 + - - -
1767X CYS* 1.3 74.8 - - - +
1769X TYR* 1.3 60.8 + - - +
1770X GLY 4.1 1.2 + - - +
1772X PHE* 3.8 17.1 - - + -
1777X THR* 4.0 28.8 - - + +
1780X LEU* 4.1 30.5 - - + -
1781X GLU* 4.3 19.3 + - + +
1784X VAL* 5.2 4.3 - - - -
1791X VAL* 6.1 0.2 - - - +
1792X VAL 4.4 3.3 + - - +
1793X LYS 5.2 2.6 - - - +
1809X VAL* 3.6 19.5 - - - -
1838X VAL* 5.6 0.7 - - - -
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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