Contacts of the helix formed by residues 1747 - 1754 (chain A) in PDB entry 3RYT
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 PHE1747 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1325A TYR* 3.5 19.3 - + - -
1329A VAL* 5.8 3.1 - - + -
1440A THR* 4.9 5.6 - - - +
1443A PHE* 3.9 17.9 - - + -
1444A THR* 3.9 29.8 - - + -
1447A LEU* 3.5 37.5 - - + -
1451A LEU* 3.9 20.4 - - + -
1743A LEU* 2.9 14.2 + - + +
1746A ARG* 1.3 78.1 - - + +
1748A TRP* 1.3 102.3 + + - +
1750A ASN* 3.5 16.0 - - - +
1751A VAL* 3.6 20.1 + - + +
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Residues in contact with TRP1748 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1447A LEU* 4.5 6.3 - - + -
1450A PHE* 3.9 32.5 - + - -
1451A LEU* 3.6 31.9 - - + -
1455A ALA* 4.0 8.7 - - + -
1459A LEU* 5.9 2.5 - - + -
1695A LEU* 5.9 1.8 - - + -
1699A ILE* 3.9 47.6 + - + +
1713A ILE* 5.2 3.8 - - + +
1743A LEU* 3.3 42.0 + - + +
1744A PRO* 3.3 22.1 + - + +
1747A PHE* 1.3 92.3 - + - +
1749A VAL* 1.3 63.9 + - - +
1750A ASN 2.9 6.3 + - - -
1751A VAL* 3.0 25.6 + - + +
1752A ILE* 3.1 16.7 + - + +
1778A PHE* 3.6 14.6 - - + -
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Residues in contact with VAL1749 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1744A PRO 2.9 13.0 + - - +
1745A LEU* 3.2 36.3 - - + +
1746A ARG* 3.9 4.0 - - - +
1748A TRP* 1.3 72.3 - - - +
1750A ASN* 1.3 63.5 + - - +
1752A ILE* 4.0 4.8 - - - +
1753A LYS* 3.4 23.5 + - + +
1775A ALA* 3.9 19.5 - - + +
1778A PHE* 3.6 16.5 - - + -
1779A MET* 3.8 31.4 - - + -
1705B ARG* 4.5 10.1 - - - +
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Residues in contact with ASN1750 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1329A VAL* 4.2 24.4 + - - +
1440A THR* 5.6 4.8 - - - +
1746A ARG 3.3 22.0 + - - +
1747A PHE* 3.5 11.7 + - - +
1748A TRP 2.9 0.2 + - - -
1749A VAL* 1.3 84.1 - - - +
1751A VAL* 1.3 62.3 + - - +
1753A LYS* 4.4 0.8 - - - +
1754A ASN* 3.1 39.0 + - - +
1757A PHE* 3.7 14.7 - - - -
1705B ARG* 4.1 26.6 + - - +
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Residues in contact with VAL1751 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1325A TYR* 5.4 3.6 - - + -
1329A VAL* 5.4 3.6 - - + -
1451A LEU* 5.2 1.8 - - + -
1459A LEU* 4.1 17.5 - - + +
1747A PHE* 3.8 26.2 - - + +
1748A TRP* 3.4 30.7 - - + +
1750A ASN* 1.3 83.7 - - + +
1752A ILE* 1.3 62.8 + - + +
1753A LYS 3.4 0.4 - - - -
1754A ASN 3.3 12.6 - - - +
1755A PRO* 3.1 26.9 - - - +
1757A PHE* 4.6 9.4 - - + -
1758A VAL* 3.8 27.1 - - + -
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Residues in contact with ILE1752 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1459A LEU* 5.3 7.0 - - + +
1462A LEU* 5.3 5.4 - - + -
1695A LEU* 4.6 12.8 - - + -
1696A PHE* 4.5 8.7 - - + -
1699A ILE* 4.2 18.8 - - + -
1748A TRP* 3.1 15.1 + - + +
1749A VAL* 4.1 4.9 - - - +
1751A VAL* 1.3 84.1 - - + +
1753A LYS* 1.3 62.7 + - - +
1754A ASN 3.2 0.2 - - - -
1755A PRO* 3.9 1.4 - - - +
1771A LEU* 3.4 34.5 - - + +
1774A VAL* 4.5 11.2 - - + -
1775A ALA* 4.1 21.3 - - + +
1778A PHE* 4.0 39.0 - - + -
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Residues in contact with LYS1753 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1749A VAL* 3.4 16.3 + - + +
1750A ASN* 4.4 2.0 - - - +
1752A ILE* 1.3 79.6 - - - +
1754A ASN* 1.3 80.4 + - - +
1755A PRO* 3.5 4.1 - - - +
1763A LYS* 3.0 15.3 + - - +
1768A ASP* 2.8 37.7 + - - +
1771A LEU* 4.2 8.8 - - - +
1772A SER* 2.7 35.8 + - - +
1775A ALA* 4.2 11.0 - - + +
1706B GLY* 5.3 9.0 - - - -
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Residues in contact with ASN1754 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1750A ASN* 3.1 24.7 + - - +
1751A VAL* 3.2 16.8 - - - +
1753A LYS* 1.3 101.1 - - - +
1755A PRO* 1.3 59.6 - - - +
1756A GLN* 3.2 14.5 + - - +
1757A PHE* 3.2 47.3 + - + +
1763A LYS* 3.1 13.7 + - - -
1705B ARG* 5.9 4.4 - - - +
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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