Contacts of the helix formed by residues 1746 - 1754 (chain B) 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 ARG1746 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1428B LEU* 3.0 24.1 + - - +
1430B ARG* 3.6 25.8 - - + +
1431B THR 4.4 1.0 - - - +
1432B GLU* 4.6 9.1 + - - +
1436B GLU* 2.7 52.2 + - - +
1439B LEU* 4.4 7.4 - - - +
1440B THR* 3.3 39.8 + - + +
1741B ASN 2.8 21.8 + - - +
1742B CYS* 3.2 23.7 + - - +
1743B LEU 3.5 1.0 + - - -
1744B PRO 3.3 0.4 - - - -
1745B LEU* 1.3 80.4 - - - +
1747B PHE* 1.3 67.9 + - + +
1748B TRP 3.3 1.2 + - - -
1749B VAL* 4.1 0.3 - - - +
1750B ASN* 3.2 27.0 + - - +
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Residues in contact with PHE1747 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1325B TYR* 3.2 29.6 - + - -
1329B VAL* 5.9 3.8 - - + -
1440B THR* 4.5 8.9 - - + +
1443B PHE* 3.6 18.6 - - + -
1444B THR* 3.4 32.5 - - - -
1447B LEU* 4.0 32.1 - - + -
1451B LEU* 4.3 17.5 - - + -
1743B LEU* 3.1 19.1 + - + +
1746B ARG* 1.3 82.8 - - + +
1748B TRP* 1.3 83.0 + + - +
1750B ASN* 3.9 3.6 + - - +
1751B VAL* 3.4 39.0 + - + +
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Residues in contact with TRP1748 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1447B LEU* 5.1 5.4 - - + +
1450B PHE* 4.4 20.0 - + - -
1451B LEU* 4.3 18.2 - - + -
1455B ALA* 3.9 29.4 - - + -
1459B LEU* 5.1 7.0 - - + -
1695B LEU* 5.7 1.6 - - + -
1699B ILE* 3.8 49.3 + - + +
1700B PHE* 6.3 0.2 - + - -
1713B ILE* 5.4 3.4 - - + +
1743B LEU* 3.3 35.6 + - + +
1744B PRO* 3.2 31.4 - - + +
1747B PHE* 1.3 90.4 - + - +
1749B VAL* 1.3 64.3 + - - +
1750B ASN 3.1 2.0 - - - -
1751B VAL* 3.1 28.9 - - + +
1752B ILE* 3.1 23.3 - - + +
1778B PHE* 3.8 10.5 - - + -
1814B TYR* 5.7 0.6 + - - -
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Residues in contact with VAL1749 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1430B ARG* 5.7 0.4 - - - +
1744B PRO 2.9 14.2 + - - +
1745B LEU* 3.1 33.4 - - - +
1746B ARG 4.1 1.3 - - - +
1748B TRP* 1.3 72.6 - - - +
1750B ASN* 1.3 65.1 + - + +
1752B ILE* 4.0 10.2 - - - +
1753B LYS* 3.5 21.1 + - - +
1775B ALA* 3.4 36.5 - - + +
1778B PHE* 4.2 8.1 - - + -
1779B MET* 3.6 24.7 - - + -
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Residues in contact with ASN1750 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1329B VAL* 4.5 20.8 + - - +
1440B THR* 5.9 3.8 - - - +
1746B ARG 3.2 18.2 + - - +
1747B PHE* 3.9 5.4 + - - +
1748B TRP 3.1 1.0 - - - -
1749B VAL* 1.3 84.4 - - + +
1751B VAL* 1.3 62.3 + - - +
1753B LYS* 3.4 4.9 + - - +
1754B ASN* 2.9 41.8 + - - +
1757B PHE* 3.8 19.4 - - - -
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Residues in contact with VAL1751 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1325B TYR* 6.1 4.0 - - + -
1329B VAL* 5.7 5.4 - - + -
1451B LEU* 6.0 4.9 - - + -
1459B LEU* 4.3 23.0 - - + +
1747B PHE* 3.4 32.3 - - + +
1748B TRP* 3.1 34.5 + - + +
1750B ASN* 1.3 80.0 - - + +
1752B ILE* 1.3 64.5 + - + +
1753B LYS 3.3 0.4 - - - -
1754B ASN* 3.3 25.5 - - - +
1755B PRO* 3.4 9.4 - - - +
1757B PHE* 5.0 11.4 - - + -
1758B VAL* 5.6 9.0 - - + -
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Residues in contact with ILE1752 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1459B LEU* 5.5 7.4 - - + -
1462B LEU* 5.0 7.9 - - + -
1695B LEU* 5.0 11.4 - - + -
1696B PHE* 5.3 3.1 - - + -
1699B ILE* 4.8 10.5 - - + -
1748B TRP* 3.1 21.0 + - + +
1749B VAL* 4.1 7.4 - - - +
1751B VAL* 1.3 82.0 - - + +
1753B LYS* 1.3 61.2 + - - +
1754B ASN 3.3 0.2 - - - -
1755B PRO* 4.2 1.4 - - - +
1771B LEU* 3.5 32.8 - - + +
1774B VAL* 4.1 23.3 - - + -
1775B ALA* 4.4 11.7 - - + +
1778B PHE* 3.7 42.6 - - + -
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Residues in contact with LYS1753 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1749B VAL 3.5 14.7 + - - +
1750B ASN* 3.4 5.3 + - - +
1752B ILE* 1.3 79.4 - - - +
1754B ASN* 1.3 74.9 + - - +
1755B PRO* 3.6 4.5 - - - +
1763B LYS* 3.0 5.4 + - - +
1768B ASP* 2.9 26.3 - - - +
1771B LEU* 4.5 7.1 - - - +
1772B SER* 5.4 4.9 - - - +
1775B ALA* 4.2 13.5 - - + -
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Residues in contact with ASN1754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1750B ASN* 2.9 21.6 + - - +
1751B VAL* 3.3 15.1 - - - +
1753B LYS* 1.3 86.5 - - - +
1755B PRO* 1.3 59.2 - - - +
1756B GLN* 3.1 27.3 + - - +
1757B PHE* 3.3 41.5 + - + +
1758B VAL 4.7 0.5 + - - -
1763B LYS* 2.7 27.2 + - - -
1768B ASP* 4.4 1.2 - - - +
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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