Contacts of the strand formed by residues 1871 - 1874 (chain A) in PDB entry 5D9Y
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 ILE1871 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1230A ILE 3.8 0.9 - - - +
1231A LEU* 3.2 3.7 - - - +
1232A VAL* 2.8 50.4 + - + +
1235A GLY* 3.6 31.6 - - - +
1236A ILE* 4.1 6.3 - - + -
1333A MET* 3.9 30.7 - - + -
1336A THR* 4.3 20.2 - - + +
1394A LEU* 4.2 27.8 - - + -
1395A VAL 3.5 5.8 - - - +
1396A CYS* 4.8 7.2 - - + -
1869A GLY 4.0 1.1 + - - +
1870A SER* 1.3 78.8 - - - +
1872A LEU* 1.3 64.7 + - - +
1873A ILE* 4.4 7.0 - - + +
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Residues in contact with LEU1872 (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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1229A LEU* 4.1 18.6 - - + -
1230A ILE 3.4 4.5 - - - +
1231A LEU* 4.0 16.4 - - + -
1393A THR 3.5 0.7 - - - +
1394A LEU* 3.3 3.6 - - - -
1395A VAL* 2.7 59.7 + - + +
1397A THR* 6.0 0.7 - - - +
1416A HIS* 4.0 21.8 - - + +
1864A VAL* 3.8 28.3 - - + -
1866A PRO* 4.9 9.0 - - + -
1871A ILE* 1.3 75.3 - - - +
1873A ILE* 1.3 65.6 + - - +
1874A GLU* 4.1 26.2 - - + -
1896A ARG* 5.9 0.7 - - - +
2001A OGA 5.7 0.4 - - - +
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Residues in contact with ILE1873 (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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1151A LEU* 4.1 16.9 - - + +
1229A LEU* 3.5 3.8 - - - +
1230A ILE* 2.7 52.6 + - + +
1232A VAL* 5.8 0.2 - - + -
1336A THR* 5.6 0.9 - - + -
1337A TYR* 4.7 6.5 - - + -
1340A LEU* 4.1 31.2 - - + -
1341A ALA* 4.5 14.4 - - + -
1392A SER* 3.5 25.1 - - - +
1393A THR 3.3 4.9 - - - +
1394A LEU* 3.7 26.5 - - + -
1871A ILE* 4.4 8.5 - - + +
1872A LEU* 1.3 76.6 - - - +
1874A GLU* 1.3 65.4 + - - +
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Residues in contact with GLU1874 (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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1151A LEU* 4.1 3.8 - - - -
1228A ILE 3.8 15.7 - - - +
1229A LEU* 3.7 12.3 - - + +
1392A SER* 3.8 5.6 - - - -
1393A THR* 2.8 35.1 + - + +
1395A VAL* 5.4 2.4 - - - +
1416A HIS* 2.9 41.3 + - - -
1418A LEU* 3.8 16.3 - - - +
1872A LEU* 4.1 10.2 - - + +
1873A ILE* 1.3 77.8 - - - +
1875A CYS* 1.3 60.6 + - - +
1876A ALA* 3.1 17.0 + - + +
1879A GLU* 5.3 4.2 - - + +
1881A HIS* 3.3 22.7 + - - -
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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