Contacts of the strand formed by residues 1319 - 1324 (chain B) in PDB entry 5FO9
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 LEU1319 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ILE* 3.6 40.2 - - + -
174A PRO* 4.7 12.5 - - + +
177A GLN* 2.4 37.2 + - - +
981B LEU* 3.7 30.3 - - + -
982B LEU 3.2 28.0 - - - +
983B GLN* 3.6 25.1 - - + +
1317B SER* 3.1 1.2 - - - +
1318B LEU* 1.3 81.3 - - - +
1320B ARG* 1.3 67.0 + - - +
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Residues in contact with ARG1320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A GLN* 4.5 2.2 - - - +
980B ILE 3.8 0.3 - - - +
981B LEU* 3.4 8.5 - - - +
982B LEU* 2.9 55.7 + - + +
1309B HIS* 3.3 44.6 + - + +
1310B ARG 3.0 32.8 + - - +
1311B ILE* 3.5 22.9 - - - +
1315B SER* 4.1 12.3 - - - -
1317B SER* 2.6 39.5 + - - -
1319B LEU* 1.3 73.7 - - - +
1321B SER* 1.3 60.6 + - - +
1322B GLU* 6.0 0.2 - - + -
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Residues in contact with SER1321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PRO 4.2 11.9 - - - -
175A VAL* 3.6 21.8 + - - +
177A GLN* 4.8 5.2 - - - +
979B ARG* 4.3 13.0 + - - -
980B ILE 3.5 3.9 + - - -
981B LEU* 3.6 18.9 - - - +
1309B HIS* 4.9 1.8 + - - -
1319B LEU 4.0 1.6 + - - -
1320B ARG* 1.3 75.6 - - - +
1322B GLU* 1.3 78.9 + - - +
1323B GLU* 3.4 16.6 + - - +
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Residues in contact with GLU1322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
979B ARG* 3.7 2.4 - - - +
980B ILE* 2.9 46.8 + - + +
982B LEU* 6.2 1.1 - - + -
1298B LEU* 4.4 18.6 - - + -
1300B LEU* 6.5 1.3 - - + -
1303B ARG* 5.9 1.2 + - - -
1307B ILE* 4.0 19.5 - - + +
1309B HIS* 2.8 40.5 + - + +
1320B ARG* 5.7 0.7 - - + -
1321B SER* 1.3 83.1 + - - +
1323B GLU* 1.3 74.2 + - - +
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Residues in contact with GLU1323 (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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175A VAL 3.4 22.0 - - - +
977B GLU* 4.7 9.2 - - + +
978B THR 3.4 7.6 - - - +
979B ARG* 3.7 33.1 + - - +
980B ILE* 5.6 0.7 - - - -
1300B LEU* 5.1 4.7 - - - +
1303B ARG* 6.0 1.7 - - - -
1321B SER* 3.4 15.3 + - - +
1322B GLU* 1.3 86.8 + - - +
1324B THR* 1.3 64.1 + - - +
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Residues in contact with THR1324 (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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977B GLU* 3.8 2.8 - - - -
978B THR* 2.9 55.2 + - + +
980B ILE* 4.6 13.0 - - + -
1300B LEU* 4.2 20.4 - - + -
1302B SER* 4.0 4.9 + - - -
1323B GLU* 1.3 77.3 - - - +
1325B LYS* 1.3 63.8 + - - +
1326B GLU* 3.2 22.0 + - - +
1328B GLU* 3.4 17.4 + - + +
1330B PHE* 5.8 2.2 - - + -
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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
------------------------------------------------------------
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