Contacts of the strand formed by residues 1289 - 1294 (chain B) in PDB entry 5NPK
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 ILE1289 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1277B ILE* 4.0 15.0 - - + -
1281B VAL* 3.7 46.2 - - + +
1286B ILE* 4.5 11.6 + - + -
1287B ASP 3.6 1.7 - - - +
1288B GLY* 1.3 77.9 - - - +
1290B THR* 1.3 62.3 + - - +
1291B ASP 3.8 14.4 - - - +
1292B LEU* 4.9 5.8 - - + -
1306B ILE* 3.7 35.0 - - + -
1307B ASP 3.4 3.1 - - - +
1308B VAL* 5.6 0.4 - - + -
1309B ARG* 5.8 0.6 + - - -
1317B ILE* 3.9 26.0 - - + -
1321B LEU* 4.6 6.1 - - + -
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Residues in contact with THR1290 (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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1256B ARG* 5.1 2.9 - - - +
1289B ILE* 1.3 76.6 - - - +
1291B ASP* 1.3 58.0 + - - +
1307B ASP* 2.8 33.6 + - - +
1308B VAL 3.6 3.9 + - - +
1309B ARG* 3.7 39.9 - - + +
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Residues in contact with ASP1291 (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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1289B ILE* 3.7 8.1 - - - +
1290B THR* 1.3 82.4 + - - +
1292B LEU* 1.3 72.7 + - - +
1293B ARG* 2.7 36.8 + - - +
1305B VAL 4.5 0.7 - - - -
1306B ILE* 3.3 4.2 - - - -
1307B ASP* 2.7 46.3 + - + +
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Residues in contact with LEU1292 (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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1274B ILE* 3.6 41.2 - - + +
1277B ILE* 3.9 20.4 - - + -
1278B ALA* 3.9 23.1 - - + +
1281B VAL* 6.0 0.4 - - + -
1289B ILE* 4.9 7.0 - - + -
1291B ASP* 1.3 82.2 + - - +
1293B ARG* 1.3 65.7 + - - +
1304B VAL* 4.2 14.8 - - + -
1305B VAL 3.4 4.3 - - - +
1306B ILE* 3.7 27.1 - - + -
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Residues in contact with ARG1293 (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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1258B ARG* 4.2 14.3 - - - +
1274B ILE* 5.3 0.9 - - - -
1291B ASP* 2.7 47.1 + - - +
1292B LEU* 1.3 79.1 - - - +
1294B ASP* 1.4 60.1 + - - +
1295B GLU* 3.0 35.5 + - + -
1303B ARG* 5.6 0.2 - - - +
1304B VAL* 3.4 6.6 - - - +
1305B VAL* 2.8 64.4 + - + +
1307B ASP* 2.8 25.5 + - - -
450D ARG* 6.2 4.7 - - - +
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Residues in contact with ASP1294 (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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1114B ASP* 4.3 4.3 - - - +
1270B LYS* 2.5 28.4 + - - -
1271B ALA* 5.6 0.7 - - - -
1274B ILE* 3.7 29.8 - - + +
1293B ARG* 1.4 70.0 - - - +
1295B GLU* 1.3 60.2 + - - +
1296B THR* 2.6 30.4 + - - +
1303B ARG 3.5 4.2 - - - +
1304B VAL* 4.0 2.9 - - - +
449D SER* 5.5 2.6 + - - -
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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