Contacts of the strand formed by residues 1243 - 1247 (chain B) in PDB entry 1B08
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 LYS1243 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1239B SER* 3.2 5.2 - - - -
1240B VAL* 2.8 36.9 + - + +
1241B GLY 3.2 0.2 - - - -
1242B GLU* 1.3 79.1 - - - +
1244B ILE* 1.3 74.7 + - - +
1245B PHE* 3.6 28.3 - - + -
1270B SER 3.5 8.5 + - - -
1272B ARG* 4.6 9.3 - - - +
1276B GLU* 2.9 36.2 + - + +
1354B GLU* 3.0 36.3 + - + +
1355B PHE 3.7 8.7 - - - +
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Residues in contact with ILE1244 (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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227A GLN* 3.7 21.1 - - + +
228A TYR* 3.5 42.6 - - + +
231A VAL* 3.9 38.6 - - + -
1233B LEU* 4.0 12.8 - - + -
1238B GLN 3.5 8.3 - - - +
1239B SER* 4.1 10.5 - - - -
1242B GLU 4.9 0.9 - - - +
1243B LYS* 1.3 80.0 - - - +
1245B PHE* 1.3 75.0 + - - +
1246B LYS* 5.0 0.2 - - + -
1354B GLU* 3.2 4.3 - - - +
1355B PHE* 2.8 36.7 + - + +
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Residues in contact with PHE1245 (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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1236B ASN 4.0 0.2 - - - +
1237B GLY* 3.2 2.6 - - - -
1238B GLN* 2.7 38.3 + - + +
1240B VAL* 3.8 25.8 - - + -
1243B LYS* 3.6 15.5 - - + -
1244B ILE* 1.3 76.2 - - - +
1246B LYS* 1.3 61.5 + - - +
1269B ALA* 4.0 23.3 - - + -
1270B SER 4.3 1.1 - - - -
1271B PRO* 4.6 7.0 - - + -
1276B GLU* 3.6 33.0 - - + -
1279B ALA* 4.5 3.1 - - + -
1280B LEU* 4.1 25.1 - - + -
1283B LEU* 4.0 10.4 - - + +
1352B VAL* 3.9 11.2 - - + -
1353B CYS 3.2 5.6 - - - -
1354B GLU* 3.8 34.8 - - + -
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Residues in contact with LYS1246 (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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231A VAL* 2.9 41.3 + - + +
232A GLU* 3.9 7.3 + - - -
234A PHE* 2.8 36.7 + - + +
235A PRO* 4.7 3.7 - - - +
1232B GLU* 3.7 20.3 + - - +
1236B ASN* 3.4 28.3 - - - +
1237B GLY* 4.5 2.0 - - - +
1244B ILE 4.1 0.6 + - - -
1245B PHE* 1.3 75.0 - - - +
1247B THR* 1.3 72.5 + - - +
1352B VAL* 4.1 2.9 - - - -
1353B CYS 2.8 30.6 + - - -
1355B PHE* 4.1 16.1 - - + -
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Residues in contact with THR1247 (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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234A PHE* 4.2 2.5 - - - -
235A PRO* 4.9 1.7 - - - +
1236B ASN* 2.9 50.4 + - + +
1246B LYS* 1.3 82.6 - - - +
1248B ALA* 1.3 65.6 + - - +
1249B GLY 3.0 13.0 + - - +
1283B LEU* 4.1 15.1 - - + +
1287B LYS* 4.1 17.7 - - + -
1350B LEU* 3.7 15.6 - - - +
1351B VAL 3.1 13.1 + - - -
1352B VAL* 4.1 13.2 - - - +
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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