Contacts of the strand formed by residues 1336 - 1341 (chain B) in PDB entry 2ZEJ
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 LYS1336 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1403A SER* 2.8 40.1 + - - -
1408A PHE* 3.8 20.9 - - - +
1409A MSE 3.5 25.4 - - - +
1412A ARG* 3.2 29.0 + - - +
1413A ALA* 3.6 9.1 - - + -
1414A LEU* 3.0 26.5 + - - +
1335B MSE 1.3 82.1 - - - +
1337B LEU* 1.3 61.2 + - - +
1338B MSE 4.0 11.0 - - - -
1390B LEU* 5.4 0.8 - - - +
1391B ASN* 3.2 17.8 - - + +
1393B TRP* 3.5 26.9 - - + +
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Residues in contact with LEU1337 (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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1414A LEU* 3.2 38.6 - - + +
1416A LEU* 4.1 24.9 - - + +
1504A ILE* 4.3 11.2 - - + -
1336B LYS* 1.3 72.1 - - - +
1338B MSE 1.3 61.5 + - - +
1339B ILE* 4.0 16.6 - - + -
1351B LEU* 5.0 0.7 - - + -
1354B LEU* 5.7 0.2 - - + -
1376B TRP* 3.9 31.6 - - + -
1390B LEU* 4.3 13.7 - - + -
1391B ASN 2.9 6.1 + - - -
1392B VAL* 3.4 22.8 - - + +
1393B TRP* 2.8 28.1 + - - +
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Residues in contact with MSE1338 (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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1409A MSE 4.3 22.2 - - + +
1413A ALA* 3.5 24.9 - - + -
1414A LEU 3.0 6.9 + - - +
1415A TYR* 3.3 40.0 - - + +
1416A LEU 2.8 26.5 + - - +
1441A ARG* 5.2 3.1 - - - +
1336B LYS* 4.2 17.3 - - - -
1337B LEU* 1.3 75.6 - - - +
1339B ILE* 1.3 61.7 + - - +
1340B VAL* 3.9 2.1 + - + -
1393B TRP* 3.6 28.5 - - - -
1395B PHE* 3.8 25.6 - - + -
1401B PHE* 4.1 9.4 - - + -
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Residues in contact with ILE1339 (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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1416A LEU* 3.6 26.0 - - + +
1418A VAL* 3.8 20.2 - - + -
1337B LEU* 4.4 7.2 - - + -
1338B MSE 1.3 74.2 - - - +
1340B VAL* 1.3 62.3 + - - +
1347B LYS* 3.7 32.6 - - + +
1350B LEU* 5.3 0.9 - - + -
1351B LEU* 3.8 31.4 - - + +
1392B VAL* 3.6 26.7 - - + -
1393B TRP 2.8 16.9 + - - +
1394B ASP* 4.3 8.1 - - + -
1395B PHE* 3.0 29.8 + - - +
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Residues in contact with VAL1340 (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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1415A TYR* 4.4 13.2 - - + -
1416A LEU 2.9 16.0 + - - +
1417A ALA* 4.2 8.1 - - + -
1418A VAL* 2.9 25.1 + - - +
1434A TRP* 3.4 37.0 - - + -
1438A ILE* 3.8 22.9 - - + -
1338B MSE 4.6 0.2 - - - -
1339B ILE* 1.3 80.1 - - - +
1341B GLY* 1.3 61.2 + - - +
1347B LYS* 3.5 12.3 - - - +
1395B PHE* 3.8 21.5 - - + -
1401B PHE* 3.9 15.5 - - + -
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Residues in contact with GLY1341 (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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1418A VAL 3.6 15.0 - - - -
1431A MSE 4.5 2.7 - - - -
1434A TRP* 3.3 36.0 - - - -
1340B VAL* 1.3 80.1 - - - +
1342B ASN* 1.3 61.8 + - - -
1347B LYS* 3.3 15.4 - - - -
1397B GLY* 3.5 8.0 - - - -
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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