Contacts of the strand formed by residues 1390 - 1395 (chain A) 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 LEU1390 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1335A MSE 3.5 22.2 - - - +
1336A LYS 5.5 0.9 - - - +
1337A LEU* 4.4 15.0 - - + -
1375A ASP* 3.5 3.6 - - - -
1376A TRP* 2.8 45.3 + - + +
1378A ILE* 3.9 25.8 - - + -
1388A LEU* 4.1 17.7 - - + -
1389A VAL* 1.3 74.7 - - - +
1391A ASN* 1.3 61.9 + - - +
1392A VAL* 3.4 12.2 + - + +
1414B LEU* 6.1 0.4 - - + -
1504B ILE* 3.9 17.9 - - + -
1508B SER* 3.7 33.9 - - - +
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Residues in contact with ASN1391 (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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1335A MSE 2.8 23.0 + - + +
1336A LYS* 3.2 22.5 + - + +
1337A LEU 3.0 21.1 + - - -
1373A VAL* 3.8 14.5 - - - +
1374A LYS 3.8 6.5 + - - -
1375A ASP* 2.9 23.9 + - - +
1389A VAL 4.0 1.4 + - - -
1390A LEU* 1.3 70.7 - - - +
1392A VAL* 1.3 60.0 + - - +
1393A TRP* 2.8 28.4 + - - -
1371B ILE* 5.5 1.0 - - - +
1403B SER* 4.6 7.3 + - - -
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Residues in contact with VAL1392 (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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1337A LEU* 3.4 15.0 - - + +
1339A ILE* 3.9 17.7 - - + -
1351A LEU* 3.7 37.2 - - + -
1355A MSE 5.0 1.1 - - - -
1372A ASP 3.4 1.7 - - - +
1373A VAL* 3.3 5.2 - - - -
1374A LYS* 2.6 47.2 + - + +
1376A TRP* 3.7 33.9 - - + -
1390A LEU* 3.7 18.4 - - + +
1391A ASN* 1.3 73.5 - - - +
1393A TRP* 1.3 64.3 + - - +
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Residues in contact with TRP1393 (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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1336A LYS* 3.5 20.0 - - + +
1337A LEU 2.7 12.4 + - - +
1338A MSE 3.5 8.1 - - - -
1339A ILE* 2.8 28.6 + - - +
1371A ILE* 3.8 19.7 - - + -
1372A ASP 3.5 4.0 - - - -
1373A VAL* 3.7 17.3 - - + +
1391A ASN* 2.8 33.9 + - - -
1392A VAL* 1.3 79.0 - - - +
1394A ASP* 1.3 60.8 + - - +
1395A PHE* 3.7 27.8 + + + -
1404A THR* 4.3 2.5 - - + -
1371B ILE* 4.0 19.7 - - + -
1393B TRP* 3.6 40.6 - + - -
1403B SER* 5.3 0.7 - - - -
1404B THR* 4.1 7.4 - - + -
1409B MSE 3.7 35.7 - - + -
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Residues in contact with ASP1394 (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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1A GDP 4.8 0.2 + - - -
2A MG 4.1 1.3 - - - -
1339A ILE* 4.1 8.6 - - + +
1347A LYS* 3.6 26.1 - - - +
1348A THR* 2.6 38.3 + - - +
1351A LEU* 4.3 22.6 - - + +
1369A VAL* 5.0 1.6 - - - +
1370A GLY 3.7 0.7 - - - +
1371A ILE* 3.4 5.2 - - - +
1372A ASP* 2.7 54.9 + - + +
1392A VAL* 4.0 0.6 - - + -
1393A TRP* 1.3 71.7 - - - +
1395A PHE* 1.3 65.1 + - - +
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Residues in contact with PHE1395 (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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1338A MSE 4.0 20.9 - - + -
1339A ILE 2.9 22.0 + - - +
1340A VAL* 3.8 16.2 - - + -
1347A LYS* 3.0 27.9 + - - +
1370A GLY 3.6 1.6 - - - -
1371A ILE* 3.6 30.1 - - + -
1393A TRP* 3.8 40.8 - + + -
1394A ASP* 1.3 76.9 - - - +
1396A ALA* 1.3 60.1 + - - +
1397A GLY 4.2 11.4 - - - +
1400A GLU* 3.7 4.3 - - + -
1401A PHE* 3.6 42.0 - + + +
1404A THR* 3.6 17.7 - - + -
1409B MSE 5.2 0.2 - - + -
1434B TRP* 5.3 0.7 - - + -
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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