Contacts of the strand formed by residues 1345 - 1352 (chain E) in PDB entry 6BAA
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 ILE1345 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1343E GLY 3.8 2.7 + - - +
1344E LYS* 1.3 75.3 - - - +
1346E GLN* 1.3 59.2 + - - +
1347E ILE* 6.2 1.8 - - + -
1368E LEU* 3.3 2.6 - - - +
1369E ILE* 2.4 59.4 + - + +
1392E PHE* 6.0 5.8 - - + -
1404E ILE 3.9 16.2 - - - +
1405E ILE* 5.3 0.9 - - - -
1406E ASP 5.2 2.7 - - - +
1532E THR* 5.8 5.4 - - - -
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Residues in contact with GLN1346 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1345E ILE* 1.3 75.0 - - - +
1347E ILE* 1.3 66.1 + - - +
1348E GLN* 4.1 2.4 + - + -
1367E THR 3.3 9.0 - - - +
1368E LEU* 4.3 11.2 - - + -
1402E ARG 4.3 1.7 - - - +
1404E ILE* 3.7 30.7 + - + +
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Residues in contact with ILE1347 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1345E ILE* 6.1 2.2 - - + -
1346E GLN* 1.3 82.5 - - - +
1348E GLN* 1.3 62.9 + - - +
1350E LEU* 3.7 22.4 - - + -
1365E VAL* 3.4 33.2 - - + +
1366E ASN* 3.3 6.9 - - - +
1367E THR* 2.6 40.7 + - - +
1402E ARG 4.0 1.3 - - - +
1403E ILE* 3.8 28.0 - - + -
1404E ILE 4.5 4.7 - - - +
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Residues in contact with GLN1348 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1346E GLN* 4.1 2.6 + - + +
1347E ILE* 1.3 74.7 - - - +
1349E ASN* 1.3 69.6 + - + +
1350E LEU 3.4 1.3 - - - -
1366E ASN* 4.9 2.0 - - - +
1401E GLY* 3.2 19.4 - - - -
1402E ARG* 3.2 16.0 + - + +
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Residues in contact with ASN1349 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1348E GLN* 1.3 72.2 - - + +
1350E LEU* 1.3 61.3 + - - +
1351E SER* 3.4 4.5 + - - -
1364E HIS* 4.2 17.0 - - + +
1365E VAL 2.9 15.7 + - - -
1366E ASN* 4.6 4.6 - - - +
1400E GLU* 3.2 15.9 - - + +
1401E GLY* 3.3 8.3 - - - +
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Residues in contact with LEU1350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1347E ILE* 3.7 25.1 - - + -
1348E GLN 3.4 1.7 + - - -
1349E ASN* 1.3 75.8 - - - +
1351E SER* 1.3 59.1 + - - +
1362E LEU* 3.6 23.6 - - + +
1364E HIS 3.5 4.9 + - - -
1365E VAL* 3.2 25.1 + - + +
1398E MET* 4.8 8.7 - - + -
1400E GLU 3.3 7.9 - - - +
1401E GLY* 4.4 0.4 - - - -
1402E ARG 4.7 9.4 - - - +
1403E ILE* 5.8 2.2 - - + -
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Residues in contact with SER1351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1349E ASN 3.4 3.8 + - - -
1350E LEU* 1.3 76.5 + - - +
1352E VAL* 1.3 55.9 + - - +
1360E PRO* 5.8 2.5 - - - -
1362E LEU 3.3 9.3 + - - -
1363E LYS* 4.3 1.6 - - - -
1364E HIS* 3.8 13.2 + - - -
1398E MET* 3.2 5.0 - - - -
1399E PHE* 2.4 39.8 + - - -
1400E GLU* 3.0 25.5 + - - +
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Residues in contact with VAL1352 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1351E SER* 1.3 75.5 - - - +
1353E ARG* 1.3 62.2 + - - +
1354E TYR* 5.1 3.8 - - + +
1360E PRO* 3.4 5.3 - - - +
1361E VAL* 2.4 41.0 + - + -
1362E LEU* 3.2 40.7 + - + +
1387E SER* 4.6 7.0 - - - +
1391E ALA* 5.6 5.4 - - + -
1396E VAL* 3.7 21.3 - - + +
1397E ASP 3.3 25.6 - - - +
1398E MET* 4.3 3.6 - - + -
1399E PHE* 4.1 6.9 - - - +
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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