Contacts of the strand formed by residues 1362 - 1369 (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 LEU1362 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1347E ILE* 6.4 0.2 - - + -
1350E LEU* 3.6 26.7 - - + +
1351E SER* 3.3 18.7 - - - -
1352E VAL* 3.2 24.1 + - + +
1360E PRO* 3.8 7.8 - - - +
1361E VAL* 1.3 84.7 - - - +
1363E LYS* 1.3 60.9 + - - +
1365E VAL* 3.6 16.2 - - + -
1384E GLY* 3.7 24.2 - - - +
1387E SER* 3.7 15.7 - - - +
1388E PHE* 3.7 26.9 - - + +
1391E ALA* 4.8 7.2 - - + -
1555E GLY 3.4 17.9 - - - +
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Residues in contact with LYS1363 (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* 4.3 2.9 - - - -
1360E PRO* 4.8 13.2 - - + +
1362E LEU* 1.3 74.6 - - - +
1364E HIS* 1.3 70.6 + - + +
1365E VAL 3.2 2.2 + - - -
1554E ARG 5.3 7.9 - - - +
1555E GLY 3.8 7.2 + - - +
1556E ALA* 3.6 20.7 - - + +
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Residues in contact with HIS1364 (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* 4.2 17.3 - - + +
1350E LEU 3.5 7.8 + - - -
1351E SER* 3.8 8.3 + - - -
1363E LYS* 1.3 73.1 - - + +
1365E VAL* 1.3 65.3 + - - +
1366E ASN* 3.4 6.8 + - - +
1556E ALA* 5.3 2.3 - - - +
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Residues in contact with VAL1365 (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* 3.4 25.8 - - + +
1349E ASN 2.9 23.0 + - - -
1350E LEU* 3.2 14.2 + - + +
1362E LEU* 3.6 32.5 - - + -
1363E LYS 3.9 5.4 - - - +
1364E HIS* 1.3 76.0 - - - +
1366E ASN* 1.3 64.5 + - - +
1367E THR* 5.5 2.2 - - - -
1388E PHE* 5.7 6.1 - - + -
1552E LEU* 5.9 3.1 - - + -
1555E GLY 3.5 24.7 - - - +
1556E ALA* 4.2 5.6 - - - +
1557E ILE* 4.7 16.2 - - + +
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Residues in contact with ASN1366 (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 3.3 11.0 - - - +
1348E GLN* 5.0 0.9 - - - -
1349E ASN* 4.6 5.2 - - - +
1364E HIS 3.4 6.7 + - - +
1365E VAL* 1.3 78.8 - - - +
1367E THR* 1.3 63.8 + - - +
1557E ILE* 3.9 17.3 + - - +
1560E PHE* 5.9 1.2 - - - +
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Residues in contact with THR1367 (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* 3.3 1.6 - - - +
1347E ILE* 2.6 47.0 + - - +
1365E VAL* 5.5 3.1 - - - -
1366E ASN* 1.3 76.2 - - - +
1368E LEU* 1.3 60.5 + - - +
1550E MET* 5.8 2.0 - - - -
1557E ILE* 4.8 8.7 - - - -
1560E PHE* 4.2 28.3 - - - -
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Residues in contact with LEU1368 (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 3.4 8.1 - - - +
1346E GLN* 4.0 10.1 - - + +
1367E THR* 1.3 76.6 - - - +
1369E ILE* 1.3 61.3 + - - +
1370E SER 4.1 1.1 + - - -
1560E PHE* 3.2 29.6 - - - -
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Residues in contact with ILE1369 (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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1343E GLY 4.2 0.3 - - - +
1344E LYS* 3.6 1.2 - - - +
1345E ILE* 2.4 59.8 + - + +
1368E LEU* 1.3 72.8 - - - +
1370E SER* 1.3 66.2 + - - +
1373E GLN* 5.4 4.3 - - + +
1375E ILE* 5.0 16.4 - - + -
1532E THR* 5.8 5.6 - - - -
1560E PHE* 5.0 3.8 - - + -
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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