Contacts of the strand formed by residues 1362 - 1369 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1350G LEU* 3.6 25.4 - - + +
1351G SER* 3.3 19.4 - - - -
1352G VAL* 3.2 24.0 + - + +
1360G PRO* 3.8 8.2 - - - +
1361G VAL* 1.3 84.5 - - - +
1363G LYS* 1.3 60.6 + - - +
1365G VAL* 3.6 15.0 - - + -
1384G GLY* 3.7 24.5 - - - +
1387G SER* 3.7 16.2 - - - +
1388G PHE* 3.7 25.6 - - + +
1391G ALA* 4.8 7.6 - - + -
1555G GLY 3.4 18.6 - - - +
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Residues in contact with LYS1363 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1351G SER* 4.3 3.1 - - - -
1360G PRO* 4.8 13.2 - - + +
1362G LEU* 1.3 74.3 - - - +
1364G HIS* 1.3 70.9 + - + +
1365G VAL 3.2 2.6 + - - -
1554G ARG 5.3 8.3 - - - +
1555G GLY 3.8 7.4 + - - +
1556G ALA* 3.6 21.1 - - + +
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Residues in contact with HIS1364 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1349G ASN* 4.2 17.4 - - + +
1350G LEU 3.5 7.3 + - - -
1351G SER* 3.8 8.1 + - - -
1363G LYS* 1.3 72.9 - - + +
1365G VAL* 1.3 64.7 + - - +
1366G ASN* 3.4 6.6 + - - +
1556G ALA* 5.3 2.1 - - - +
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Residues in contact with VAL1365 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1347G ILE* 3.4 24.9 - - + +
1349G ASN 2.9 23.6 + - - -
1350G LEU* 3.2 15.9 + - + +
1362G LEU* 3.6 30.7 - - + -
1363G LYS 3.9 5.6 - - - +
1364G HIS* 1.3 76.7 - - - +
1366G ASN* 1.3 64.8 + - - +
1367G THR* 5.5 2.5 - - - -
1388G PHE* 5.7 6.3 - - + -
1552G LEU* 5.9 3.8 - - + -
1555G GLY 3.5 25.6 - - - +
1556G ALA* 4.2 4.9 - - - +
1557G ILE* 4.7 15.7 - - + +
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Residues in contact with ASN1366 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1347G ILE 3.3 10.8 - - - +
1348G GLN* 5.0 1.1 - - - -
1349G ASN 4.6 5.2 - - - +
1364G HIS 3.4 6.7 + - - +
1365G VAL* 1.3 77.9 - - - +
1367G THR* 1.3 64.5 + - - +
1557G ILE* 3.9 17.9 + - - +
1560G PHE* 5.9 1.2 - - - +
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Residues in contact with THR1367 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1346G GLN* 3.3 1.6 - - - +
1347G ILE* 2.6 47.8 + - - +
1365G VAL* 5.5 2.9 - - - -
1366G ASN* 1.3 75.6 - - - +
1368G LEU* 1.3 59.9 + - - +
1550G MET* 5.8 1.8 - - - -
1557G ILE* 4.8 9.0 - - - -
1560G PHE* 4.2 27.8 - - - -
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Residues in contact with LEU1368 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1345G ILE 3.4 8.3 - - - +
1346G GLN* 4.0 10.5 - - + +
1367G THR* 1.3 77.2 - - - +
1369G ILE* 1.3 60.4 - - - +
1370G SER 4.1 1.3 + - - -
1560G PHE* 3.2 29.3 - - - -
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Residues in contact with ILE1369 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1343G GLY 4.2 0.5 - - - +
1344G LYS* 3.6 1.7 - - - +
1345G ILE* 2.4 59.4 + - + +
1368G LEU* 1.3 73.0 - - - +
1370G SER* 1.3 65.1 + - - +
1373G GLN* 5.4 5.2 - - + +
1375G ILE* 5.0 16.4 - - + -
1532G THR* 5.8 6.1 - - - -
1560G 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