Contacts of the strand formed by residues 1345 - 1352 (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 ILE1345 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1343G GLY 3.8 3.1 + - - +
1344G LYS* 1.3 75.4 - - - +
1346G GLN* 1.3 58.8 + - - +
1347G ILE* 6.2 1.8 - - + -
1368G LEU* 3.3 2.1 - - - +
1369G ILE* 2.4 60.3 + - + +
1392G PHE* 6.0 5.8 - - + -
1404G ILE* 3.9 15.7 - - - +
1405G ILE* 5.3 1.1 - - - -
1406G ASP 5.2 2.5 - - - +
1532G THR* 5.8 5.2 - - - -
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Residues in contact with GLN1346 (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* 1.3 75.8 - - - +
1347G ILE* 1.3 66.9 + - - +
1348G GLN* 4.1 2.3 + - + -
1367G THR 3.3 10.8 - - - +
1368G LEU* 4.3 10.1 - - + -
1402G ARG 4.3 1.7 - - - +
1404G ILE* 3.7 29.6 + - + +
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Residues in contact with ILE1347 (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* 6.2 1.8 - - + -
1346G GLN* 1.3 81.7 - - - +
1348G GLN* 1.3 61.2 + - - +
1350G LEU* 3.7 22.4 - - + -
1365G VAL* 3.4 34.1 - - + +
1366G ASN* 3.3 6.8 - - - +
1367G THR* 2.6 40.6 + - - +
1402G ARG 4.0 1.6 - - - +
1403G ILE* 3.8 28.5 - - + -
1404G ILE 4.5 4.5 - - - +
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Residues in contact with GLN1348 (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* 4.1 2.1 + - + +
1347G ILE* 1.3 74.3 - - - +
1349G ASN* 1.3 69.0 + - + +
1350G LEU 3.4 1.5 + - - -
1366G ASN* 4.9 2.0 - - - +
1401G GLY* 3.2 18.5 - - - -
1402G ARG* 3.2 16.3 + - + +
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Residues in contact with ASN1349 (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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1348G GLN* 1.3 72.2 - - + +
1350G LEU* 1.3 62.2 + - - +
1351G SER* 3.4 4.9 + - - -
1364G HIS* 4.2 16.4 - - + +
1365G VAL 2.9 16.4 + - - -
1366G ASN* 4.6 4.2 - - - +
1400G GLU* 3.2 15.0 - - + +
1401G GLY* 3.3 8.0 + - - +
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Residues in contact with LEU1350 (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* 3.7 25.6 - - + -
1348G GLN 3.4 1.5 + - - -
1349G ASN* 1.3 75.7 - - - +
1351G SER* 1.3 60.3 + - - +
1362G LEU* 3.6 23.0 - - + +
1364G HIS 3.5 4.5 + - - -
1365G VAL* 3.2 26.0 + - + +
1398G MET* 4.8 9.2 - - + -
1400G GLU 3.3 8.1 - - - +
1401G GLY* 4.4 0.2 - - - -
1402G ARG 4.7 9.4 - - - +
1403G ILE* 5.8 2.5 - - + -
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Residues in contact with SER1351 (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 3.4 3.8 + - - -
1350G LEU* 1.3 75.7 + - - +
1352G VAL* 1.3 55.1 + - - +
1360G PRO* 5.8 2.2 - - - -
1362G LEU 3.3 9.6 + - - -
1363G LYS* 4.3 1.6 - - - -
1364G HIS* 3.8 13.3 + - - -
1398G MET* 3.2 5.5 - - - -
1399G PHE* 2.4 40.1 + - - -
1400G GLU* 3.0 25.4 + - - +
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Residues in contact with VAL1352 (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* 1.3 76.3 - - - +
1353G ARG* 1.3 62.6 + - - +
1354G TYR* 5.1 3.8 - - + +
1360G PRO* 3.4 5.1 - - - +
1361G VAL* 2.4 40.2 + - + -
1362G LEU* 3.2 40.3 + - + +
1387G SER* 4.6 6.7 - - - +
1391G ALA* 5.6 5.6 - - + -
1396G VAL* 3.7 22.0 - - + +
1397G ASP 3.3 25.4 - - - +
1398G MET* 4.3 3.8 - - + -
1399G PHE* 4.1 6.7 - - - +
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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