Contacts of the strand formed by residues 1409 - 1413 (chain H) in PDB entry 2BT4
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 ILE1409 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1404H LEU* 4.2 20.4 - - + -
1408H PRO* 1.4 71.0 - - - +
1410H MET* 1.3 72.2 + - - +
1411H ILE* 3.6 13.7 + - + -
1444H ALA* 4.3 6.7 - - + -
1450H THR 2.9 18.2 + - - +
1451H VAL* 3.3 6.0 - - + +
1452H ASP 2.9 23.1 + - - -
1473H HIS* 4.2 0.4 - - - -
1474H CYS* 3.6 20.0 - - - -
1475H GLY 3.8 13.2 - - - +
1477H VAL* 4.1 15.5 - - + -
1542H VAL* 3.8 30.7 - - + +
1545H ILE* 4.0 17.9 - - + -
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Residues in contact with MET1410 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1408H PRO 3.7 3.6 + - - -
1409H ILE* 1.3 71.4 - - - +
1411H ILE* 1.3 61.3 + - - +
1412H LEU* 3.7 22.7 - - + -
1452H ASP* 3.5 18.4 - - - +
1454H ARG* 3.5 41.7 - - - +
1465H TRP* 3.5 24.2 - - + +
1468H GLU* 4.3 2.5 - - + -
1469H ALA* 3.7 18.8 - - + +
1473H HIS* 3.5 31.9 - - + -
1475H GLY 2.9 14.9 + - - +
1476H ILE* 3.3 5.9 - - + +
1477H VAL 2.9 25.6 + - - +
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Residues in contact with ILE1411 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1409H ILE* 4.0 9.9 - - + +
1410H MET* 1.3 76.8 - - - +
1412H LEU* 1.3 62.6 + - - +
1413H ASN* 3.8 4.4 + - - +
1440H CYS* 3.6 25.4 - - + -
1451H VAL* 3.7 27.6 - - + -
1452H ASP 2.9 11.2 + - - +
1453H PHE* 3.4 28.2 - - + -
1454H ARG* 2.9 28.2 + - - +
1477H VAL* 3.2 18.8 - - + +
1538H TYR* 4.0 20.9 - - + -
1542H VAL* 4.0 15.3 - - + -
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Residues in contact with LEU1412 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1410H MET* 3.7 28.7 - - + -
1411H ILE* 1.3 79.4 - - - +
1413H ASN* 1.3 63.2 + - - +
1454H ARG* 3.7 8.5 - - + -
1462H LEU* 4.4 11.2 - - + +
1465H TRP* 3.8 35.2 - - + -
1466H ILE* 3.7 38.6 - - + +
1476H ILE* 4.2 15.3 - - + -
1477H VAL 2.9 7.4 + - - +
1478H ILE* 3.3 20.4 - - + +
1479H ASN 3.0 25.3 + - - +
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Residues in contact with ASN1413 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1411H ILE* 3.8 6.3 + - - +
1412H LEU* 1.3 79.9 - - - +
1414H GLY* 1.3 59.1 + - - +
1417H LEU* 3.8 10.3 - - + +
1433H LEU* 4.1 6.9 - - + +
1453H PHE* 3.3 33.0 - - - -
1454H ARG 2.9 25.2 + - - +
1455H GLN* 3.3 14.7 - - + -
1456H SER 3.0 27.4 + - - +
1462H LEU* 3.7 8.4 - - - +
1479H ASN* 3.5 4.3 - - - +
1538H TYR* 2.8 36.6 + - - -
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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