Contacts of the helix formed by residues 1487 - 1496 (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 SER1487 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1459H GLU* 2.7 23.8 + - - -
1483H TYR* 3.0 34.0 + - - +
1485H HIS 3.9 0.6 - - - -
1486H THR* 1.3 73.2 + - - +
1488H VAL* 1.3 61.7 + - - +
1490H ILE* 2.9 33.1 + - - +
1491H LEU 3.3 13.2 + - - -
1521H TYR* 3.9 14.9 - - - +
1522H VAL* 5.2 1.4 - - - +
2407H TRS 3.5 5.4 - - - -
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Residues in contact with VAL1488 (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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1282G ALA* 3.6 22.4 - - + +
1285G HIS* 4.3 8.5 - - + -
1286G THR* 3.6 24.9 - - + +
1316G PHE* 3.9 26.9 - - + -
1317G ARG* 3.9 9.2 - - - +
1486H THR 3.4 2.2 + - - -
1487H SER* 1.3 74.0 - - - +
1489H ALA* 1.3 51.5 + - - +
1491H LEU* 3.1 9.1 + - + +
1492H ASP* 2.8 42.1 + - - +
1521H TYR* 3.7 32.5 - - + +
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Residues in contact with ALA1489 (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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1215G PRO* 4.1 10.5 - - + -
1216G ASN* 3.0 12.4 + - - +
1282G ALA* 3.4 17.4 - - + +
1283G TYR* 3.8 25.1 - - + +
1286G THR* 5.5 0.4 - - - +
1459H GLU* 3.7 17.5 + - - +
1463H VAL* 3.9 11.5 - - + +
1487H SER* 3.1 0.6 - - - +
1488H VAL* 1.3 77.8 - - - +
1490H ILE* 1.3 57.7 + - - +
1492H ASP 3.4 0.3 + - - -
1493H ALA* 2.9 24.9 + - - +
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Residues in contact with ILE1490 (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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1459H GLU* 4.2 5.8 - - + +
1462H LEU* 4.0 31.6 - - + -
1463H VAL* 4.0 17.3 - - + -
1466H ILE* 3.9 16.4 - - + -
1478H ILE* 4.3 9.0 - - + -
1480H PRO* 5.2 4.9 - - + -
1483H TYR* 3.9 25.4 - - + +
1487H SER* 2.9 26.1 + - - +
1489H ALA* 1.3 73.7 - - - +
1491H LEU* 1.4 66.6 + - - +
1493H ALA* 3.2 6.4 + - - +
1494H LEU* 2.9 30.3 + - + +
1522H VAL* 4.1 20.4 - - + -
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Residues in contact with LEU1491 (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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1316G PHE* 4.0 27.6 - - + -
1317G ARG* 4.5 7.0 - - - +
1487H SER 3.3 10.1 + - - +
1488H VAL* 3.1 11.5 + - - +
1490H ILE* 1.4 78.6 - - - +
1492H ASP* 1.3 59.0 + - - +
1494H LEU* 3.2 6.6 + - - -
1495H ASN* 2.9 37.7 + - - +
1521H TYR* 3.5 36.6 - - + +
1522H VAL* 4.6 4.8 - - - +
1524H GLN* 4.1 13.9 - - + +
1525H ARG* 3.4 34.8 - - + +
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Residues in contact with ASP1492 (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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1216G ASN* 3.3 21.0 + - + +
1228G TYR* 5.8 0.2 + - - -
1282G ALA* 3.3 15.4 + - - +
1317G ARG* 2.8 32.4 + - - -
1360G CA2 2.5 38.8 + - + +
1488H VAL 2.8 18.3 + - - +
1489H ALA 4.3 0.2 - - - -
1491H LEU* 1.3 76.4 - - - +
1493H ALA* 1.3 61.6 + - - +
1495H ASN* 3.4 11.2 + - - +
1496H THR* 3.2 24.4 + - - +
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Residues in contact with ALA1493 (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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1216G ASN* 3.2 22.8 - - - +
1463H VAL* 4.2 8.7 - - + -
1466H ILE* 3.6 34.0 - - + +
1467H HIS* 4.2 5.6 - - - +
1489H ALA 2.9 13.6 + - - +
1490H ILE* 3.2 8.7 + - - +
1492H ASP* 1.3 77.2 - - - +
1494H LEU* 1.4 59.6 + - - +
1496H THR* 2.6 26.3 + - - -
1497H CYS* 3.8 1.4 - - - -
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Residues in contact with LEU1494 (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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1466H ILE* 3.9 18.6 - - + -
1476H ILE* 3.7 33.7 - - + -
1478H ILE* 4.5 7.0 - - + -
1490H ILE* 2.9 28.9 + - + +
1491H LEU* 3.7 5.4 - - - +
1493H ALA* 1.4 76.5 - - - +
1495H ASN* 1.3 57.6 + - - +
1497H CYS* 3.0 26.2 + - - +
1502H VAL* 4.1 23.3 - - + -
1522H VAL* 3.7 33.7 - - + +
1525H ARG* 3.4 27.2 + - + -
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Residues in contact with ASN1495 (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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1223G ARG* 2.9 37.0 + - - +
1317G ARG* 4.3 7.3 - - - +
1491H LEU* 2.9 31.9 + - - +
1492H ASP* 3.5 20.3 + - - +
1493H ALA 3.2 0.2 - - - -
1494H LEU* 1.3 76.5 - - - +
1496H THR* 1.3 58.4 + - + +
1497H CYS 3.1 1.3 + - - -
1498H ASP* 4.1 3.1 + - - +
1524H GLN 5.4 0.5 - - - +
1525H ARG* 3.5 30.6 + - - +
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Residues in contact with THR1496 (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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1216G ASN* 4.6 5.4 - - + +
1219G LEU* 3.8 21.3 - - + +
1223G ARG* 3.5 19.9 - - - +
1360G CA2 4.4 17.5 - - + -
1467H HIS* 4.2 3.3 - - - -
1470H ARG* 2.8 42.9 + - - -
1492H ASP 3.2 17.0 - - - +
1493H ALA* 2.6 19.7 + - - +
1495H ASN* 1.3 75.8 - - + +
1497H CYS* 1.3 56.4 + - - +
1498H ASP* 3.0 15.9 + - - +
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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