Contacts of the helix formed by residues 1521 - 1525 (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 TYR1521 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1286G THR* 5.4 2.6 - - + +
1316G PHE* 3.9 30.9 - + + +
1484H SER 2.9 9.2 + - - +
1485H HIS 3.3 31.2 - - - -
1486H THR* 4.0 11.4 - - - -
1487H SER 3.9 26.7 - - - +
1488H VAL* 3.7 26.8 - - + +
1491H LEU* 3.5 25.0 - - + +
1519H HIS* 3.8 20.0 - + - -
1520H SER* 1.3 73.2 - - - +
1522H VAL* 1.3 63.7 + - + +
1524H GLN* 3.0 31.2 + - - +
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Residues in contact with VAL1522 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1478H ILE* 4.4 4.7 - - + -
1480H PRO* 3.7 27.6 - - + -
1483H TYR 4.8 2.5 - - - +
1484H SER* 4.4 7.2 - - - +
1487H SER 5.2 0.7 - - - +
1490H ILE* 4.1 22.9 - - + -
1491H LEU* 4.7 8.7 - - - +
1494H LEU* 3.7 21.1 - - + -
1504H GLU* 3.7 26.5 - - + +
1520H SER* 2.9 10.3 + - - +
1521H TYR* 1.3 80.1 - - + +
1523H SER* 1.3 58.5 + - - +
1525H ARG* 3.0 6.4 + - - +
1526H ALA* 2.9 27.0 + - + -
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Residues in contact with SER1523 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1109F ASN* 3.0 24.1 + - - -
1111F HIS* 3.9 25.6 + - - +
1112F GLN* 3.6 4.0 + - - +
1504H GLU* 2.6 26.3 + - - -
1506H HIS* 5.3 0.2 + - - -
1520H SER* 3.2 19.6 + - - -
1521H TYR 3.2 0.4 - - - -
1522H VAL* 1.3 77.6 - - - +
1524H GLN* 1.3 59.6 + - - +
1525H ARG 3.2 1.1 + - - -
1526H ALA 3.9 2.1 - - - +
1529H VAL* 3.4 23.2 - - - +
2411H GOL 4.2 2.2 + - - -
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Residues in contact with GLN1524 (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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1111F HIS 4.7 11.7 - - - +
1112F GLN* 3.3 22.4 + - - +
1314G GLU* 5.0 6.1 - - - +
1316G PHE* 3.3 34.6 - - - -
1491H LEU* 4.1 11.4 - - + +
1495H ASN* 5.4 0.9 - - - +
1519H HIS* 3.4 23.4 + - - -
1520H SER 4.0 7.9 - - - +
1521H TYR* 3.2 22.6 - - - +
1522H VAL 3.0 0.8 + - - -
1523H SER* 1.3 77.4 - - - +
1525H ARG* 1.3 56.5 + - - +
2411H GOL 5.0 3.7 - - - -
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Residues in contact with ARG1525 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1112F GLN* 3.6 5.7 + - - +
1491H LEU* 3.4 24.4 - - + +
1494H LEU* 3.4 33.4 + - + -
1495H ASN* 3.5 24.4 + - - +
1497H CYS 2.9 23.4 + - - -
1498H ASP* 4.9 0.8 - - - +
1499H GLY 4.4 4.0 - - - +
1500H LEU 2.8 24.7 + - - +
1502H VAL* 3.8 14.9 - - + +
1522H VAL 3.0 4.2 + - - +
1524H GLN* 1.3 77.8 - - - +
1526H ALA* 1.3 69.4 + - - +
1527H ASP* 3.0 28.9 + - - +
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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