Contacts of the helix formed by residues 1552 - 1561 (chain B) in PDB entry 1PXX
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 GLY1552 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A MET* 3.5 18.4 - - - -
1547B PRO* 2.8 29.7 + - - +
1551B GLY* 1.3 78.6 - - - +
1553B GLU* 1.3 61.1 + - - -
1554B VAL 3.1 3.1 - - - -
1555B GLY 3.4 0.7 + - - -
1556B PHE* 3.0 24.9 + - - +
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Residues in contact with GLU1553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1547B PRO* 3.0 27.2 - - + +
1552B GLY* 1.3 70.3 - - - -
1554B VAL* 1.3 62.2 + - + +
1556B PHE* 3.6 23.3 - - - +
1557B LYS* 3.1 28.1 + - - +
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Residues in contact with VAL1554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1315B ILE* 3.7 28.5 - - + -
1316B LEU* 5.9 1.1 - - + -
1319B GLU* 3.2 39.7 - - + +
1551B GLY 5.3 3.8 - - - +
1552B GLY 3.1 0.8 - - - -
1553B GLU* 1.3 78.2 - - + +
1555B GLY* 1.3 64.2 + - - +
1557B LYS* 3.5 6.5 + - - +
1558B ILE* 3.2 25.7 + - + +
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Residues in contact with GLY1555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1316B LEU* 4.9 4.4 - - - +
1335B ILE* 3.8 15.3 - - - +
1550B PHE* 3.1 26.5 + - - -
1551B GLY 4.7 2.2 + - - -
1552B GLY 3.4 4.2 + - - -
1554B VAL* 1.3 76.4 - - - +
1556B PHE* 1.3 66.3 + - - +
1558B ILE* 3.1 24.0 + - - +
1559B ILE* 3.5 8.8 + - - +
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Residues in contact with PHE1556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1364B GLU* 5.6 2.5 - - - -
1545B TRP* 3.5 47.1 - + - -
1546B LYS* 4.1 10.8 - - - -
1547B PRO* 4.0 21.8 - - + -
1550B PHE* 3.0 44.6 - + - +
1552B GLY 3.0 18.0 + - - +
1553B GLU* 3.6 23.3 - - - +
1555B GLY* 1.3 75.1 - - - +
1557B LYS* 1.3 61.4 + - - +
1559B ILE* 3.2 8.7 + - + +
1560B ASN* 3.1 42.0 + - - -
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Residues in contact with LYS1557 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1553B GLU* 3.1 19.7 + - - +
1554B VAL* 3.6 7.6 - - - +
1555B GLY 3.2 0.2 - - - -
1556B PHE* 1.3 74.6 - - - +
1558B ILE* 1.3 66.0 + - + +
1560B ASN* 4.4 6.1 - - + +
1561B THR* 2.9 48.3 + - + +
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Residues in contact with ILE1558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1308B GLU* 4.4 1.8 - - - +
1311B ARG* 4.8 8.1 - - - +
1312B VAL* 4.0 24.5 - - + -
1315B ILE* 3.8 39.3 - - + -
1316B LEU* 6.0 0.2 - - + -
1335B ILE* 3.6 10.5 - - + -
1339B GLU* 3.5 27.8 - - - +
1554B VAL* 3.2 16.6 - - + +
1555B GLY* 3.1 14.3 + - - +
1557B LYS* 1.3 79.3 - - + +
1559B ILE* 1.3 61.5 + - - +
1561B THR* 3.5 6.7 + - - -
1562B ALA* 3.2 21.5 + - - +
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Residues in contact with ILE1559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1335B ILE* 3.7 23.6 - - + +
1338B GLY* 3.4 37.5 - - - +
1339B GLU* 4.1 7.6 - - - -
1342B LYS* 3.4 14.7 - - - +
1361B PHE* 4.3 4.7 - - + -
1545B TRP* 4.1 20.6 - - + -
1550B PHE* 3.7 45.1 - - + -
1555B GLY 3.8 10.5 - - - +
1556B PHE* 3.3 6.5 - - + +
1557B LYS 3.1 0.4 - - - -
1558B ILE* 1.3 72.9 - - - +
1560B ASN* 1.3 61.7 + - - +
1561B THR 3.0 10.1 + - - -
1562B ALA* 3.2 10.9 + - - +
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Residues in contact with ASN1560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1342B LYS* 3.5 22.0 + - - +
1361B PHE* 4.8 9.0 - - - +
1545B TRP* 3.5 21.9 - - - -
1556B PHE* 3.1 55.3 + - - +
1557B LYS* 3.3 7.3 + - + +
1559B ILE* 1.3 80.8 - - - +
1561B THR* 1.3 61.7 + - + +
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Residues in contact with THR1561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1342B LYS* 4.5 0.9 - - - +
1557B LYS* 2.9 48.6 + - + +
1558B ILE* 3.5 7.3 + - - -
1560B ASN* 1.3 81.7 - - + +
1562B ALA* 1.3 68.8 + - - +
1563B SER* 3.5 4.9 + - - -
1566B SER* 4.0 8.4 + - - -
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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