Contacts of the helix formed by residues 1447 - 1458 (chain B) in PDB entry 5XA0
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 TRP1447 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1406B VAL* 5.3 14.3 - - + +
1446B MET* 1.3 77.9 - - + +
1448B LYS* 1.3 64.2 + - - +
1449B LEU 3.4 2.5 - - - -
1450B PHE* 3.4 11.1 + - + +
1451B GLU* 3.1 23.4 + - - +
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Residues in contact with LYS1448 (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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1402B LEU* 5.6 6.2 - - + +
1406B VAL* 5.9 3.4 - - - -
1428B HIS* 4.3 6.7 - - - +
1431B VAL* 4.6 20.4 - - + -
1445B HIS* 4.6 18.3 - - + +
1446B MET 3.8 1.8 - - - +
1447B TRP* 1.3 74.4 - - - +
1449B LEU* 1.3 60.9 + - - +
1451B GLU* 3.5 5.8 + - - +
1452B ASN* 3.0 29.0 + - - +
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Residues in contact with LEU1449 (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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1446B MET 5.3 3.7 + - - +
1447B TRP 3.4 0.8 - - - +
1448B LYS* 1.3 77.4 - - - +
1450B PHE* 1.3 58.1 + - - +
1452B ASN* 3.4 6.3 + - - +
1453B PHE* 2.9 32.0 + - - +
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Residues in contact with PHE1450 (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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1446B MET 5.4 1.5 + - - +
1447B TRP* 3.4 16.6 + - + +
1448B LYS 3.3 0.6 - - - -
1449B LEU* 1.3 76.1 - - - +
1451B GLU* 1.3 62.3 + - - +
1453B PHE* 4.6 4.3 - - - -
1454B LEU* 2.8 30.7 + - - +
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Residues in contact with GLU1451 (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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1406B VAL* 5.8 8.1 - - + -
1428B HIS* 4.8 2.9 - - + -
1447B TRP 3.1 17.2 + - - +
1448B LYS* 3.9 5.6 - - - +
1450B PHE* 1.3 75.0 - - - +
1452B ASN* 1.3 58.1 + - - +
1454B LEU* 3.3 7.8 + - - +
1455B VAL* 2.9 29.7 + - - +
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Residues in contact with ASN1452 (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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1428B HIS* 2.9 39.0 - - + +
1448B LYS 3.0 15.4 + - - +
1449B LEU* 3.6 8.3 - - - +
1450B PHE 3.3 0.2 - - - -
1451B GLU* 1.3 77.5 - - - +
1453B PHE* 1.3 56.9 + - - +
1455B VAL* 3.4 4.9 + - - +
1456B ASP* 2.8 29.8 + - - +
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Residues in contact with PHE1453 (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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1449B LEU 2.9 17.7 + - - +
1450B PHE* 4.2 3.8 - - - +
1452B ASN* 1.3 71.5 - - - +
1454B LEU* 1.3 61.9 + - - +
1456B ASP* 4.4 6.3 - - - +
1457B ILE* 2.8 36.5 + - + +
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Residues in contact with LEU1454 (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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1450B PHE 2.8 21.3 + - - +
1451B GLU* 3.3 8.5 - - - +
1453B PHE* 1.3 75.7 - - - +
1455B VAL* 1.3 50.3 + - - +
1457B ILE* 4.8 0.9 - - - -
1458B CYS* 2.2 42.1 + - - -
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Residues in contact with VAL1455 (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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1421B ALA* 5.4 8.3 - - + -
1425B PHE* 4.3 26.7 - - + -
1451B GLU 2.9 16.9 + - - +
1452B ASN* 3.7 7.0 - - - +
1453B PHE 3.3 0.2 - - - -
1454B LEU* 1.3 76.1 - - - +
1456B ASP* 1.3 58.0 + - - +
1458B CYS* 2.9 23.6 - - - +
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Residues in contact with ASP1456 (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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1452B ASN 2.8 20.6 + - - +
1453B PHE* 4.5 4.5 - - - -
1455B VAL* 1.3 73.6 - - - +
1457B ILE* 1.3 65.5 - - - +
1458B CYS* 3.8 2.4 - - - +
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Residues in contact with ILE1457 (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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1453B PHE* 2.8 25.4 + - + +
1454B LEU* 4.1 1.3 - - - +
1456B ASP* 1.3 74.9 - - - +
1458B CYS* 1.3 73.6 + - - +
1459B ARG* 3.6 1.6 + - - +
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Residues in contact with CYS1458 (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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1454B LEU* 2.2 30.4 + - - +
1455B VAL* 2.9 21.5 - - - +
1456B ASP 3.8 2.9 - - - +
1457B ILE* 1.3 76.4 - - - +
1459B ARG* 1.3 73.0 + - - +
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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