Contacts of the helix formed by residues 147 - 159 (chain 6) in PDB entry 2X17
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 SER 147 (chain 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1436 PHE 5.6 0.2 - - - -
1446 ALA* 3.9 16.5 - - - +
1456 LYS 3.3 5.6 + - - -
1466 ASP* 1.3 78.6 - - - +
1486 PRO* 1.3 62.8 - - - +
1496 GLN* 2.9 16.5 + - - -
1506 ILE* 3.4 31.1 + - - +
1516 LEU* 3.5 17.2 + - - +
149N GLN* 3.4 19.6 + - - +
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Residues in contact with PRO 148 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1466 ASP 3.9 7.2 - - - +
1476 SER* 1.3 84.4 - - - +
1496 GLN* 1.3 76.6 + - - +
1506 ILE 3.4 0.2 - - - -
1516 LEU* 3.7 10.0 - - + +
1526 PHE* 3.1 23.9 + - - +
143M PHE* 3.6 35.6 - - + +
150M ILE* 4.1 11.2 - - + +
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Residues in contact with GLN 149 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1476 SER* 2.9 22.2 + - - +
1486 PRO* 1.3 91.0 - - - +
1506 ILE* 1.3 60.7 + - + +
1526 PHE* 3.4 5.9 + - - +
1536 MET* 3.2 29.8 + - + +
147M SER* 3.3 24.3 + - - +
149M GLN* 3.6 23.9 + - + +
150M ILE* 3.8 24.9 - - + +
153M MET* 4.1 7.2 - - + +
149N GLN* 4.3 20.7 + - + -
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Residues in contact with ILE 150 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1406 LYS 5.0 2.0 - - - +
1436 PHE* 4.4 15.5 - - + +
1446 ALA* 3.6 24.5 - - + -
1476 SER* 3.4 25.7 + - - +
1486 PRO 3.4 0.2 - - - -
1496 GLN* 1.3 73.0 - - - +
1516 LEU* 1.3 56.1 + - - +
1526 PHE 3.2 0.4 - - - -
1536 MET* 3.2 10.7 + - + -
1546 LEU* 2.8 39.8 + - + +
148N PRO* 4.0 21.5 - - + +
149N GLN* 3.9 26.5 - - + +
152N PHE* 4.0 32.3 - - + -
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Residues in contact with LEU 151 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366 LEU* 4.3 18.5 - - + +
396 PHE* 4.0 14.9 - - + -
836 PRO* 4.4 19.3 - - + -
1416 LEU* 3.8 28.5 - - + -
1446 ALA* 4.5 6.8 - - + +
1476 SER 3.5 11.9 + - - +
1486 PRO* 3.5 11.4 + - + +
1506 ILE* 1.3 77.4 - - - +
1526 PHE* 1.3 55.7 - - - +
1546 LEU* 3.6 7.2 + - - +
1556 ASP* 3.1 26.7 + - - +
143M PHE* 3.8 24.7 - - + -
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Residues in contact with PHE 152 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366 LEU* 5.5 2.0 - - - -
1486 PRO 3.1 13.9 + - - +
1496 GLN* 3.5 9.9 - - - +
1506 ILE 3.2 0.2 - - - -
1516 LEU* 1.3 77.2 - - - +
1536 MET* 1.3 61.8 + - + +
1556 ASP* 3.4 11.5 + - + +
1566 LYS* 3.4 21.8 + - + +
140M LYS* 4.4 29.4 - - + -
143M PHE* 4.5 15.2 - + + -
150M ILE* 4.1 19.5 - - + -
153M MET* 3.7 44.4 - - + -
154M LEU* 4.4 15.0 - - + -
157M GLU* 3.6 33.0 - - - -
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Residues in contact with MET 153 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1496 GLN* 3.2 20.1 + - + +
1506 ILE* 3.2 15.8 + - + +
1526 PHE* 1.3 78.6 - - + +
1546 LEU* 1.3 63.8 + - - +
1566 LYS* 3.3 9.3 + - + +
1576 GLU* 3.2 26.2 + - - +
11736 AG 3.0 25.1 - - - -
153M MET* 3.7 20.4 - - + +
149N GLN* 4.3 11.2 - - + +
152N PHE* 3.7 33.4 - - + -
153N MET* 3.7 24.7 - - + +
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Residues in contact with LEU 154 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396 PHE* 4.0 10.5 - - + -
1376 ILE* 4.7 15.3 - - + -
1406 LYS* 3.8 55.6 - - + +
1416 LEU* 4.4 17.7 - - + -
1446 ALA* 4.9 1.8 - - + -
1506 ILE* 2.8 30.9 + - + +
1516 LEU* 3.8 7.6 - - - +
1536 MET* 1.3 69.2 - - - +
1556 ASP* 1.3 64.6 + - - +
1576 GLU* 3.4 13.9 + - - +
1586 LEU* 3.2 38.6 + - + +
152N PHE* 4.4 12.3 - - + -
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Residues in contact with ASP 155 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356 GLY 4.7 2.3 - - - +
366 LEU* 3.2 26.3 - - + -
376 GLU* 3.8 6.8 + - - +
386 GLY* 2.9 50.0 + - - -
396 PHE* 3.2 24.4 + - + +
1516 LEU 3.1 15.0 + - - +
1526 PHE* 3.4 16.1 - - + +
1546 LEU* 1.3 78.0 - - - +
1566 LYS* 1.3 59.4 - - - +
1586 LEU 3.7 0.2 + - - -
1596 SER* 3.4 7.8 + - - -
140M LYS* 5.4 7.6 + - - -
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Residues in contact with LYS 156 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1526 PHE* 3.4 10.6 + - + +
1536 MET* 3.3 12.7 + - + +
1546 LEU 3.3 0.8 - - - -
1556 ASP* 1.3 79.6 + - - +
1576 GLU* 1.3 62.1 + - + +
1596 SER* 2.6 25.8 + - - +
1606 ALA* 4.3 1.6 + - - +
156M LYS* 5.1 15.4 - - - +
157M GLU* 3.8 31.3 - - - +
156N LYS* 6.0 2.2 - - - +
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Residues in contact with GLU 157 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1406 LYS* 3.8 21.7 + - - -
1536 MET 3.2 12.0 + - - +
1546 LEU* 3.8 13.2 - - + +
1556 ASP 3.4 0.4 - - - -
1566 LYS* 1.3 77.5 - - + +
1586 LEU* 1.3 64.1 + - + +
1596 SER 3.4 0.5 + - - -
1606 ALA* 3.5 19.9 + - - +
152N PHE* 3.7 28.1 - - + -
156N LYS* 4.3 30.4 - - + +
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Residues in contact with LEU 158 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386 GLY 3.5 20.3 - - - +
396 PHE* 3.6 42.6 - - + -
426 TRP* 3.7 28.4 - - + +
876 PHE* 5.0 1.1 - - + -
1376 ILE* 3.8 33.7 - - + -
1546 LEU* 3.2 24.2 + - + +
1556 ASP 4.4 0.2 - - - +
1566 LYS 3.4 0.2 - - - -
1576 GLU* 1.3 75.4 - - + +
1596 SER* 1.3 59.4 + - - +
1606 ALA 3.1 5.8 - - - -
1616 ARG* 3.2 25.0 + - - +
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Residues in contact with SER 159 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376 GLU 5.4 0.4 - - - -
386 GLY* 3.9 14.6 - - - -
416 ASN* 5.3 9.2 + - - -
1556 ASP 3.4 12.8 + - - -
1566 LYS* 2.6 28.1 + - - +
1576 GLU 3.2 0.2 - - - -
1586 LEU* 1.3 74.7 - - - +
1606 ALA* 1.3 62.5 + - - +
1616 ARG 3.2 9.2 + - - +
1626 ALA* 4.7 5.5 - - - +
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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