Contacts of the helix formed by residues 147 - 159 (chain 3) 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 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1443 ALA* 3.9 15.4 + - - +
1453 LYS 3.5 4.6 + - - -
1463 ASP* 1.3 79.4 - - - +
1483 PRO* 1.3 62.2 - - - +
1493 GLN* 2.8 20.6 + - - +
1503 ILE* 3.4 37.9 + - - +
1513 LEU* 3.6 17.8 + - - +
149K GLN* 3.6 10.7 + - - -
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Residues in contact with PRO 148 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1463 ASP 3.9 6.7 - - - +
1473 SER* 1.3 83.8 - - - +
1493 GLN* 1.3 73.3 + - - +
1503 ILE 3.4 0.2 - - - -
1513 LEU* 3.7 7.9 - - + +
1523 PHE* 3.0 29.6 + - - +
143Q PHE* 3.7 38.8 - - + +
150Q ILE* 4.2 11.8 - - + +
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Residues in contact with GLN 149 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1463 ASP 4.9 0.5 - - - +
1473 SER* 2.8 29.1 + - - +
1483 PRO* 1.3 93.0 - - - +
1503 ILE* 1.3 57.3 + - - +
1523 PHE* 3.5 4.6 + - - +
1533 MET* 3.2 36.0 + - + +
149K GLN* 3.7 26.6 + - + -
147Q SER* 3.5 22.5 + - - +
149Q GLN* 4.3 19.9 + - + +
150Q ILE* 4.0 24.4 - - + +
153Q MET* 4.5 6.5 - - + +
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Residues in contact with ILE 150 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1403 LYS 4.9 2.7 - - - +
1433 PHE* 4.5 10.8 - - + +
1443 ALA* 3.6 27.4 - - + -
1473 SER* 3.4 24.3 + - - +
1483 PRO 3.4 0.2 - - - -
1493 GLN* 1.3 74.3 - - - +
1513 LEU* 1.3 56.4 + - - +
1533 MET* 3.7 8.8 - - + -
1543 LEU* 2.8 42.4 + - + +
148K PRO* 4.2 33.0 - - + +
149K GLN* 4.1 18.8 - - + +
152K PHE* 4.4 26.9 - - + -
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Residues in contact with LEU 151 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363 LEU* 4.2 20.3 - - + +
393 PHE* 4.0 15.4 - - + -
833 PRO* 4.3 18.6 - - + -
1413 LEU* 3.8 28.7 - - + -
1443 ALA* 4.5 4.8 - - + +
1473 SER 3.6 11.8 + - - +
1483 PRO* 3.5 9.4 + - + +
1493 GLN 3.3 0.4 - - - -
1503 ILE* 1.3 76.2 - - - +
1523 PHE* 1.3 59.3 + - - +
1543 LEU* 3.5 7.0 + - - +
1553 ASP* 3.1 26.9 + - - +
143Q PHE* 4.0 25.1 - - + -
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Residues in contact with PHE 152 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363 LEU* 5.4 3.6 - - + -
1483 PRO 3.0 18.3 + - - +
1493 GLN* 3.6 6.3 - - - +
1513 LEU* 1.3 77.0 - - - +
1533 MET* 1.3 63.3 + - + +
1553 ASP* 3.5 12.0 - - + +
1563 LYS* 3.4 22.4 + - + +
140Q LYS* 4.6 26.2 - - + -
143Q PHE* 4.5 16.3 - + + -
150Q ILE* 4.4 20.6 - - + -
153Q MET* 3.9 42.8 - - + -
154Q LEU* 4.7 12.3 - - + -
157Q GLU* 3.3 32.5 - - + -
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Residues in contact with MET 153 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1493 GLN* 3.2 27.1 + - + +
1503 ILE* 3.9 10.3 - - + +
1523 PHE* 1.3 77.2 - - + +
1543 LEU* 1.3 64.4 - - - +
1563 LYS* 3.6 7.6 + - + +
1573 GLU* 3.4 25.1 + - - +
11723 AG 2.8 29.2 - - - -
149K GLN* 4.1 19.7 - - + +
152K PHE* 3.8 34.8 - - + -
153K MET* 3.9 16.2 - - + +
153Q MET* 4.0 15.0 - - + +
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Residues in contact with LEU 154 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393 PHE* 4.1 9.9 - - + -
1373 ILE* 4.8 13.9 - - + -
1403 LYS* 3.7 57.0 - - + +
1413 LEU* 4.3 20.0 - - + +
1443 ALA* 5.2 1.6 - - + -
1503 ILE* 2.8 29.1 + - + +
1513 LEU* 3.8 7.2 - - - +
1523 PHE 3.4 0.2 - - - -
1533 MET* 1.3 73.6 - - - +
1553 ASP* 1.3 65.1 + - - +
1573 GLU* 3.2 15.7 + - - +
1583 LEU* 3.1 36.8 + - + +
152K PHE* 4.8 6.0 - - + -
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Residues in contact with ASP 155 (chain 3).
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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353 GLY 4.6 1.9 - - - +
363 LEU* 3.2 24.9 - - + +
373 GLU* 3.8 7.1 + - - +
383 GLY* 2.8 40.2 + - - -
393 PHE* 3.2 24.6 + - + +
1513 LEU 3.1 13.5 + - - +
1523 PHE* 3.5 15.8 - - + +
1533 MET 3.3 0.2 - - - -
1543 LEU* 1.3 76.7 - - - +
1563 LYS* 1.3 55.7 + - - +
1583 LEU 3.4 1.0 + - - -
1593 SER* 3.1 23.7 + - - -
140Q LYS* 5.8 3.3 + - - -
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Residues in contact with LYS 156 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1523 PHE* 3.4 12.7 + - + +
1533 MET* 3.9 10.1 - - - +
1543 LEU 3.3 0.6 - - - -
1553 ASP* 1.3 76.9 - - - +
1573 GLU* 1.3 64.7 + - + +
1593 SER* 2.6 25.9 + - - +
1603 ALA* 4.0 2.9 + - - +
156K LYS* 5.1 11.9 - - - +
156Q LYS* 5.4 9.9 - - - +
157Q GLU* 4.8 20.1 - - + +
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Residues in contact with GLU 157 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1403 LYS* 3.7 21.3 + - - -
1533 MET 3.4 10.6 + - - +
1543 LEU* 3.2 16.8 + - + +
1563 LYS* 1.3 78.7 - - + +
1583 LEU* 1.3 66.9 + - + +
1603 ALA* 3.5 19.2 - - - +
152K PHE* 3.3 29.6 - - + -
156K LYS* 4.6 25.7 - - + +
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Residues in contact with LEU 158 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383 GLY 3.5 17.6 - - - +
393 PHE* 3.6 45.8 - - + -
423 TRP* 3.6 29.9 - - + +
873 PHE* 5.0 1.3 - - + -
1373 ILE* 3.8 33.2 - - + -
1543 LEU* 3.1 22.0 + - + +
1553 ASP 4.0 3.1 - - - +
1573 GLU* 1.3 77.3 - - + +
1593 SER* 1.3 56.5 + - - +
1603 ALA 3.0 5.8 - - - -
1613 ARG* 3.1 28.7 + - - +
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Residues in contact with SER 159 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383 GLY* 3.8 17.3 - - - -
413 ASN* 5.2 10.2 + - - -
1553 ASP* 3.1 14.8 + - - -
1563 LYS* 2.6 28.0 + - - +
1583 LEU* 1.3 74.1 - - - +
1603 ALA* 1.3 62.5 + - - +
1613 ARG 3.2 8.3 + - - +
1623 ALA* 5.0 4.7 - - - +
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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