Contacts of the helix formed by residues 147 - 159 (chain 0) 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 0).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1440 ALA* 3.9 16.8 + - - +
1450 LYS 3.4 4.2 + - - -
1460 ASP* 1.3 78.1 - - - +
1480 PRO* 1.3 62.2 - - - +
1490 GLN* 3.2 18.3 + - - +
1500 ILE* 3.4 36.8 + - - +
1510 LEU* 3.6 18.5 + - - +
149H GLN* 3.7 10.8 + - - -
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Residues in contact with PRO 148 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1460 ASP 3.4 11.9 - - - +
1470 SER* 1.3 83.3 - - - +
1490 GLN* 1.3 79.7 + - - +
1500 ILE 3.3 0.2 - - - -
1510 LEU* 3.9 8.9 - - + +
1520 PHE* 3.1 24.3 + - - +
143G PHE* 3.9 32.8 - - + +
150G ILE* 4.2 12.0 - - + +
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Residues in contact with GLN 149 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1460 ASP 5.2 0.2 - - - +
1470 SER* 3.2 19.2 + - - +
1480 PRO* 1.3 96.5 - - - +
1500 ILE* 1.3 60.8 + - - +
1520 PHE* 3.5 5.2 - - - +
1530 MET* 3.4 29.0 + - + +
146G ASP 5.5 0.4 + - - -
147G SER* 3.5 24.6 + - - +
149G GLN* 4.4 19.2 + - + +
150G ILE* 3.9 25.8 - - + +
153G MET* 4.2 8.1 - - + +
149H GLN* 4.4 21.5 + - + +
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Residues in contact with ILE 150 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1400 LYS* 4.9 1.3 - - + +
1430 PHE* 4.5 10.8 - - + +
1440 ALA* 3.6 26.9 - - + -
1470 SER* 3.4 24.9 + - - +
1480 PRO 3.3 0.2 - - - -
1490 GLN* 1.3 72.9 - - - +
1510 LEU* 1.3 55.7 + - - +
1520 PHE 3.1 1.6 - - - -
1530 MET* 3.0 11.6 + - + +
1540 LEU* 2.8 41.7 + - + +
148H PRO* 4.2 20.9 - - + +
149H GLN* 4.1 31.2 - - + +
152H PHE* 4.3 28.0 - - + -
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Residues in contact with LEU 151 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360 LEU* 4.4 15.7 - - + +
390 PHE* 3.9 16.6 - - + -
830 PRO* 4.3 24.9 - - + -
1410 LEU* 3.8 28.7 - - + -
1440 ALA* 4.7 5.2 - - + +
1470 SER 3.6 15.3 + - - +
1480 PRO* 3.9 6.7 - - + +
1490 GLN 3.5 0.2 - - - -
1500 ILE* 1.3 77.7 - - - +
1520 PHE* 1.3 60.5 + - - +
1540 LEU* 3.6 8.1 + - - +
1550 ASP* 3.2 22.5 + - - +
143G PHE* 4.0 23.6 - - + -
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Residues in contact with PHE 152 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360 LEU* 5.6 1.3 - - - -
1480 PRO 3.1 18.7 + - - +
1490 GLN* 3.5 6.3 - - - +
1510 LEU* 1.3 77.0 - - - +
1530 MET* 1.3 64.5 + - + +
1550 ASP* 3.4 21.4 + - + +
1560 LYS* 3.5 10.8 + - + +
140G LYS* 4.5 26.0 - - + -
143G PHE* 4.6 17.0 - + + -
150G ILE* 4.3 22.2 - - + -
153G MET* 3.9 42.2 - - + -
154G LEU* 4.8 10.3 - - + -
157G GLU* 3.7 34.8 - - + -
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Residues in contact with MET 153 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1490 GLN* 3.4 19.9 + - + +
1500 ILE* 3.0 18.8 + - + +
1520 PHE* 1.3 76.7 - - + +
1540 LEU* 1.3 64.4 + - - +
1560 LYS* 3.3 9.3 + - - +
1570 GLU* 3.2 25.8 + - - +
153G MET* 3.9 18.2 - - + +
1173G AG 2.9 27.8 - - - -
149H GLN* 4.3 12.1 - - + +
152H PHE* 3.9 31.4 - - + -
153H MET* 4.0 19.3 - - + +
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Residues in contact with LEU 154 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390 PHE* 4.0 10.1 - - + -
1370 ILE* 4.8 13.7 - - + +
1400 LYS* 3.8 54.3 - - + +
1410 LEU* 4.1 22.7 - - + -
1440 ALA* 5.5 0.9 - - + -
1500 ILE* 2.8 27.9 + - + +
1510 LEU* 3.7 9.4 - - - +
1530 MET* 1.3 71.2 - - - +
1550 ASP* 1.3 64.0 + - - +
1570 GLU* 3.3 14.1 + - - +
1580 LEU* 3.1 39.0 + - + +
152H PHE* 4.7 11.4 - - + -
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Residues in contact with ASP 155 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350 GLY 4.9 1.6 - - - +
360 LEU* 3.3 20.7 - - + -
370 GLU* 3.8 8.8 + - - +
380 GLY* 2.9 40.3 + - - -
390 PHE* 3.2 27.4 + - + -
1510 LEU 3.2 14.1 + - - +
1520 PHE* 3.4 14.7 - - + +
1530 MET 3.3 0.4 - - - -
1540 LEU* 1.3 75.3 - - - +
1560 LYS* 1.3 58.4 + - - +
1580 LEU* 4.9 0.2 - - - -
1590 SER* 3.1 22.5 + - - -
140G LYS* 5.8 3.8 + - - -
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Residues in contact with LYS 156 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1520 PHE* 3.5 11.4 + - + +
1530 MET* 3.3 12.9 + - - +
1540 LEU 3.2 0.4 - - - -
1550 ASP* 1.3 77.6 + - - +
1570 GLU* 1.3 63.8 + - + +
1590 SER* 2.6 25.9 + - - +
1600 ALA* 4.0 2.8 + - - +
157G GLU* 3.6 35.6 + - - +
156H LYS* 6.2 4.0 - - - +
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Residues in contact with GLU 157 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1400 LYS* 3.7 21.8 + - - -
1530 MET 3.2 10.1 + - - +
1540 LEU* 3.3 13.9 + - + +
1560 LYS* 1.3 82.5 - - + +
1580 LEU* 1.3 64.6 + - + +
1600 ALA* 3.4 20.5 - - - +
1610 ARG 4.8 0.2 + - - -
152H PHE* 3.3 32.9 - - - -
156H LYS* 4.6 24.1 - - - +
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Residues in contact with LEU 158 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380 GLY 3.4 19.8 - - - +
390 PHE* 3.6 46.0 - - + +
420 TRP* 3.6 29.1 - - + +
870 PHE* 4.9 1.6 - - + -
1370 ILE* 3.7 34.8 - - + -
1540 LEU* 3.1 22.7 + - + +
1570 GLU* 1.3 76.1 - - + +
1590 SER* 1.3 60.6 + - - +
1600 ALA 3.1 5.8 - - - -
1610 ARG* 3.2 24.2 + - - +
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Residues in contact with SER 159 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370 GLU* 5.3 0.7 - - - -
380 GLY* 3.7 15.5 - - - -
410 ASN* 5.0 10.1 + - - +
1550 ASP* 3.1 16.2 + - - -
1560 LYS* 2.6 27.6 + - - +
1580 LEU* 1.3 74.7 - - - +
1600 ALA* 1.3 62.8 + - - +
1610 ARG 3.2 8.1 + - - +
1620 ALA* 4.6 6.1 + - - +
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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