Contacts of the helix formed by residues 147 - 159 (chain 1) 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 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1441 ALA* 3.5 14.5 + - - +
1451 LYS 3.3 4.7 - - - -
1461 ASP* 1.3 78.1 - - - +
1481 PRO* 1.3 62.1 - - - +
1491 GLN* 2.8 24.0 + - - +
1501 ILE* 3.3 39.3 + - - +
1511 LEU* 3.5 17.0 + - - +
149O GLN* 3.5 11.9 + - - -
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Residues in contact with PRO 148 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1461 ASP 3.4 10.1 - - - +
1471 SER* 1.3 83.1 - - - +
1491 GLN* 1.3 78.0 + - - +
1501 ILE 3.5 0.2 - - - -
1511 LEU* 3.9 6.0 - - + +
1521 PHE* 3.3 22.3 + - - +
143I PHE* 3.6 43.7 - - + +
150I ILE* 4.1 12.9 - - + +
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Residues in contact with GLN 149 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1461 ASP 5.2 0.3 - - - +
1471 SER* 2.8 23.5 + - - +
1481 PRO* 1.3 97.8 - - - +
1501 ILE* 1.3 61.2 + - - +
1521 PHE* 3.4 6.6 - - - +
1531 MET* 3.3 27.3 + - + +
147I SER* 3.4 30.1 + - - +
149I GLN* 4.2 20.9 + - + +
150I ILE* 4.0 17.0 - - + +
153I MET* 4.1 9.5 - - + +
149O GLN* 3.7 24.2 + - + +
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Residues in contact with ILE 150 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1401 LYS 5.1 1.3 - - - +
1431 PHE* 4.5 6.3 - - + +
1441 ALA* 3.5 29.8 - - + -
1471 SER* 3.3 25.2 + - - +
1491 GLN* 1.3 72.0 - - - +
1511 LEU* 1.3 60.2 + - - +
1521 PHE 3.1 2.0 - - - -
1531 MET* 3.1 9.2 + - + -
1541 LEU* 2.8 34.7 + - + +
148O PRO* 4.1 15.5 - - + +
149O GLN* 3.9 36.6 - - + +
152O PHE* 4.0 34.5 - - + -
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Residues in contact with LEU 151 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361 LEU* 4.3 21.6 - - + +
391 PHE* 4.0 11.5 - - + -
831 PRO* 4.3 22.0 - - + -
1411 LEU* 3.8 28.3 - - + -
1441 ALA* 4.7 7.2 - - + +
1471 SER 3.5 15.7 + - - +
1481 PRO* 3.9 6.3 - - + +
1501 ILE* 1.3 78.0 - - - +
1521 PHE* 1.3 56.7 + - - +
1541 LEU* 3.6 9.0 + - - +
1551 ASP* 3.1 25.6 + - - +
143I PHE* 3.7 28.0 - - + -
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Residues in contact with PHE 152 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361 LEU* 5.7 2.5 - - - -
1481 PRO 3.3 12.9 + - - +
1491 GLN* 3.4 10.8 - - - +
1501 ILE 3.1 0.2 - - - -
1511 LEU* 1.3 79.3 - - - +
1531 MET* 1.3 64.5 + - + +
1551 ASP* 3.2 18.7 + - + +
1561 LYS* 3.3 14.1 + - + +
140I LYS* 4.7 22.9 - - + -
143I PHE* 5.0 11.8 - + + -
150I ILE* 4.4 20.6 - - + -
153I MET* 3.9 45.1 - - + -
154I LEU* 4.8 7.6 - - + -
157I GLU* 3.3 41.1 - - + -
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Residues in contact with MET 153 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1491 GLN* 3.3 19.0 + - + +
1501 ILE* 3.1 20.9 + - + +
1521 PHE* 1.3 76.2 - - + +
1541 LEU* 1.3 64.3 + - - +
1561 LYS* 3.6 7.2 + - - +
1571 GLU* 3.3 26.9 + - - +
11741 AG 2.7 30.5 - - - -
153I MET* 3.9 13.7 - - + +
149O GLN* 4.1 19.7 - - + +
152O PHE* 3.7 32.1 - - + -
153O MET* 3.5 15.3 - - - +
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Residues in contact with LEU 154 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391 PHE* 4.1 9.9 - - + -
1371 ILE* 4.6 15.3 - - + -
1401 LYS* 3.8 55.0 - - + +
1411 LEU* 4.1 23.1 - - + -
1441 ALA* 5.0 1.6 - - + -
1501 ILE* 2.8 25.3 + - + +
1511 LEU* 3.8 7.4 - - - +
1531 MET* 1.3 73.6 - - - +
1551 ASP* 1.3 64.8 + - - +
1571 GLU* 3.3 15.3 + - + +
1581 LEU* 3.1 37.3 + - + +
152O PHE* 4.5 10.1 - - + -
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Residues in contact with ASP 155 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351 GLY 4.8 1.7 - - - +
361 LEU* 3.4 22.4 - - + +
371 GLU* 3.8 6.9 + - - +
381 GLY* 2.9 39.3 + - - -
391 PHE* 3.2 24.3 + - + +
1511 LEU 3.1 15.4 + - - +
1521 PHE* 3.2 16.5 + - + +
1541 LEU* 1.3 78.7 - - - +
1561 LYS* 1.3 60.9 + - - +
1581 LEU 3.7 0.2 + - - -
1591 SER* 3.3 18.9 + - - -
140I LYS* 5.6 5.0 + - - -
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Residues in contact with LYS 156 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1521 PHE* 3.3 10.6 + - + +
1531 MET* 3.9 9.6 - - - +
1541 LEU 3.3 0.8 - - - -
1551 ASP* 1.3 76.9 - - - +
1571 GLU* 1.3 65.3 + - + +
1591 SER* 2.6 25.1 + - - +
1601 ALA* 4.1 3.3 + - - +
156I LYS* 4.8 15.4 - - - +
157I GLU* 4.5 25.6 - - + +
156O LYS* 5.3 11.9 - - - +
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Residues in contact with GLU 157 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1401 LYS* 3.6 23.3 + - - -
1531 MET 3.3 16.6 + - - +
1541 LEU* 3.3 12.0 + - + +
1561 LYS* 1.3 80.2 - - + +
1581 LEU* 1.3 65.2 + - + +
1591 SER 3.8 0.2 + - - -
1601 ALA* 3.8 15.6 - - - +
152O PHE* 3.8 22.8 - - + -
156O LYS* 3.9 37.2 - - + +
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Residues in contact with LEU 158 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381 GLY 3.8 19.7 - - - +
391 PHE* 3.6 44.0 - - + -
421 TRP* 3.6 30.9 - - + +
871 PHE* 4.9 1.1 - - + -
1371 ILE* 3.8 28.7 - - + -
1541 LEU* 3.1 26.7 + - + +
1551 ASP 4.3 0.4 - - - +
1561 LYS 3.3 0.2 - - - -
1571 GLU* 1.3 78.6 - - + +
1591 SER* 1.3 58.3 + - - +
1601 ALA 3.0 9.8 + - - -
1611 ARG* 3.2 23.7 + - - +
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Residues in contact with SER 159 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371 GLU 5.3 0.4 - - - -
381 GLY* 4.0 15.0 - - - -
411 ASN* 5.4 7.5 + - - +
1551 ASP* 3.3 15.2 + - - -
1561 LYS* 2.6 29.2 + - - +
1581 LEU* 1.3 73.9 - - - +
1601 ALA* 1.3 61.7 + - - +
1611 ARG 3.2 7.9 + - - +
1621 ALA* 4.9 4.9 - - - +
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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