Contacts of the helix formed by residues 147 - 159 (chain 7) 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 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1447 ALA* 3.6 30.0 - - - +
1457 LYS 3.3 3.8 + - - -
1467 ASP* 1.3 78.2 - - - +
1487 PRO* 1.3 61.9 - - - +
1497 GLN* 3.1 9.4 + - - -
1507 ILE* 3.4 17.3 + - - +
1517 LEU* 3.6 15.1 + - - +
148I PRO* 6.4 0.4 - - - -
149I GLN* 2.9 31.1 + - - -
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Residues in contact with PRO 148 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1467 ASP 3.3 11.4 - - - +
1477 SER* 1.3 83.1 - - - +
1497 GLN* 1.3 80.6 + - - +
1517 LEU* 3.6 7.3 + - + +
1527 PHE* 3.2 17.8 + - - +
143O PHE* 3.5 43.4 - - + +
150O ILE* 4.1 9.1 - - + +
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Residues in contact with GLN 149 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1477 SER* 3.1 20.4 + - - +
1487 PRO* 1.3 95.8 - - - +
1507 ILE* 1.3 58.1 + - - +
1527 PHE* 3.4 5.7 + - - +
1537 MET* 3.2 34.6 + - + +
149I GLN* 3.6 23.4 + - + -
147O SER* 3.3 31.3 + - - +
149O GLN* 4.0 20.6 + - + +
150O ILE* 3.9 17.9 - - + +
153O MET* 4.2 4.6 - - + +
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Residues in contact with ILE 150 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1407 LYS* 5.0 2.2 - - + +
1437 PHE* 4.5 10.3 - - + +
1447 ALA* 3.5 28.3 - - + -
1477 SER* 3.4 20.9 + - - +
1497 GLN* 1.3 72.9 - - - +
1517 LEU* 1.3 56.0 + - - +
1527 PHE 3.2 0.4 - - - -
1537 MET* 3.2 10.2 + - + -
1547 LEU* 2.7 40.7 + - + +
148I PRO* 4.1 15.5 - - + +
149I GLN* 3.8 39.0 - - + +
152I PHE* 4.2 29.8 - - + -
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Residues in contact with LEU 151 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367 LEU* 4.3 18.9 - - + +
397 PHE* 4.1 14.0 - - + -
837 PRO* 4.2 20.4 - - + -
1417 LEU* 3.8 29.2 - - + -
1447 ALA* 4.7 6.4 - - + +
1477 SER 3.6 11.5 + - - +
1487 PRO* 3.6 10.7 + - + +
1497 GLN 3.4 0.2 - - - -
1507 ILE* 1.3 78.4 - - - +
1527 PHE* 1.3 57.2 + - - +
1547 LEU* 3.9 5.5 - - - +
1557 ASP* 3.1 27.5 + - - +
143O PHE* 3.8 25.4 - - + -
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Residues in contact with PHE 152 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367 LEU* 5.6 1.8 - - + -
1487 PRO 3.2 13.7 + - - +
1497 GLN* 3.4 11.2 - - - +
1507 ILE 3.2 0.2 - - - -
1517 LEU* 1.3 75.7 - - - +
1537 MET* 1.3 63.6 + - + +
1557 ASP* 3.4 10.2 + - + +
1567 LYS* 3.3 22.1 + - + +
140O LYS* 4.5 23.1 - - + -
143O PHE* 4.4 15.9 - + + -
150O ILE* 3.9 22.0 - - + -
153O MET* 3.5 41.7 - - + -
154O LEU* 4.3 21.5 - - + -
157O GLU* 3.5 32.5 - - - -
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Residues in contact with MET 153 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11741 AG 3.0 26.7 - - - -
1497 GLN* 3.2 19.7 + - + +
1507 ILE* 3.2 17.8 + - + +
1527 PHE* 1.3 78.6 - - + +
1547 LEU* 1.3 63.0 + - - +
1567 LYS* 3.5 9.1 + - + +
1577 GLU* 3.3 26.4 + - - +
149I GLN* 4.2 13.9 - - + +
152I PHE* 3.9 26.0 - - + -
153I MET* 3.7 27.6 - - + +
153O MET* 3.8 17.9 - - + +
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Residues in contact with LEU 154 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397 PHE* 4.1 5.6 - - + -
1377 ILE* 4.2 16.4 - - + +
1407 LYS* 3.8 50.5 - - + +
1417 LEU* 4.1 21.3 - - + -
1447 ALA* 6.0 0.9 - - + -
1507 ILE* 2.7 23.9 + - + +
1517 LEU* 3.9 8.7 - - - +
1537 MET* 1.3 72.4 - - - +
1557 ASP* 1.3 63.8 + - - +
1577 GLU* 3.3 11.1 + - - +
1587 LEU* 3.2 48.0 + - + +
152I PHE* 4.8 10.5 - - + -
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Residues in contact with ASP 155 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357 GLY 4.6 2.1 - - - +
367 LEU* 3.3 23.7 - - + +
377 GLU* 3.7 6.6 + - - +
387 GLY* 2.9 50.9 + - - -
397 PHE* 3.1 27.8 + - + -
1517 LEU 3.1 18.4 + - - +
1527 PHE* 3.5 10.1 - - + +
1547 LEU* 1.3 77.0 - - - +
1567 LYS* 1.3 61.3 + - - +
1587 LEU* 3.6 0.9 + - - -
1597 SER* 3.3 7.4 + - - -
140O LYS* 5.5 6.1 + - - -
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Residues in contact with LYS 156 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1527 PHE* 3.3 11.2 + - + +
1537 MET* 3.8 11.7 - - + +
1547 LEU 3.3 1.0 - - - -
1557 ASP* 1.3 79.3 + - - +
1577 GLU* 1.3 63.4 + - + +
1597 SER* 2.6 25.9 + - - +
1607 ALA* 4.0 3.6 + - - +
156I LYS* 5.3 8.9 - - - +
156O LYS* 5.4 9.9 - - - +
157O GLU* 4.2 28.7 - - - +
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Residues in contact with GLU 157 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1407 LYS* 4.1 16.5 + - - -
1537 MET 3.3 12.4 + - - +
1547 LEU* 3.3 14.5 + - + +
1567 LYS* 1.3 80.4 - - + +
1587 LEU* 1.3 64.6 + - + +
1607 ALA* 3.5 19.5 - - - +
152I PHE* 3.3 36.3 - - - -
156I LYS* 4.4 27.3 - - - +
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Residues in contact with LEU 158 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387 GLY 3.4 20.0 - - - +
397 PHE* 3.6 47.1 - - + -
427 TRP* 3.7 28.8 - - + +
877 PHE* 4.8 1.6 - - + -
1377 ILE* 3.8 32.3 - - + -
1547 LEU* 3.2 21.7 + - + +
1557 ASP 3.6 0.2 + - - -
1567 LYS 3.3 0.2 - - - -
1577 GLU* 1.3 76.7 - - + +
1597 SER* 1.3 60.2 + - - +
1607 ALA 3.1 5.4 - - - -
1617 ARG* 3.3 23.6 + - - +
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Residues in contact with SER 159 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377 GLU 5.3 0.7 - - - -
387 GLY* 3.7 15.9 - - - -
417 ASN* 5.2 9.3 + - - -
1557 ASP 3.3 12.7 + - - -
1567 LYS* 2.6 29.5 + - - +
1577 GLU 3.3 0.2 - - - -
1587 LEU* 1.3 74.7 - - - +
1607 ALA* 1.3 63.1 + - - +
1617 ARG 3.2 8.9 + - - +
1627 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