Contacts of the helix formed by residues 147 - 159 (chain 4) 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 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1444 ALA* 4.1 15.2 - - - +
1454 LYS 3.4 4.8 + - - -
1464 ASP* 1.3 79.0 - - - +
1484 PRO* 1.3 63.5 - - - +
1494 GLN* 3.1 18.0 + - - -
1504 ILE* 3.4 29.9 + - - +
1514 LEU* 3.4 19.6 + - - +
149R GLN* 3.3 18.0 + - - +
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Residues in contact with PRO 148 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1464 ASP 3.7 7.0 - - - +
1474 SER* 1.3 83.8 - - - +
1494 GLN* 1.3 73.7 + - - +
1514 LEU* 3.8 11.2 - - + +
1524 PHE* 3.0 29.3 + - - +
143P PHE* 4.2 25.4 - - + +
147P SER* 6.4 0.4 - - - -
150P ILE* 3.8 18.8 - - + +
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Residues in contact with GLN 149 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1464 ASP 5.2 0.2 - - - +
1474 SER* 3.1 21.1 + - - +
1484 PRO* 1.3 91.5 - - - +
1504 ILE* 1.3 58.3 + - - +
1524 PHE* 3.5 4.5 + - - +
1534 MET* 3.2 36.3 + - + +
147P SER* 3.5 21.4 + - - -
149P GLN* 3.8 32.9 + - + +
150P ILE* 4.3 13.7 - - + +
153P MET* 4.2 6.2 - - + +
149R GLN* 4.1 24.5 + - + +
149Z GLN* 6.2 1.1 - - + -
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Residues in contact with ILE 150 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1404 LYS* 4.9 1.1 - - + +
1434 PHE* 4.1 17.9 - - + +
1444 ALA* 3.6 24.7 - - + -
1474 SER* 3.4 25.4 + - - +
1484 PRO 3.4 0.2 - - - -
1494 GLN* 1.3 74.4 - - - +
1514 LEU* 1.3 61.0 + - - +
1524 PHE 3.2 0.4 - - - -
1534 MET* 3.4 8.9 + - + -
1544 LEU* 2.9 39.4 + - + +
148R PRO* 3.9 29.6 - - + +
149R GLN* 3.9 20.9 - - + +
152R PHE* 4.3 26.7 - - + -
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Residues in contact with LEU 151 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364 LEU* 4.5 15.0 - - + +
394 PHE* 4.1 14.7 - - + -
834 PRO* 4.3 23.8 - - + -
1414 LEU* 3.9 27.8 - - + -
1444 ALA* 4.6 7.0 - - + +
1474 SER 3.4 15.2 + - - +
1484 PRO* 3.8 8.3 - - + +
1504 ILE* 1.3 79.7 - - - +
1524 PHE* 1.3 59.0 + - - +
1544 LEU* 3.7 5.6 + - - +
1554 ASP* 3.3 21.1 + - - +
143P PHE* 3.7 27.4 - - + -
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Residues in contact with PHE 152 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364 LEU* 5.8 1.6 - - - -
1484 PRO 3.0 18.4 + - - +
1494 GLN* 3.6 6.5 - - - +
1514 LEU* 1.3 76.8 - - - +
1534 MET* 1.3 63.5 + - - +
1554 ASP* 3.3 17.1 + - + +
1564 LYS* 3.4 15.9 + - + +
140P LYS* 4.8 17.7 - - + -
143P PHE* 5.1 12.5 - + + -
150P ILE* 4.0 23.6 - - + -
153P MET* 3.7 48.9 - - + -
154P LEU* 4.6 11.2 - - + -
157P GLU* 3.3 37.5 - - + -
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Residues in contact with MET 153 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1494 GLN* 3.2 28.7 + - + +
1504 ILE* 3.4 10.3 + - + +
1524 PHE* 1.3 79.0 - - + +
1544 LEU* 1.3 63.8 + - - +
1564 LYS* 3.7 7.4 + - - +
1574 GLU* 3.4 27.1 + - - +
11744 AG 2.9 25.8 - - - -
153P MET* 3.8 19.7 - - + +
149R GLN* 4.4 9.9 - - + +
152R PHE* 3.9 28.9 - - + -
153R MET* 3.7 29.2 - - + +
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Residues in contact with LEU 154 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394 PHE* 4.1 10.5 - - + -
1374 ILE* 4.8 12.8 - - + -
1404 LYS* 3.8 56.5 - - + +
1414 LEU* 4.2 19.3 - - + -
1444 ALA* 5.0 1.8 - - + -
1504 ILE* 2.9 32.4 + - + +
1514 LEU* 3.9 6.7 - - - +
1524 PHE 3.3 0.2 - - - -
1534 MET* 1.3 74.6 - - - +
1554 ASP* 1.3 65.5 + - - +
1574 GLU* 3.3 14.0 + - + +
1584 LEU* 3.1 34.9 + - + +
152R PHE* 4.7 7.0 - - + -
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Residues in contact with ASP 155 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354 GLY 4.7 1.9 - - - +
364 LEU* 3.3 24.5 - - + +
374 GLU* 3.8 5.9 + - - +
384 GLY* 2.9 52.4 + - - -
394 PHE* 3.2 24.7 + - + -
1514 LEU 3.3 12.4 + - - +
1524 PHE* 3.3 15.4 + - + +
1544 LEU* 1.3 79.1 - - - +
1564 LYS* 1.3 61.4 + - - +
1584 LEU 3.6 0.2 + - - -
1594 SER* 3.3 7.3 + - - -
140P LYS* 5.4 6.9 + - - -
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Residues in contact with LYS 156 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1524 PHE* 3.4 13.1 + - + +
1534 MET* 4.0 9.2 - - - +
1544 LEU 3.3 0.4 - - - -
1554 ASP* 1.3 77.3 + - - +
1574 GLU* 1.3 63.7 + - + +
1594 SER* 2.6 26.2 + - - +
1604 ALA* 4.0 2.8 + - - +
156P LYS* 5.0 13.7 - - - +
157P GLU* 4.5 23.5 - - + +
156R LYS* 5.7 5.6 - - - +
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Residues in contact with GLU 157 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1404 LYS* 3.9 17.8 + - - -
1534 MET 3.4 11.1 + - - +
1544 LEU* 3.3 14.3 + - + +
1564 LYS* 1.3 79.8 - - + +
1584 LEU* 1.3 65.2 + - + +
1604 ALA* 3.5 20.5 - - - +
1614 ARG 4.8 0.2 + - - -
152R PHE* 3.4 32.4 - - - -
156R LYS* 4.2 29.7 - - + +
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Residues in contact with LEU 158 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384 GLY 3.3 21.7 - - - +
394 PHE* 3.6 43.1 - - + -
424 TRP* 3.6 37.9 - - + +
874 PHE* 4.7 1.6 - - + -
1374 ILE* 3.9 32.5 - - + -
1544 LEU* 3.1 21.3 + - + +
1554 ASP 3.6 0.4 + - - -
1564 LYS 3.4 0.2 - - - -
1574 GLU* 1.3 77.9 - - + +
1594 SER* 1.3 59.9 + - - +
1604 ALA 3.1 5.9 + - - -
1614 ARG 3.3 18.7 + - - +
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Residues in contact with SER 159 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374 GLU 5.3 0.7 - - - -
384 GLY* 3.8 16.4 - - - -
414 ASN* 5.3 8.3 + - - -
1554 ASP 3.3 15.0 + - - -
1564 LYS* 2.6 27.2 + - - +
1584 LEU* 1.3 74.3 - - - +
1604 ALA* 1.3 63.6 + - - +
1614 ARG 3.2 8.6 + - - +
1624 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