Contacts of the helix formed by residues 24 - 34 (chain D) in PDB entry 2PY2
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 HIS 24 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D LEU* 1.3 79.0 - - - +
25D TRP* 1.3 67.1 + - - +
26D ALA* 3.4 17.6 + - + +
27D ASP* 3.0 59.7 + - - +
28D ALA* 3.0 17.0 + - - +
30D GLU* 4.8 0.9 - - - -
63D TRP* 3.7 0.2 - - - -
117D CYS 3.3 13.5 - - - +
118D THR* 3.5 27.6 - - + +
119D HIS 3.3 9.0 - - - -
120D LEU* 3.5 11.9 - - + +
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Residues in contact with TRP 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D HIS* 1.3 70.9 - - - +
26D ALA* 1.3 67.6 + - + +
28D ALA* 3.2 3.7 + - - +
29D GLN* 2.9 39.9 + - + -
39D LEU* 3.4 16.6 - - + +
63D TRP* 3.4 33.9 - + + +
64D ILE 3.0 21.1 + - - -
65D GLY 4.2 5.4 - - - -
66D GLY 4.2 0.6 + - - -
67D THR* 3.6 25.5 - - + +
78D MET* 3.4 43.3 - - + -
101D CYS* 3.5 36.4 - - + +
117D CYS* 2.9 21.6 + - + +
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Residues in contact with ALA 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D HIS* 3.3 17.3 + - + -
25D TRP* 1.3 91.1 - - + +
27D ASP* 1.3 58.7 + - - +
29D GLN* 3.3 3.4 + - - +
30D GLU* 3.0 42.2 + - + +
117D CYS* 4.8 1.2 + - - +
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Residues in contact with ASP 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 3.8 27.5 - - + +
24D HIS* 3.0 43.5 + - - +
26D ALA* 1.3 76.6 - - - +
28D ALA* 1.3 58.6 + - - +
30D GLU* 3.4 21.3 + - - +
31D SER* 3.0 28.9 + - - -
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Residues in contact with ALA 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 3.9 16.3 - - + +
24D HIS 3.0 13.5 + - - +
25D TRP 3.2 10.1 + - - +
27D ASP* 1.3 77.4 - - - +
29D GLN* 1.3 61.7 + - - +
31D SER* 3.3 4.9 + - - -
32D CYS* 3.2 25.6 + - - -
39D LEU* 4.0 9.6 - - + +
63D TRP* 4.2 9.6 - - + -
121D HIS 5.2 0.2 - - - +
123D SER* 3.8 29.9 + - - +
125D CYS* 4.6 0.3 - - - -
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Residues in contact with GLN 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D TRP* 2.9 31.6 + - + +
26D ALA* 3.7 4.5 - - - +
27D ASP 3.3 0.2 - - - -
28D ALA* 1.3 74.9 - - - +
30D GLU* 1.3 66.7 + - + +
32D CYS* 3.1 3.9 + - - +
33D MET* 3.0 47.1 + - - +
38D ASN* 2.9 27.5 + - - +
39D LEU* 2.9 45.2 + - + +
78D MET* 3.9 27.5 - - + +
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Residues in contact with GLU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D HIS* 4.8 0.7 - - - -
26D ALA* 3.0 38.7 + - + +
27D ASP* 3.4 23.8 + - - +
29D GLN* 1.3 77.9 - - + +
31D SER* 1.3 62.7 + - - +
33D MET* 3.3 17.5 + - - +
34D LYS* 3.3 28.7 + - - +
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Residues in contact with SER 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ASN* 3.8 22.8 + - - -
23D LEU* 4.4 6.5 - - - +
27D ASP 3.0 17.2 + - - -
28D ALA 3.5 6.5 - - - -
30D GLU* 1.3 73.7 - - - +
32D CYS* 1.3 65.7 + - - +
34D LYS* 3.3 34.0 + - - +
35D GLU* 3.9 9.0 + - - +
125D CYS* 4.8 0.7 - - - -
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Residues in contact with CYS 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ALA 3.2 18.6 + - - -
29D GLN 3.1 7.6 + - - +
31D SER* 1.3 76.5 - - - +
33D MET* 1.3 58.6 + - - +
35D GLU* 3.0 15.7 + - - +
37D ALA* 2.9 28.9 + - - +
38D ASN 3.6 17.0 - - - -
39D LEU* 3.7 22.9 - - - +
123D SER* 5.2 0.2 - - - -
125D CYS* 2.0 55.9 - - + -
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Residues in contact with MET 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D GLN* 3.0 47.3 + - - +
30D GLU* 3.5 19.3 - - - +
31D SER 3.2 0.2 - - - -
32D CYS* 1.3 77.6 - - - +
34D LYS* 1.3 60.5 + - - +
35D GLU 3.0 0.4 - - - -
36D GLY* 3.1 12.4 + - - -
37D ALA 3.3 11.9 - - - +
38D ASN* 4.7 1.3 - - - +
78D MET* 6.1 0.4 - - - -
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Residues in contact with LYS 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D GLU* 3.3 10.2 + - - +
31D SER* 3.6 31.5 + - - +
32D CYS 3.2 1.0 - - - -
33D MET* 1.3 76.4 - - + +
35D GLU* 1.3 70.8 + - + +
36D GLY 3.4 0.4 + - - -
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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