Contacts of the helix formed by residues 36 - 52 (chain D) in PDB entry 5Y39
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 ASP 36 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 5.1 3.6 - - + +
26D VAL* 5.5 2.0 - - - +
32D ASP 4.2 10.9 - - - +
33D LEU* 3.3 24.5 + - - +
34D GLU 3.3 2.0 - - - +
35D ASN* 1.3 75.8 - - - +
37D GLU* 1.3 63.7 + - - +
38D GLN* 3.5 24.1 + - - +
39D ALA* 3.3 34.0 + - + +
40D ALA* 3.0 22.7 + - - +
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Residues in contact with GLU 37 (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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26D VAL* 4.4 16.1 - - - +
35D ASN 3.8 4.1 + - - -
36D ASP* 1.3 73.4 + - - +
38D GLN* 1.3 63.5 + - + +
40D ALA* 3.4 8.1 + - + +
41D SER* 3.0 29.3 + - - -
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Residues in contact with GLN 38 (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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35D ASN 5.2 2.4 + - - -
36D ASP* 3.5 18.1 + - - +
37D GLU* 1.3 80.3 - - + +
39D ALA* 1.3 64.6 + - - +
41D SER* 3.4 6.5 + - - -
42D ALA* 3.0 22.9 + - - +
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Residues in contact with ALA 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 5.2 2.2 - - + -
33D LEU* 5.3 7.6 - - + -
36D ASP* 3.3 32.6 + - + +
38D GLN* 1.3 76.1 - - - +
40D ALA* 1.3 57.2 + - - +
42D ALA* 3.1 6.9 + - - +
43D ILE* 2.8 52.1 + - + +
75D LEU* 6.4 0.9 - - + -
137E LEU* 4.6 7.9 - - + +
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Residues in contact with ALA 40 (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 LEU* 4.0 16.2 - - + +
21D LEU* 3.8 24.1 - - + +
24D GLY 5.0 5.6 - - - +
26D VAL* 4.1 15.0 - - + -
36D ASP 3.0 18.6 + - - +
37D GLU* 3.4 8.7 - - + +
39D ALA* 1.3 75.8 - - - +
41D SER* 1.3 52.7 + - - +
43D ILE* 3.6 0.6 + - - -
44D SER* 2.6 38.8 + - - -
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Residues in contact with SER 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D GLY 5.5 1.5 + - - -
37D GLU 3.0 16.5 + - - -
38D GLN* 3.7 6.3 - - - -
40D ALA* 1.3 73.2 - - - +
42D ALA* 1.3 60.8 + - - +
44D SER* 3.4 6.7 + - - -
45D GLU* 3.0 33.1 + - - +
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Residues in contact with ALA 42 (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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38D GLN 3.0 17.6 + - - +
39D ALA* 3.6 4.7 - - - +
41D SER* 1.3 76.1 - - - +
43D ILE* 1.3 57.7 + - - +
45D GLU* 3.6 8.5 + - - +
46D LEU* 3.0 30.2 + - - +
133E GLN* 4.9 5.6 - - - +
136E LYS* 4.6 24.7 - - + +
137E LEU* 3.7 21.8 - - + -
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Residues in contact with ILE 43 (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 LEU* 3.8 25.1 - - + -
21D LEU* 4.7 5.6 - - + -
33D LEU* 4.9 4.7 - - + -
39D ALA* 2.8 31.7 + - + +
40D ALA 4.0 2.9 - - - +
42D ALA* 1.3 68.4 - - - +
44D SER* 1.3 59.0 + - - +
46D LEU* 3.3 8.2 + - + +
47D VAL* 2.8 50.0 + - + +
75D LEU* 4.9 7.4 - - + -
77D VAL* 4.2 12.1 - - + -
84D VAL* 4.7 0.2 - - + -
86D VAL* 3.7 37.9 - - + -
137E LEU* 3.5 24.2 - - + -
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Residues in contact with SER 44 (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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21D LEU* 3.3 18.4 - - - +
24D GLY* 4.0 22.7 + - - -
40D ALA 2.6 24.5 + - - -
41D SER* 3.5 8.0 - - - -
42D ALA 3.3 0.2 - - - -
43D ILE* 1.3 76.1 - - - +
45D GLU* 1.3 57.4 + - - +
47D VAL* 3.2 7.1 + - - +
48D SER* 2.9 31.0 + - - -
84D VAL* 6.0 1.8 - - - -
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Residues in contact with GLU 45 (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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14C PRO 5.4 5.3 - - - +
17C GLU* 2.8 30.4 - - - +
41D SER* 3.0 19.1 + - - +
42D ALA* 3.9 6.9 - - - +
44D SER* 1.3 75.5 - - - +
46D LEU* 1.3 60.5 + - - +
48D SER* 3.0 18.6 + - - +
49D THR* 3.1 20.7 + - - +
133E GLN* 3.3 22.2 + - + +
136E LYS* 3.3 19.9 + - - -
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Residues in contact with LEU 46 (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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42D ALA 3.0 18.6 + - - +
43D ILE* 3.4 10.1 - - + +
45D GLU* 1.3 76.5 - - - +
47D VAL* 1.3 56.2 + - - +
49D THR* 3.3 2.9 + - - -
50D ALA* 2.9 30.6 + - - +
66D LEU* 3.8 17.5 - - + -
68D VAL* 3.7 30.3 - - + -
77D VAL* 5.7 0.9 - - + -
130E LEU* 3.5 46.0 - - + +
133E GLN* 3.4 22.1 + - + +
134E ALA* 4.3 7.4 - - + +
137E LEU* 3.8 15.9 - - + -
147E VAL* 5.0 3.4 - - + -
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Residues in contact with VAL 47 (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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108A LEU* 4.4 6.3 - - + -
43D ILE* 2.8 29.8 + - + +
44D SER* 3.2 5.6 + - - +
46D LEU* 1.3 71.7 - - - +
48D SER* 1.3 54.0 - - - +
50D ALA* 3.2 7.3 + - - +
51D CYS* 2.8 43.0 + - - -
63D PHE* 5.6 4.0 - - + -
66D LEU* 4.5 9.6 - - + -
77D VAL* 3.5 32.3 - - + -
79D VAL* 4.0 26.2 - - + -
84D VAL* 4.0 16.6 - - + -
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Residues in contact with SER 48 (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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108A LEU* 4.1 18.6 - - - +
44D SER 2.9 18.2 + - - -
45D GLU* 3.0 18.2 + - - +
47D VAL* 1.3 73.2 - - - +
49D THR* 1.3 62.5 + - - -
51D CYS* 3.4 3.6 + - - +
52D GLY* 3.3 15.9 + - - -
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Residues in contact with THR 49 (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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15C SER 4.8 9.4 + - - -
102C LEU* 4.8 9.0 - - + +
45D GLU* 3.1 12.0 + - - +
46D LEU 3.5 1.8 - - - -
48D SER* 1.3 74.1 + - - +
50D ALA* 1.3 58.4 - - - +
52D GLY* 2.9 22.7 + - - -
53D PHE 3.7 2.6 + - - -
126E VAL* 3.8 18.3 - - + +
129E VAL* 3.6 26.8 - - + +
130E LEU* 3.8 15.0 - - + -
133E GLN* 3.1 29.1 + - - +
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Residues in contact with ALA 50 (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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46D LEU 2.9 19.2 + - - +
47D VAL* 3.5 7.4 - - - +
49D THR* 1.3 75.3 - - - +
51D CYS* 1.3 56.5 + - - +
52D GLY 3.1 0.2 - - - -
53D PHE* 3.0 28.1 + - - +
63D PHE* 3.5 30.0 - - + -
66D LEU* 4.4 9.4 - - + -
130E LEU* 3.6 24.7 - - + -
149E LEU* 4.8 4.9 - - + +
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Residues in contact with CYS 51 (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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108A LEU* 3.8 21.1 - - + -
109A PRO* 3.8 30.4 - - + +
111A LEU* 4.7 9.4 - - - -
47D VAL* 2.8 32.5 + - - +
48D SER 3.8 5.8 - - - +
49D THR 3.3 0.4 - - - -
50D ALA* 1.3 73.3 - - - +
52D GLY* 1.3 51.4 + - - +
53D PHE 3.2 1.6 - - - -
54D ARG* 2.4 33.6 + - - -
62D PRO* 4.4 7.0 - - - -
63D PHE* 4.5 13.5 - - - -
79D VAL* 4.7 2.9 - - - -
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Residues in contact with GLY 52 (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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48D SER 3.3 7.0 + - - -
49D THR* 2.9 14.7 + - - -
51D CYS* 1.3 77.1 - - - +
53D PHE* 1.3 61.1 + - - +
54D ARG* 3.5 7.6 + - - +
126E VAL* 4.5 9.7 - - - +
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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