Contacts of the helix formed by residues 38 - 53 (chain D) in PDB entry 1OIK
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 38 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D ASP 3.7 2.2 + - - -
37D LEU* 1.3 76.6 - - - +
39D ALA* 1.3 64.1 + - - +
40D ALA* 2.8 14.6 + - - +
41D THR* 2.8 34.1 + - - -
42D VAL* 3.0 19.3 + - - +
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Residues in contact with ALA 39 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D LEU 3.9 1.0 + - - -
38D ASP* 1.3 73.5 - - - +
40D ALA* 1.3 52.0 + - - +
42D VAL* 3.6 9.7 + - - +
43D GLU* 2.9 33.7 + - - +
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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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38D ASP* 2.8 11.9 + - - +
39D ALA* 1.3 74.8 - - - +
41D THR* 1.3 62.0 + - - +
43D GLU* 3.2 10.7 + - - +
44D ALA* 2.9 29.1 + - - +
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Residues in contact with THR 41 (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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15D LEU* 4.5 12.1 - - + +
31D VAL* 4.3 20.2 - - + -
37D LEU* 4.0 26.8 - - + +
38D ASP* 2.8 28.9 + - - -
40D ALA* 1.3 72.1 - - - +
42D VAL* 1.3 68.4 + - - +
44D ALA* 3.2 5.9 + - - +
45D ILE* 2.9 40.8 + - + +
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Residues in contact with VAL 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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37D LEU* 4.0 15.3 - - + +
38D ASP 3.0 19.4 + - - +
39D ALA* 3.7 8.1 - - - +
41D THR* 1.3 76.4 - - - +
43D GLU* 1.3 57.7 + - - +
45D ILE* 3.1 10.4 + - + +
46D GLN* 2.9 33.1 + - + +
71D PHE* 5.6 0.9 - - + -
74D LEU* 3.5 56.5 - - + +
75D LEU* 3.8 14.6 - - + -
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Residues in contact with GLU 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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39D ALA 2.9 21.6 + - - +
40D ALA* 3.2 10.1 + - - +
41D THR 3.2 0.2 - - - -
42D VAL* 1.3 74.0 - - - +
44D ALA* 1.3 59.6 + - - +
46D GLN* 3.3 9.8 + - + +
47D ALA* 3.1 28.1 + - + +
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Residues in contact with ALA 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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14D GLU* 5.4 5.8 - - - +
15D LEU* 3.7 32.4 - - + +
40D ALA 2.9 17.3 + - - +
41D THR* 3.2 3.1 + - - +
43D GLU* 1.3 78.7 - - - +
45D ILE* 1.3 55.1 + - - +
47D ALA* 3.6 6.6 + - - +
48D ALA* 3.1 27.4 + - - +
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Residues in contact with ILE 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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15D LEU* 4.0 16.4 - - + -
28D ILE* 4.9 0.7 - - + -
31D VAL* 4.6 1.6 - - + -
33D LEU* 4.2 8.3 - - + -
37D LEU* 4.0 26.0 - - + -
41D THR* 2.9 23.1 + - + +
42D VAL* 3.4 10.8 - - + +
44D ALA* 1.3 75.4 - - - +
46D GLN* 1.3 60.3 + - - +
48D ALA* 3.4 3.6 + - - +
49D LEU* 2.9 30.4 + - + +
55D ILE* 3.8 20.6 - - + +
57D PHE* 4.1 24.9 - - + -
71D PHE* 4.4 5.2 - - + -
75D LEU* 4.2 19.1 - - + -
256D ILE* 4.5 8.1 - - + -
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Residues in contact with GLN 46 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D VAL* 2.9 22.6 + - + +
43D GLU* 3.5 11.0 - - + +
45D ILE* 1.3 78.3 - - - +
47D ALA* 1.3 56.5 + - - +
49D LEU* 3.5 21.3 - - - +
50D VAL* 3.1 34.4 + - + +
74D LEU 4.8 1.6 + - - -
75D LEU* 2.9 50.5 + - + +
119D LYS* 4.2 8.2 + - - +
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Residues in contact with ALA 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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43D GLU* 3.1 17.9 + - + +
44D ALA* 3.9 7.9 - - - +
46D GLN* 1.3 73.5 - - - +
48D ALA* 1.3 58.5 + - - +
49D LEU 3.1 1.1 - - - -
50D VAL* 3.4 6.6 + - - +
51D ARG* 3.0 30.2 + - - +
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Residues in contact with ALA 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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15D LEU* 5.2 0.4 - - + -
17D VAL* 4.7 12.6 - - + -
28D ILE* 3.9 25.1 - - + -
44D ALA 3.1 18.3 + - - +
45D ILE 3.4 4.0 + - - +
47D ALA* 1.3 75.3 - - - +
49D LEU* 1.3 57.0 + - - +
51D ARG* 4.5 0.9 - - - +
52D HIS* 2.9 49.7 + - + +
55D ILE* 4.0 4.9 - - + -
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Residues in contact with LEU 49 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D ILE* 2.9 18.5 + - + +
46D GLN* 3.5 21.3 - - - +
47D ALA 3.1 0.2 - - - -
48D ALA* 1.3 75.1 - - - +
50D VAL* 1.3 62.7 + - + +
53D LYS* 2.9 34.4 + - - +
55D ILE* 4.0 17.2 - - + +
75D LEU* 5.6 3.6 - - + -
120D ALA* 4.6 14.8 - - + -
256D ILE* 3.3 44.9 - - + +
257D TRP* 3.6 2.0 - - - -
258D ASP* 3.6 30.6 - - + +
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Residues in contact with VAL 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 GLN* 3.1 19.7 + - + +
47D ALA* 3.4 6.9 + - - +
49D LEU* 1.3 78.2 - - + +
51D ARG* 1.3 59.2 + - - +
53D LYS* 3.1 26.9 + - - +
202D HIS* 4.5 9.6 - - + +
204D ILE* 4.4 24.7 - - + -
205D SER* 3.8 33.0 - - - +
207D GLU* 5.7 0.7 - - - +
258D ASP* 4.0 17.2 - - - +
260D ARG* 5.5 0.9 - - - +
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Residues in contact with ARG 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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19D PRO* 6.2 1.0 - - - +
47D ALA 3.0 18.2 + - - +
48D ALA* 3.9 3.6 - - - +
50D VAL* 1.3 78.9 - - - +
52D HIS* 1.3 89.0 + - + +
53D LYS* 3.5 16.8 + - - +
139D ASN* 5.6 0.7 + - - -
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Residues in contact with HIS 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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17D VAL* 3.8 16.4 - - + +
19D PRO* 4.4 18.7 - - + +
24D ILE* 3.4 6.8 - - - +
25D GLY 2.8 34.0 + - - +
26D ALA* 3.7 31.4 - - + +
48D ALA* 2.9 35.9 + - + +
51D ARG* 1.3 111.6 + - + +
53D LYS* 1.3 61.9 - - - +
54D VAL 2.8 18.9 + - - +
55D ILE* 4.2 1.8 - - + -
139D ASN* 5.9 0.2 - - - -
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Residues in contact with LYS 53 (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 ILE* 3.9 11.7 - - + -
49D LEU* 2.9 20.2 + - - -
50D VAL 3.1 21.6 + - - +
51D ARG* 3.5 13.3 + - - +
52D HIS* 1.3 80.6 - - - +
54D VAL* 1.3 57.4 + - - +
139D ASN* 3.9 28.0 - - - +
141D ALA* 4.3 2.8 - - - +
202D HIS* 6.3 0.7 - - - -
207D GLU* 2.9 33.9 + - - -
257D TRP* 3.3 3.6 - - - +
258D ASP* 2.8 31.9 + - + -
261D ALA* 3.8 35.2 - - + +
262D THR* 3.7 15.5 - - + +
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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