Contacts of the helix formed by residues 38 - 53 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ASP 3.6 2.9 + - - +
37A LEU* 1.3 77.9 - - - +
39A ALA* 1.3 63.2 + - - +
40A ALA* 3.0 12.3 + - - +
41A THR* 2.7 44.9 + - - -
42A VAL* 3.0 19.8 + - - +
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Residues in contact with ALA 39 (chain A).
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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37A LEU 4.0 0.2 + - - -
38A ASP* 1.3 74.4 - - - +
40A ALA* 1.3 57.3 + - - +
42A VAL* 3.8 7.3 - - - +
43A GLU* 2.9 30.1 + - - +
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 4.3 22.1 + - + +
38A ASP* 3.0 11.0 + - - +
39A ALA* 1.3 75.6 - - - +
41A THR* 1.3 61.0 + - - +
43A GLU* 3.5 9.8 + - - +
44A ALA* 3.0 28.4 + - - +
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Residues in contact with THR 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 5.1 7.5 - - - +
15A LEU* 4.5 16.6 - - + +
31A VAL* 4.4 12.6 - - + -
37A LEU* 4.1 26.3 - - + +
38A ASP* 2.7 34.2 + - - -
40A ALA* 1.3 68.6 - - - +
42A VAL* 1.3 61.4 + - - +
44A ALA* 3.2 6.5 + - - +
45A ILE* 2.9 45.0 + - + +
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 4.0 15.7 - - + +
38A ASP 3.0 17.1 + - - +
39A ALA* 3.8 7.0 - - - +
41A THR* 1.3 77.5 - - - +
43A GLU* 1.3 57.2 + - - +
45A ILE* 3.3 10.0 + - + +
46A GLN* 3.0 33.7 + - + +
71A PHE* 5.7 0.9 - - + -
74A LEU* 3.6 53.8 - - + +
75A LEU* 3.8 15.3 - - + -
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Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU 5.6 3.1 + - - -
39A ALA 2.9 18.9 + - - +
40A ALA* 3.7 9.5 - - - +
42A VAL* 1.3 78.4 - - - +
44A ALA* 1.3 56.5 + - - +
46A GLN* 3.2 8.4 + - + +
47A ALA* 3.0 30.0 + - + +
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 4.1 25.6 - - + +
15A LEU* 3.7 30.5 - - + +
40A ALA 3.0 18.4 + - - +
41A THR 3.2 2.4 + - - +
43A GLU* 1.3 76.5 - - - +
45A ILE* 1.3 56.9 - - - +
47A ALA* 3.6 6.7 + - - +
48A ALA* 3.0 27.7 + - - +
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 4.1 16.4 - - + -
28A ILE* 5.0 0.2 - - - -
31A VAL* 4.8 1.8 - - + -
33A LEU* 4.3 7.2 - - + -
37A LEU* 4.1 26.0 - - + -
41A THR* 2.9 24.9 + - + +
42A VAL* 3.5 10.1 - - - +
43A GLU 3.2 0.2 - - - -
44A ALA* 1.3 75.0 - - - +
46A GLN* 1.3 60.6 + - - +
48A ALA* 3.2 4.2 + - - -
49A LEU* 2.9 30.2 + - + +
55A ILE* 3.8 20.9 - - + +
57A PHE* 4.2 25.1 - - + -
71A PHE* 4.3 5.6 - - + -
75A LEU* 4.3 17.7 - - + -
256A ILE* 4.5 9.2 - - + -
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Residues in contact with GLN 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 3.0 23.7 + - + +
43A GLU* 3.5 11.0 - - + +
45A ILE* 1.3 76.5 - - - +
47A ALA* 1.3 56.6 + - - +
49A LEU* 3.5 20.6 - - - +
50A VAL* 3.1 35.0 + - + +
74A LEU 4.8 1.6 + - - -
75A LEU* 3.1 50.8 + - + +
119A LYS* 4.4 7.1 + - - +
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A GLU* 3.0 18.6 + - + +
44A ALA* 3.8 8.3 - - - +
45A ILE 3.2 0.2 - - - -
46A GLN* 1.3 75.6 - - - +
48A ALA* 1.3 64.6 + - - +
50A VAL* 3.9 5.6 - - - +
51A ARG* 3.0 24.8 + - - +
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 5.3 0.2 - - + -
17A VAL* 4.7 11.9 - - + -
28A ILE* 3.9 25.6 - - + -
44A ALA 3.0 18.5 + - - +
45A ILE 3.2 4.7 + - - +
47A ALA* 1.3 74.5 - - - +
49A LEU* 1.3 57.5 + - - +
51A ARG* 3.4 1.7 + - - -
52A HIS* 2.8 48.9 + - + +
55A ILE* 3.9 7.2 - - + -
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ILE* 2.9 18.4 + - + +
46A GLN* 3.5 22.7 - - - +
48A ALA* 1.3 77.4 - - - +
50A VAL* 1.3 57.9 + - + +
53A LYS* 2.8 37.1 + - - +
55A ILE* 4.0 17.6 - - + +
75A LEU* 5.7 3.1 - - + -
120A ALA* 4.6 11.2 - - + -
256A ILE* 3.4 42.6 - - + +
257A TRP* 3.7 2.0 - - - -
258A ASP* 3.6 34.3 - - + +
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLN* 3.1 24.0 + - + +
47A ALA* 3.9 6.5 - - - +
48A ALA 3.4 0.2 - - - -
49A LEU* 1.3 78.5 - - + +
51A ARG* 1.3 60.5 + - - +
53A LYS* 3.1 27.2 + - - +
202A HIS* 4.5 10.5 - - + +
204A ILE* 4.3 28.5 - - + -
205A SER* 3.8 29.2 - - - +
207A GLU* 5.7 0.7 - - - +
258A ASP* 4.1 16.9 - - - +
260A ARG* 5.6 0.7 - - - +
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Residues in contact with ARG 51 (chain A).
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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19A PRO* 6.0 1.6 - - - +
47A ALA 3.0 17.6 + - - +
48A ALA* 3.7 3.8 - - - +
50A VAL* 1.3 80.2 - - - +
52A HIS* 1.3 90.3 + - + +
53A LYS* 3.4 16.6 + - - +
139A ASN* 5.5 0.7 + - - -
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Residues in contact with HIS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL* 3.9 17.7 - - + +
19A PRO* 4.3 23.6 - - + +
24A ILE* 3.5 5.3 - - - +
25A GLY 2.9 31.0 + - - +
26A ALA* 3.6 22.5 - - + +
48A ALA* 2.8 33.0 + - + +
51A ARG* 1.3 114.0 + - + +
53A LYS* 1.3 60.7 + - - +
54A VAL 2.8 26.7 + - - +
55A ILE* 4.1 2.0 - - + -
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Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 4.0 12.3 - - + -
49A LEU* 2.8 19.2 + - - -
50A VAL 3.1 20.6 + - - +
51A ARG* 3.4 13.1 + - - +
52A HIS* 1.3 79.9 - - - +
54A VAL* 1.3 55.8 + - - +
139A ASN* 3.8 29.0 - - - +
141A ALA* 4.2 7.1 - - - +
202A HIS* 6.4 0.7 - - - -
207A GLU* 2.9 33.3 + - - -
257A TRP* 3.2 4.9 - - - +
258A ASP* 2.9 32.5 + - + -
261A ALA* 3.8 30.1 - - + +
262A THR* 3.7 16.4 - - + +
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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