Contacts of the helix formed by residues 44 - 59 (chain A) in PDB entry 1ORN
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 THR 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A CYS* 1.3 77.8 - - - +
45A ASP* 1.3 65.9 + - - +
46A ALA* 3.9 7.9 + - - +
47A LEU* 3.3 28.8 + - - +
48A VAL* 3.1 22.2 + - - +
8B G 4.8 8.5 - - - +
9B G 5.6 6.5 - - - +
17C A 3.6 36.0 + - + +
18C PED 3.4 7.9 - - - -
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Residues in contact with ASP 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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24A GLU* 3.6 21.7 + - + +
25A LEU* 3.6 28.0 - - + +
40A SER* 4.0 12.0 + - - -
44A THR* 1.3 70.9 - - - +
46A ALA* 1.3 64.4 + - - +
48A VAL* 3.0 3.4 + - - +
49A ASN* 2.8 37.3 + - - +
186A ARG* 3.2 30.3 + - - -
18C PED 2.9 24.6 + - - +
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Residues in contact with ALA 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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44A THR* 3.2 8.9 - - - +
45A ASP* 1.3 78.7 - - - +
47A LEU* 1.3 62.1 + - + +
49A ASN* 3.5 7.4 + - - +
50A LYS* 3.1 27.9 + - - +
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A CYS* 3.9 13.7 - - - -
44A THR* 3.2 21.1 + - + +
46A ALA* 1.3 82.4 - - + +
48A VAL* 1.3 64.5 + - - +
50A LYS* 2.9 37.5 - - + +
51A VAL* 3.1 13.5 + - - +
79A SER* 3.9 22.7 - - - +
80A ILE* 4.2 2.0 - - + -
8B G 3.7 44.2 - - - +
9B G 3.8 19.1 - - - +
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.8 17.3 - - + -
36A ALA* 3.8 22.7 - - + +
39A LEU* 4.1 7.0 - - + +
40A SER* 3.8 29.6 - - - +
43A CYS* 3.9 13.7 - - + -
44A THR 3.1 15.2 + - - +
45A ASP 3.0 7.2 + - - +
47A LEU* 1.3 76.7 - - - +
49A ASN* 1.3 61.3 + - - +
51A VAL* 3.3 1.4 + - - +
52A THR* 2.8 44.2 + - + +
80A ILE* 3.7 10.3 - - + -
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Residues in contact with ASN 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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24A GLU* 3.1 22.4 + - - +
25A LEU* 3.5 8.7 - - - +
26A VAL* 2.8 44.7 + - + +
36A ALA* 6.1 0.2 - - - +
45A ASP* 2.8 27.4 + - - +
46A ALA* 3.9 6.5 - - - +
48A VAL* 1.3 76.3 - - - +
50A LYS* 1.3 64.0 + - - +
52A THR* 3.5 7.0 + - - -
53A LYS* 3.1 23.2 + - - +
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Residues in contact with LYS 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 ALA 3.1 11.8 + - - +
47A LEU* 2.9 50.5 - - + +
49A ASN* 1.3 76.6 - - - +
51A VAL* 1.3 65.9 + - + +
53A LYS* 3.3 16.6 - - - +
54A ARG* 3.2 21.6 + - - +
79A SER* 6.0 0.2 - - - -
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Residues in contact with VAL 51 (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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39A LEU* 5.0 4.5 - - + -
47A LEU* 3.1 18.5 + - + +
48A VAL 3.7 2.7 - - - +
50A LYS* 1.3 85.4 - - + +
52A THR* 1.3 67.8 + - - +
53A LYS 3.1 2.1 + - - -
54A ARG* 3.2 21.9 - - - +
55A LEU* 3.0 20.1 + - + +
76A ASP 3.8 22.4 - - - +
77A ILE* 4.2 10.5 - - + -
79A SER* 4.1 22.2 - - - +
80A ILE* 3.6 31.4 - - + -
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Residues in contact with THR 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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26A VAL* 4.3 9.5 + - - +
36A ALA* 4.6 3.5 - - + +
39A LEU* 4.0 19.7 - - + -
48A VAL* 2.8 40.9 + - + +
49A ASN* 3.5 10.7 + - - -
51A VAL* 1.3 70.7 - - - +
53A LYS* 1.3 68.6 + - - +
55A LEU* 3.5 9.6 - - + -
56A PHE* 2.8 67.2 + - + +
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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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49A ASN 3.1 14.3 + - - +
50A LYS* 3.3 16.6 - - - +
51A VAL 3.1 0.2 - - - -
52A THR* 1.3 81.2 + - - +
54A ARG* 1.3 61.0 + - + +
56A PHE* 4.8 0.5 - - - +
57A GLU* 3.4 21.5 + - - +
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Residues in contact with ARG 54 (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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50A LYS* 3.2 24.4 + - - +
51A VAL* 3.2 31.8 + - - +
53A LYS* 1.3 81.4 - - + +
55A LEU* 1.3 65.0 + - - +
56A PHE 3.3 0.4 - - - -
57A GLU* 3.0 19.0 + - - +
58A LYS* 3.2 13.2 + - - +
76A ASP 4.6 12.1 + - - +
79A SER* 4.7 10.5 + - - -
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Residues in contact with LEU 55 (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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35A ILE* 4.2 4.0 - - + -
39A LEU* 4.1 24.2 - - + -
51A VAL* 3.0 20.0 + - + +
52A THR* 3.7 6.3 - - + -
54A ARG* 1.3 79.5 - - + +
56A PHE* 1.3 69.0 + - + +
57A GLU 3.2 0.3 + - - -
58A LYS* 3.2 2.7 + - - -
59A TYR* 2.9 58.8 + - + +
65A TYR* 3.6 21.5 - - + +
73A LEU* 4.3 3.6 - - + -
76A ASP* 4.0 15.0 - - + +
77A ILE* 3.8 25.6 - - + -
90A ILE* 5.8 0.9 - - + -
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Residues in contact with PHE 56 (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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26A VAL* 3.9 16.4 - - + -
27A HIS* 5.2 0.2 - - - -
28A ARG* 3.5 26.5 + - - +
32A GLU* 3.3 60.5 - - + +
35A ILE* 4.0 14.8 - - + -
36A ALA* 4.2 6.7 - - + -
52A THR* 2.8 54.4 + - + +
53A LYS 4.8 0.7 - - - +
55A LEU* 1.3 76.6 - - + +
57A GLU* 1.3 61.7 + - - +
59A TYR 3.2 16.4 - - - +
60A ARG* 3.9 10.7 - - - +
65A TYR* 3.8 20.2 - - - -
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Residues in contact with GLU 57 (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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28A ARG* 3.3 34.3 + - - -
53A LYS 3.4 19.1 - - - +
54A ARG* 3.0 10.9 + - - +
56A PHE* 1.3 78.8 - - - +
58A LYS* 1.3 64.3 + - - +
59A TYR 4.9 0.2 - - - -
60A ARG* 3.6 33.7 + - - +
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Residues in contact with LYS 58 (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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54A ARG 3.2 10.9 + - - +
55A LEU* 3.8 7.6 - - - +
57A GLU* 1.3 80.8 - - - +
59A TYR* 1.3 81.4 + - + +
60A ARG* 4.3 5.3 + - - -
64A ASP* 4.5 6.4 - - - +
68A VAL* 5.1 2.9 - - - -
72A GLU* 3.1 28.0 + - - +
76A ASP* 2.8 39.1 + - - +
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Residues in contact with TYR 59 (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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31A PHE* 5.7 0.2 - - - -
32A GLU* 5.6 1.0 - - - +
55A LEU* 2.9 38.3 + - + +
56A PHE* 3.2 25.5 - - - +
58A LYS* 1.3 102.7 + - + +
60A ARG* 1.3 61.1 + - - +
64A ASP* 3.5 39.0 - - + -
65A TYR* 3.4 39.3 + + + -
68A VAL* 3.7 31.7 - - + +
72A GLU* 4.4 0.9 - - - +
73A LEU* 3.8 14.9 + - + +
76A ASP* 2.6 30.1 + - - -
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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