Contacts of the helix formed by residues 44 - 59 (chain A) in PDB entry 1OZ7
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 SER 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ILE* 3.7 2.1 - - - +
43A GLU* 1.3 80.8 - - - +
45A LYS* 1.3 55.1 + - - +
46A LYS* 3.6 9.7 + - - +
47A GLU* 3.0 24.4 + - - +
48A GLU* 2.7 35.9 + - - +
87B TYR* 3.8 14.5 - - - -
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Residues in contact with LYS 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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44A SER* 1.3 74.3 - - - +
46A LYS* 1.3 72.0 + - - +
48A GLU* 3.5 2.4 - - + +
49A ILE* 3.0 57.2 + - + +
110A ARG* 5.8 3.1 - - - +
87B TYR* 3.5 33.6 - - + +
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Residues in contact with LYS 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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9A ASN* 4.9 11.9 - - - +
44A SER* 3.1 9.3 + - - +
45A LYS* 1.3 98.9 - - - +
47A GLU* 1.3 58.7 + - - +
49A ILE* 3.2 13.3 + - + +
50A LEU* 3.0 24.7 + - + +
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Residues in contact with GLU 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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9A ASN* 4.0 12.3 - - - +
12A TYR* 5.5 0.4 - - - -
14A TYR* 2.6 39.5 + - + +
41A SER 3.2 12.4 - - - +
42A ILE* 4.2 1.8 - - + -
43A GLU* 2.8 32.1 + - - +
44A SER* 3.0 21.5 + - - +
46A LYS* 1.3 72.9 - - - +
48A GLU* 1.3 65.8 + - - +
49A ILE 2.9 1.6 - - - -
50A LEU* 2.7 17.9 + - + +
51A VAL* 2.9 20.0 + - + +
126A LYS* 2.8 22.4 + - - -
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Residues in contact with GLU 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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42A ILE* 3.5 25.2 - - + +
44A SER 2.7 21.0 + - - +
45A LYS* 3.5 6.1 - - + +
47A GLU* 1.3 70.8 - - - +
49A ILE* 1.3 60.9 + - + +
51A VAL* 3.5 2.4 + - - +
52A ASP* 3.3 23.9 + - - +
103A LEU* 5.9 0.7 - - - +
109A PHE 4.8 3.5 - - - +
110A ARG* 4.9 17.4 - - + +
112A TRP* 6.0 0.9 - - - +
87B TYR* 4.0 18.8 - - + +
89B ALA* 5.9 0.2 - - + -
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Residues in contact with ILE 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 LYS* 3.0 53.8 + - + +
46A LYS* 3.3 14.4 - - + +
47A GLU 2.9 0.8 - - - -
48A GLU* 1.3 77.7 - - + +
50A LEU* 1.3 63.6 + - + +
51A VAL 3.2 1.1 + - - -
52A ASP* 3.7 3.9 + - - +
53A ILE* 3.0 29.3 + - + +
110A ARG* 4.0 38.8 - - - +
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Residues in contact with LEU 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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7A SER* 5.8 7.2 - - - -
8A SER 4.6 7.2 - - - +
9A ASN* 3.4 45.1 - - + +
14A TYR* 4.3 27.8 - - + -
46A LYS* 3.0 12.4 + - + +
47A GLU 2.7 12.6 + - - +
49A ILE* 1.3 75.8 - - + +
51A VAL* 1.3 62.2 + - + +
53A ILE* 2.9 23.5 - - + +
54A VAL* 3.4 15.8 + - + +
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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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14A TYR* 4.3 27.4 - - + -
40A LEU* 5.2 3.6 - - + -
42A ILE* 3.5 27.6 - - + -
47A GLU 2.9 18.9 + - - +
48A GLU 3.9 3.8 - - - +
50A LEU* 1.3 77.9 - - + +
52A ASP* 1.3 61.4 + - - +
53A ILE 3.1 1.6 - - - -
54A VAL* 3.0 9.2 + - + +
55A VAL* 2.8 39.1 + - + +
67A THR* 5.6 0.7 - - + -
103A LEU* 4.1 22.4 - - + -
124A MET* 4.5 17.9 - - + -
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Residues in contact with ASP 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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48A GLU 3.3 12.5 + - - +
49A ILE* 3.7 4.5 + - - +
51A VAL* 1.3 77.8 - - - +
53A ILE* 1.3 50.4 + - - +
55A VAL* 3.1 5.3 + - - +
56A SER* 2.5 40.6 + - - +
103A LEU* 5.3 0.2 - - - -
108A VAL* 3.2 29.2 - - + +
109A PHE* 3.6 26.1 + - + +
110A ARG* 4.5 8.1 - - + +
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Residues in contact with ILE 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 ILE* 3.0 19.1 + - + +
50A LEU* 2.9 33.9 - - + +
52A ASP* 1.3 75.6 - - - +
54A VAL* 1.3 63.3 + - + +
56A SER* 3.7 9.6 - - - -
57A GLU* 3.3 29.6 + - + +
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Residues in contact with VAL 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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7A SER* 4.1 26.2 - - - +
14A TYR* 5.1 14.4 - - + +
15A MET* 5.4 1.8 - - - -
16A LEU* 4.1 21.5 - - + +
50A LEU* 3.6 16.8 - - + +
51A VAL* 3.0 21.1 + - + +
53A ILE* 1.3 79.6 - - + +
55A VAL* 1.3 72.2 + - + +
57A GLU* 4.0 3.1 - - - +
58A ASN* 3.0 43.0 + - - +
124A MET* 5.4 3.1 - - + -
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Residues in contact with VAL 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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16A LEU* 5.0 2.0 - - + -
51A VAL* 2.8 32.1 + - + +
52A ASP* 3.2 10.5 - - - +
54A VAL* 1.3 81.8 - - + +
56A SER* 1.3 64.1 + - - +
57A GLU 3.0 1.7 + - - -
59A ILE* 3.1 44.9 + - + +
65A ILE* 3.8 35.0 - - + -
103A LEU* 4.7 5.4 - - + -
109A PHE* 3.6 32.1 - - + -
124A MET* 5.3 1.6 - - + -
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Residues in contact with SER 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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52A ASP 2.5 29.9 + - - -
53A ILE* 3.7 12.0 - - - -
55A VAL* 1.3 75.5 - - - +
57A GLU* 1.3 55.8 + - - +
59A ILE 4.8 5.7 - - - +
108A VAL* 4.6 10.6 - - - +
109A PHE* 4.0 16.1 - - - -
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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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53A ILE* 3.3 21.1 + - + +
54A VAL* 5.3 1.9 - - - +
55A VAL 3.1 0.6 - - - -
56A SER* 1.3 79.6 - - - +
58A ASN* 1.3 81.8 + - - +
59A ILE 3.8 0.9 - - - -
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Residues in contact with ASN 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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5A GLY 5.7 1.0 - - - +
7A SER* 5.7 0.2 + - - -
15A MET* 6.2 1.7 - - - +
16A LEU* 4.5 17.6 - - + +
18A LYS* 4.5 8.3 - - - +
54A VAL* 3.0 40.0 + - - +
57A GLU* 1.3 103.5 - - - +
59A ILE* 1.3 65.0 + - - +
60A GLY 4.0 1.6 + - - -
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Residues in contact with ILE 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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16A LEU* 3.5 29.8 - - + -
17A PHE 4.3 0.7 - - - +
18A LYS* 3.4 41.1 - - + +
55A VAL* 3.1 37.6 + - + +
56A SER* 4.8 5.5 - - - +
57A GLU 5.3 0.4 - - - -
58A ASN* 1.3 82.4 - - - +
60A GLY* 1.4 60.0 + - - +
61A LYS* 3.6 7.1 + - - +
62A MET* 4.7 6.7 - - + +
65A ILE* 4.2 11.0 - - + -
109A PHE* 6.2 1.1 - - + -
122A PRO* 4.0 24.2 - - + -
123A PHE 4.2 8.3 - - - +
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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