Contacts of the strand formed by residues 55 - 65 (chain A) in PDB entry 1O4H
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 GLY 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A PHE* 3.3 18.4 - - - -
51A ASP 2.6 35.6 + - - -
52A ASN 4.3 1.5 + - - -
53A ALA 3.5 1.6 - - - -
54A LYS* 1.3 74.4 - - - +
56A LEU* 1.3 57.4 + - - -
57A ASN* 3.0 20.1 + - - -
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Residues in contact with LEU 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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21A LEU 4.4 7.6 - - - +
22A LEU* 3.3 27.4 - - + +
23A ASN 3.2 44.4 - - - +
24A ALA* 3.8 10.1 - - - +
26A ASN 4.3 15.0 - - - +
27A PRO 6.0 0.7 - - - -
48A SER* 4.6 8.7 - - - +
49A ASP 3.5 17.7 - - - +
50A PHE* 3.5 19.3 - - + -
54A LYS 3.6 4.4 + - - +
55A GLY* 1.3 67.1 - - - -
57A ASN* 1.3 65.3 + - - +
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Residues in contact with ASN 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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22A LEU* 3.9 7.4 - - - -
48A SER* 3.5 4.5 - - - -
49A ASP* 2.8 53.9 + - - +
50A PHE* 4.2 1.4 - - - +
51A ASP* 4.8 2.2 + - - +
54A LYS* 3.5 36.5 - - + +
55A GLY 3.0 24.2 + - - +
56A LEU* 1.3 76.4 - - - +
58A VAL* 1.3 68.8 + - - +
59A LYS* 4.1 17.3 - - - -
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Residues in contact with VAL 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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18A GLU* 4.0 19.3 - - + +
21A LEU* 3.8 42.8 - - + +
22A LEU* 4.0 21.6 - - + +
47A VAL 3.5 9.2 - - - +
48A SER* 4.6 1.3 - - - -
57A ASN* 1.3 85.6 - - - +
59A LYS* 1.3 82.0 + - - +
60A HIS* 3.7 27.7 + - + -
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Residues in contact with LYS 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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45A LEU 3.7 0.5 - - - +
46A SER* 3.4 3.1 - - - -
47A VAL* 2.8 31.9 + - - +
49A ASP* 5.1 2.0 - - + -
54A LYS* 3.6 23.3 - - - +
57A ASN* 4.1 17.9 - - - +
58A VAL* 1.3 79.4 - - - +
60A HIS* 1.3 64.9 + - - +
61A TYR* 3.3 34.8 - - + +
97A CYS* 3.8 23.3 - - + -
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Residues in contact with HIS 60 (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 ARG* 3.6 45.8 + - + +
17A SER* 3.3 23.8 - - - -
18A GLU* 2.9 27.3 + - + +
34A ARG* 3.1 12.4 + - - +
44A CYS* 4.7 5.2 - - - -
45A LEU 3.5 3.6 - - - +
46A SER* 2.8 20.8 + - - +
58A VAL* 3.7 20.7 - - + +
59A LYS* 1.3 78.6 - - - +
61A TYR* 1.3 66.5 + - - +
62A LYS 4.3 0.3 + - - -
300A 772 4.4 2.2 - - - +
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Residues in contact with TYR 61 (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 CYS* 3.4 4.5 - - - -
45A LEU* 2.8 50.8 + - + +
47A VAL* 3.8 23.3 - - + -
59A LYS* 3.3 36.8 - - + +
60A HIS* 1.3 76.0 - - - +
62A LYS* 1.3 62.4 + - - +
63A ILE* 3.6 0.9 + - - +
73A ILE* 4.0 29.2 - - + -
95A GLY 4.5 6.4 + - - -
96A LEU* 3.6 31.0 - - + -
97A CYS* 2.9 30.3 + - - +
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Residues in contact with LYS 62 (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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36A SER* 4.4 1.3 + - - +
38A THR* 4.9 1.6 + - - -
39A THR* 2.7 39.8 + - + +
42A ALA* 3.6 21.3 - - + -
43A TYR 3.5 6.3 - - - +
44A CYS* 4.5 3.8 - - - -
60A HIS 4.2 0.6 + - - -
61A TYR* 1.3 72.7 - - - +
63A ILE* 1.3 60.9 + - - +
64A ARG* 3.8 18.1 + - - +
72A TYR 3.7 0.7 - - - +
73A ILE* 3.5 26.7 - - - +
300A 772 3.6 52.8 + - - -
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Residues in contact with ILE 63 (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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33A VAL* 4.5 10.5 - - + -
42A ALA* 3.2 6.2 - - - -
43A TYR* 2.9 57.5 + - + +
45A LEU* 3.9 28.3 - - + +
61A TYR 4.3 0.7 - - - +
62A LYS* 1.3 73.0 - - - +
64A ARG* 1.3 72.0 + - - +
65A LYS 4.1 0.2 + - - -
71A PHE* 4.5 3.8 - - + -
72A TYR 3.4 7.6 - - - +
73A ILE* 4.1 15.5 - - + -
82A LEU* 3.7 35.4 - - + -
85A LEU* 4.0 24.5 - - + -
86A VAL* 5.7 0.2 - - + -
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Residues in contact with ARG 64 (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 THR* 3.4 30.9 - - - +
40A LYS* 4.1 16.0 + - - +
41A GLY 4.7 4.4 + - - -
42A ALA* 3.7 7.3 - - - +
62A LYS* 3.9 29.0 - - - +
63A ILE* 1.3 76.3 - - - +
65A LYS* 1.3 63.5 + - - +
66A LEU* 4.2 1.1 - - + -
71A PHE* 3.2 3.1 - - - -
72A TYR* 2.7 73.7 + - + +
73A ILE 5.0 2.5 - - - +
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Residues in contact with LYS 65 (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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41A GLY 4.0 18.8 + - - +
43A TYR* 5.0 7.4 - - + -
64A ARG* 1.3 78.5 + - - +
66A LEU* 1.3 84.1 + - - +
67A ASP* 4.6 7.4 + - - +
69A GLY* 3.2 20.9 - - - -
70A GLY 3.4 10.5 - - - +
71A PHE* 3.4 42.0 - - + +
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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