Contacts of the helix formed by residues 53 - 63 (chain A) in PDB entry 1OX4
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 TYR 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A GLY 3.3 2.4 + - - -
52A ASN* 1.3 74.2 + - - +
54A GLY* 1.3 66.2 + - - +
56A PHE* 3.3 1.6 + - - +
57A VAL* 2.9 47.7 + - + +
84A VAL* 4.6 10.3 - - + -
87A GLN* 3.2 55.9 + - + +
88A ALA* 3.8 3.3 - - - -
90A PHE 3.8 0.2 + - - -
92A GLY* 3.4 26.3 + - - -
93A SER* 3.3 30.3 - - - +
95A GLU* 2.6 20.9 + - - +
96A SER* 3.9 5.8 - - - +
99A SER* 3.7 23.1 - - - -
100A THR 4.7 2.9 - - - -
101A GLY* 3.5 17.8 - - - -
109A LEU* 4.0 2.7 - - + -
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Residues in contact with GLY 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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52A ASN* 2.9 3.9 + - - -
53A TYR* 1.3 69.5 - - - +
55A HIS* 1.3 57.6 + - - +
57A VAL* 4.5 0.4 - - - -
58A ASP* 2.6 47.2 + - - -
96A SER* 2.8 20.7 + - - -
99A SER* 2.8 26.9 - - - -
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Residues in contact with HIS 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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11A SER* 4.6 15.7 + - - -
51A GLY* 5.4 0.7 - - - -
52A ASN* 2.8 30.7 + - + +
54A GLY* 1.3 71.5 - - - +
56A PHE* 1.3 57.8 + - - +
58A ASP* 3.7 6.2 + - - +
59A ASN* 3.0 39.8 + - + +
392A LYS 4.9 0.7 - - - +
393A ALA* 3.2 41.7 - - - +
394A TYR* 6.3 0.4 - - - -
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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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7A ILE 5.9 0.2 - - - -
9A VAL* 4.1 32.0 - - + +
47A LEU* 3.8 21.8 - - + -
48A PRO 3.4 26.5 - - - -
49A GLY* 3.6 15.3 - - - -
50A VAL 4.5 13.2 - - - +
52A ASN 3.1 6.9 + - - +
53A TYR 3.8 2.5 - - - +
55A HIS* 1.3 79.4 - - - +
57A VAL* 1.3 65.5 + - + +
59A ASN* 3.7 5.3 - - - +
60A LEU* 2.9 50.7 + - + +
84A VAL* 3.2 42.6 - - + -
85A GLY* 4.5 1.3 - - - -
88A ALA* 4.2 7.6 - - + -
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Residues in contact with VAL 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 TYR* 2.9 51.6 + - + +
54A GLY* 4.0 2.9 - - - +
56A PHE* 1.3 86.2 - - + +
58A ASP* 1.3 67.5 + - - +
60A LEU* 4.3 5.2 - - + -
61A PHE* 2.9 43.2 + - + +
88A ALA* 4.6 11.9 - - + -
99A SER* 4.8 2.5 - - - +
100A THR 3.1 28.9 - - - +
101A GLY* 4.9 0.9 - - - -
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Residues in contact with ASP 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 GLY* 2.6 35.1 + - - +
55A HIS* 3.7 5.0 + - - +
57A VAL* 1.3 71.6 - - - +
59A ASN* 1.3 58.4 + - - +
61A PHE* 4.1 1.5 - - - +
62A ASN* 2.7 54.2 + - - +
99A SER* 4.7 7.2 + - - -
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Residues in contact with ASN 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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9A VAL* 3.4 37.4 + - + +
11A SER* 4.9 6.3 - - - -
55A HIS* 3.0 27.2 + - - +
56A PHE* 3.7 6.7 - - - +
58A ASP* 1.3 82.0 - - - +
60A LEU* 1.3 66.0 + - - +
62A ASN* 3.8 4.9 - - - +
63A ARG* 2.8 51.5 + - - +
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Residues in contact with LEU 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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7A ILE* 4.0 20.0 - - + -
9A VAL* 4.3 11.8 - - + +
47A LEU* 4.2 14.4 - - + -
56A PHE* 2.9 40.7 + - + +
57A VAL* 3.8 5.6 - - + +
59A ASN* 1.3 79.5 - - - +
61A PHE* 1.3 80.0 + - + +
63A ARG* 3.2 8.1 + - - -
65A PHE* 3.4 54.7 + - + -
69A ILE* 4.1 16.4 - - + -
88A ALA* 4.9 7.4 - - + -
102A LEU* 5.8 1.6 - - + -
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Residues in contact with PHE 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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57A VAL* 2.9 31.7 + - + +
58A ASP* 4.1 2.0 - - - +
60A LEU* 1.3 93.9 - - + +
62A ASN* 1.3 59.5 + - - +
64A GLY* 3.0 19.6 + - - +
65A PHE 4.6 2.5 - - - +
66A GLU* 3.8 47.0 + - + +
69A ILE* 5.8 0.2 - - + -
88A ALA* 6.4 0.7 - - + -
100A THR* 3.8 31.6 - - + -
101A GLY 4.1 11.7 - - - -
102A LEU* 3.5 34.1 - - + -
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Residues in contact with ASN 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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58A ASP* 2.7 43.9 + - - +
59A ASN* 3.8 5.2 - - - +
61A PHE* 1.3 75.3 - - - +
63A ARG* 1.3 59.6 + - + +
64A GLY 3.0 4.0 + - - -
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Residues in contact with ARG 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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8A ASP 3.3 19.8 + - - -
9A VAL* 2.8 29.5 + - - +
10A GLU* 3.6 20.3 + - - +
32A LYS 3.0 26.5 + - - -
33A SER* 5.6 0.2 - - - -
34A PRO* 3.0 27.1 - - + +
59A ASN* 2.8 35.6 + - - +
60A LEU 3.2 5.6 + - - +
62A ASN* 1.3 76.9 - - + +
64A GLY* 1.3 57.3 + - - +
65A PHE* 3.5 17.0 - - + -
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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