Contacts of the strand formed by residues 69 - 76 (chain A) in PDB entry 2NUO
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 ILE 69 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TYR* 3.7 5.5 - - - +
29A LEU* 2.9 51.4 + - + +
63A ILE* 3.9 16.2 - - + -
64A ARG 3.7 7.6 - - - +
65A SER* 3.9 11.4 - - - -
68A TYR* 1.3 73.1 - - - +
70A ASP* 1.3 59.3 + - - +
71A ASN 3.8 10.8 - - - +
72A ILE* 5.1 0.4 - - + -
111A LEU* 2.9 40.2 + - + +
113A SER* 4.0 8.1 - - - -
114A LEU* 4.0 13.9 - - + +
7B PHE* 3.5 33.9 - - + +
8B GLY* 3.9 2.2 - - - -
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Residues in contact with ASP 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER 3.4 6.9 - - - +
28A TYR* 3.5 22.4 - - - +
29A LEU 4.2 1.8 - - - -
64A ARG* 2.8 15.9 + - + +
65A SER* 3.4 4.2 - - - -
66A GLY 3.3 12.3 + - - -
69A ILE* 1.3 73.0 - - - +
71A ASN* 1.3 55.5 + - - +
86A GLY* 3.3 5.2 - - - -
87A GLY 2.9 26.4 + - - +
89A GLY* 3.4 33.7 + - - +
90A GLY 3.6 1.0 + - - -
303A BGC 2.6 48.0 + - - -
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Residues in contact with ASN 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 4.4 2.2 - - - +
62A THR* 4.5 1.3 - - - +
63A ILE* 3.4 4.2 - - - -
64A ARG* 2.9 49.0 + - + +
69A ILE* 3.6 9.6 - - - +
70A ASP* 1.3 77.9 - - - +
72A ILE* 1.3 82.2 + - - +
73A SER* 4.3 0.7 + - - -
84A PRO* 3.4 21.4 - - - +
85A TYR 3.1 15.6 + - - +
86A GLY 3.3 18.0 + - - -
87A GLY 3.0 24.0 + - - +
88A SER* 5.7 0.2 + - - -
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Residues in contact with ILE 72 (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 ILE* 6.1 2.0 - - + -
23A VAL* 4.2 6.7 - - + -
29A LEU* 3.6 23.1 - - + +
32A ILE* 4.9 12.3 - - + -
61A MET* 3.9 22.7 - - + -
62A THR 3.5 7.6 - - - +
63A ILE* 4.5 4.0 - - + -
69A ILE* 5.1 0.9 - - + -
71A ASN* 1.3 79.2 + - - +
73A SER* 1.3 71.4 + - - +
74A PHE* 4.8 10.5 - - + -
82A PHE* 4.2 21.2 - - + -
83A GLY* 4.0 2.4 - - - -
84A PRO* 3.4 0.7 - - - +
85A TYR* 3.0 29.8 + - + +
103A ILE* 5.9 4.7 - - + -
114A LEU* 4.0 23.8 - - + -
116A ILE* 6.0 0.4 - - + -
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Residues in contact with SER 73 (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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61A MET* 3.3 5.2 - - - +
62A THR* 3.0 48.8 + - - +
71A ASN* 4.9 0.7 - - - -
72A ILE* 1.3 77.8 - - - +
74A PHE* 1.3 64.6 + - - +
82A PHE 3.2 14.1 - - - -
83A GLY 4.2 0.4 - - - -
84A PRO* 3.8 23.1 - - - +
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Residues in contact with PHE 74 (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 ILE* 3.7 31.6 - - + -
50A PHE* 3.9 35.7 - + + -
52A PHE* 4.0 1.8 - + - -
58A ILE* 3.6 34.3 - - + -
60A ASN* 3.3 15.0 - - - +
61A MET* 4.1 11.7 - - + +
72A ILE* 4.8 6.5 - - + -
73A SER* 1.3 76.7 - - - +
75A GLU* 1.3 68.1 - - - +
76A THR* 4.1 6.1 - - + -
81A ARG* 3.3 7.2 - - - +
82A PHE* 3.0 75.1 + + + +
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Residues in contact with GLU 75 (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 ILE* 3.6 3.3 - - - -
59A SER* 2.9 23.8 + - - +
60A ASN* 2.9 39.4 + - - +
74A PHE* 1.3 76.5 - - - +
76A THR* 1.3 75.9 + - - +
79A GLY* 3.9 16.7 - - - +
80A ARG 3.2 12.6 - - - +
81A ARG* 3.0 39.4 + - + +
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Residues in contact with THR 76 (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 PHE* 3.7 25.1 - - + -
52A PHE* 4.2 5.6 - - + -
56A GLU* 2.7 37.5 + - + +
57A TYR 3.1 15.3 - - - +
59A SER* 3.2 9.9 + - - -
74A PHE* 4.1 11.2 - - + -
75A GLU* 1.3 81.0 - - - +
77A ASN* 1.3 59.9 + - - +
78A MET 3.2 8.3 + - - -
79A GLY* 3.0 16.6 + - - -
80A ARG 2.8 23.4 + - - +
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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