Contacts of the strand formed by residues 57 - 63 (chain A) in PDB entry 2NBV
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 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A LEU* 4.5 11.0 - - + -
49A ILE* 3.6 23.6 - - + -
50A GLN 3.5 2.0 - - - +
51A GLN* 4.1 32.1 - - + +
55A SER 3.9 4.7 + - - +
56A LEU* 1.3 71.0 - - - +
58A HIS* 1.3 60.6 + - - +
74A ILE* 3.2 7.1 - - - +
75A ILE* 2.7 52.8 + - + +
127A TYR* 4.0 17.5 - - + +
128A LEU* 3.7 26.0 - - + +
130A ASN 6.0 2.7 - - - +
103B LYS* 5.3 5.8 - - - +
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Residues in contact with HIS 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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48A TYR 3.6 1.4 - - - +
49A ILE* 3.6 4.9 - - - -
50A GLN* 2.7 51.8 + - + +
52A THR* 3.3 23.9 + - + +
54A ASP* 4.5 5.1 + - - -
56A LEU* 3.3 31.5 - - + +
57A ILE* 1.3 77.4 - - - +
59A PHE* 1.3 61.2 + - - +
60A CYS* 3.7 14.8 + - - -
72A ASP* 2.6 29.0 + - - +
73A LEU 3.2 4.0 + - - -
74A ILE* 3.9 23.9 - - + +
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Residues in contact with PHE 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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26A PHE* 5.3 0.2 - + - -
47A VAL* 3.5 30.7 - - + -
48A TYR 4.0 2.5 - - - -
49A ILE* 3.7 31.0 - - + -
57A ILE 4.1 1.0 + - - -
58A HIS* 1.3 70.3 - - - +
60A CYS* 1.3 63.2 + - - +
71A ASP* 3.8 2.1 - - - +
72A ASP* 3.6 1.2 - - - -
73A LEU* 2.7 34.3 + - + +
75A ILE* 3.5 23.1 - - + +
82A PHE* 5.0 7.4 - + - -
96A LEU* 3.7 28.9 - - + -
105A LEU* 5.8 2.5 - - + -
107A PHE* 4.5 16.2 - + - -
124A VAL* 3.9 28.0 - - + -
128A LEU* 3.9 15.3 - - + -
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Residues in contact with CYS 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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46A LEU 3.8 0.2 - - - +
47A VAL* 3.8 5.2 - - - +
48A TYR* 3.3 61.4 + - + +
50A GLN* 4.4 2.7 - - - -
58A HIS* 3.8 20.4 - - - -
59A PHE* 1.3 79.7 - - - +
61A TRP* 1.3 60.7 + - - +
62A LYS 3.9 0.2 - - - -
69A VAL* 3.5 17.7 - - + -
71A ASP 3.1 10.8 - - - +
72A ASP* 3.0 27.1 - - - +
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Residues in contact with TRP 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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28A ALA 3.0 18.4 + - - -
30A LYS* 3.7 41.4 - - + +
41A ASP* 5.9 0.2 - - + -
43A ARG* 3.6 31.6 - - + -
44A LYS 4.3 1.8 - - - -
45A GLY* 3.3 28.8 - - - -
46A LEU 3.9 3.4 - - - -
47A VAL* 3.8 24.2 - - + +
60A CYS* 1.3 71.2 - - - +
62A LYS* 1.3 59.9 + - - +
63A ASP* 4.0 17.0 - - - -
69A VAL* 3.7 2.8 - - - -
70A GLU* 3.2 56.9 + - + -
71A ASP* 2.9 23.0 + - + +
107A PHE* 3.8 20.4 - + + -
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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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22A TYR* 2.9 30.2 + - + +
45A GLY* 3.5 1.7 - - - -
46A LEU* 2.9 45.4 + - + +
48A TYR* 3.8 18.4 - - + -
60A CYS 3.9 1.0 + - - -
61A TRP* 1.3 76.5 - - - +
63A ASP* 1.3 70.6 + - - +
64A ARG* 3.4 1.3 + - - -
67A GLY* 3.4 33.1 + - - +
68A ASN 3.8 3.8 - - - +
69A VAL* 4.2 16.1 - - + +
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Residues in contact with ASP 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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43A ARG* 2.8 36.8 + - - +
44A LYS 4.0 2.9 - - - +
61A TRP* 3.9 20.4 + - + -
62A LYS* 1.3 73.2 - - - +
64A ARG* 1.3 58.1 + - - +
65A THR* 2.7 40.1 + - - -
66A SER* 3.3 24.6 + - - +
67A GLY* 2.9 30.1 + - - -
68A ASN* 3.0 16.4 + - + +
70A GLU* 4.2 3.8 - - + +
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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