Contacts of the strand formed by residues 54 - 61 (chain B) in PDB entry 3NIE
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 LYS 54 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B TYR* 3.2 9.9 - - - -
49B ASP* 2.6 40.5 + - + +
52B ALA* 3.0 29.6 - - + +
53B ASN* 1.3 74.1 - - - +
55B ASN* 1.3 62.3 + - - +
56B VAL* 4.8 4.5 - - + -
93B HIS* 5.2 2.9 - - + -
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Residues in contact with ASN 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LEU* 3.9 29.7 - - + +
47B ALA 3.3 4.5 - - - +
48B TYR* 3.6 26.7 + - - +
54B LYS* 1.3 76.4 - - - +
56B VAL* 1.3 66.1 + - - +
112B GLU* 5.3 0.2 - - - -
113B ILE* 3.3 30.2 + - + +
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Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B TYR* 4.1 15.5 - - + -
45B TYR 3.6 0.5 - - - +
46B LEU* 3.7 3.8 - - - -
47B ALA* 2.8 40.0 + - + +
49B ASP* 4.2 9.6 - - + -
54B LYS* 4.7 3.1 - - + +
55B ASN* 1.3 79.1 - - - +
57B ALA* 1.3 59.6 + - - +
58B ILE* 4.1 11.7 - - + -
93B HIS* 3.9 35.0 - - + +
110B VAL* 3.5 20.4 - - + -
111B LEU 3.3 13.9 - - - +
112B GLU* 5.3 1.6 - - - -
113B ILE* 3.8 10.3 - - - +
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ILE* 4.4 1.6 - - + -
44B VAL* 3.8 14.1 - - + -
45B TYR 3.4 5.2 - - - +
56B VAL* 1.3 73.8 - - - +
58B ILE* 1.3 60.5 - - - +
59B LYS 4.0 0.4 - - - -
109B ILE 3.7 0.7 - - - +
110B VAL* 3.3 2.3 - - - +
111B LEU* 2.5 44.6 + - + +
113B ILE* 4.0 7.9 - - + +
430B ANP 3.5 42.6 - - + +
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Residues in contact with ILE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B VAL* 5.1 4.5 - - + -
26B VAL* 4.4 8.1 - - + -
30B TYR* 4.1 21.5 - - + -
32B ILE* 4.0 16.2 - - + -
43B TYR 3.5 2.8 - - - +
44B VAL* 3.5 3.1 - - - -
45B TYR* 3.0 41.8 + - + +
47B ALA* 3.5 27.6 - - + -
56B VAL* 4.1 11.0 - - + -
57B ALA* 1.3 75.2 - - - +
59B LYS* 1.3 63.2 + - - +
60B LYS 5.0 0.2 - - - +
108B TYR* 4.0 32.3 - - + -
109B ILE 3.4 7.4 - - - +
110B VAL* 4.1 13.9 - - + -
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Residues in contact with LYS 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLY* 4.2 11.7 - - - -
43B TYR 3.6 3.1 - - - -
44B VAL* 3.7 21.5 - - + +
57B ALA 4.0 0.8 - - - -
58B ILE* 1.3 72.1 - - - +
60B LYS* 1.3 59.7 + - - +
61B VAL* 4.1 17.7 - - + -
77B GLU* 2.6 38.3 + - - +
107B LEU 3.6 2.1 - - - +
108B TYR* 3.4 2.9 - - - -
109B ILE* 2.7 54.5 + - + +
111B LEU* 4.7 17.0 - - + +
174B ASP* 4.0 1.0 + - - -
430B ANP 2.5 59.4 + - - +
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Residues in contact with LYS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ASN* 2.6 53.4 + - - +
24B VAL* 4.9 2.7 - - + -
41B TYR 4.2 0.2 - - - +
42B GLY* 3.5 4.3 - - - -
43B TYR* 3.0 35.0 + - + +
45B TYR* 4.5 11.0 - - + -
58B ILE* 3.7 1.4 + - + -
59B LYS* 1.3 71.9 - - - +
61B VAL* 1.3 64.2 + - - +
62B ASN* 3.8 34.4 + - - +
106B GLU* 4.7 10.1 - - + -
107B LEU 3.5 5.6 - - - +
108B TYR* 3.0 41.0 + - + -
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Residues in contact with VAL 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B TYR* 3.8 23.6 - - + +
42B GLY* 4.5 0.7 - - - -
59B LYS* 4.1 24.7 - - + +
60B LYS* 1.3 78.1 - - - +
62B ASN* 1.3 71.0 + - - +
64B MET* 4.4 5.4 - - + +
73B ARG* 6.4 0.2 - - - +
74B ILE* 2.9 40.8 - - + -
77B GLU* 6.0 0.7 - - - +
105B ASP 4.2 0.2 - - - +
106B GLU* 3.1 9.5 - - - +
107B LEU* 2.9 35.7 + - + +
109B ILE* 4.5 14.4 - - + -
430B ANP 5.5 0.2 - - - +
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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