Contacts of the strand formed by residues 54 - 61 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A TYR* 3.8 8.9 - - - -
49A ASP* 2.8 32.0 + - - +
52A ALA* 3.4 13.8 - - + +
53A ASN* 1.3 79.6 - - - +
55A ASN* 1.3 70.3 + - - +
56A VAL* 4.4 3.3 - - + +
93A HIS* 5.7 2.2 - - + -
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Residues in contact with ASN 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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33A LYS* 4.2 17.1 + - - +
46A LEU* 3.7 28.1 - - + +
47A ALA 3.5 6.4 - - - +
48A TYR* 3.6 23.5 - - - +
54A LYS* 1.3 79.0 - - - +
56A VAL* 1.3 64.6 + - - +
112A GLU* 5.5 0.2 - - - -
113A ILE* 3.5 27.4 + - + +
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Residues in contact with VAL 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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30A TYR* 4.2 14.4 - - + -
46A LEU* 3.6 8.3 - - - +
47A ALA* 2.8 50.3 + - + +
49A ASP* 4.5 5.6 - - + -
54A LYS* 4.4 6.5 - - + +
55A ASN* 1.3 79.4 - - - +
57A ALA* 1.3 59.3 + - - +
58A ILE* 4.3 2.5 - - + -
93A HIS* 3.8 40.8 - - + +
110A VAL* 3.8 18.4 - - + -
111A LEU 3.4 12.8 - - - +
112A GLU* 5.3 1.8 - - - -
113A ILE* 3.9 9.0 - - - +
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Residues in contact with ALA 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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44A VAL* 4.0 13.2 - - + -
45A TYR 3.4 4.9 - - - +
56A VAL* 1.3 73.6 - - - +
58A ILE* 1.3 62.1 + - - +
59A LYS 4.1 0.4 - - - -
109A ILE 3.7 0.3 - - - +
110A VAL* 3.3 3.8 - - - +
111A LEU* 2.6 43.2 + - + +
112A GLU 4.1 0.4 - - - +
113A ILE* 3.9 9.0 - - + +
430A ANP 3.6 41.1 - - + +
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Residues in contact with ILE 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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24A VAL* 5.0 4.0 - - + -
26A VAL* 4.6 7.6 - - + -
30A TYR* 4.3 21.1 - - + -
32A ILE* 3.5 15.7 - - + -
44A VAL* 3.2 4.3 - - - -
45A TYR* 2.9 44.4 + - + +
47A ALA* 3.4 32.1 - - + -
56A VAL* 4.3 1.3 - - + -
57A ALA* 1.3 78.4 - - - +
59A LYS* 1.3 61.2 + - - +
108A TYR* 4.0 34.3 - - + -
109A ILE 3.3 7.0 - - - +
110A VAL* 4.2 18.8 - - + -
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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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42A GLY* 4.2 10.5 - - - -
43A TYR 3.5 5.8 - - - +
44A VAL* 3.8 15.2 - - + +
57A ALA 4.1 1.0 - - - -
58A ILE* 1.3 70.9 - - - +
60A LYS* 1.3 61.9 + - - +
61A VAL* 4.0 22.2 - - + -
77A GLU* 2.5 36.1 + - - +
107A LEU 3.6 1.9 - - - +
108A TYR* 3.5 1.7 - - - -
109A ILE* 2.6 56.6 + - + +
111A LEU* 5.0 16.7 - - + +
174A ASP* 3.8 2.8 + - - -
430A ANP 2.6 60.7 + - - +
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Residues in contact with LYS 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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23A ASN* 2.5 56.5 + - - +
24A VAL* 4.8 2.5 - - + -
41A TYR 4.2 0.3 - - - +
42A GLY* 3.3 4.2 - - - -
43A TYR* 2.8 38.4 + - + +
45A TYR* 4.4 10.5 - - + -
58A ILE 3.7 1.2 + - - -
59A LYS* 1.3 72.2 - - - +
61A VAL* 1.3 65.1 + - - +
62A ASN* 3.8 24.4 + - - +
106A GLU* 3.8 25.3 + - - -
107A LEU 3.6 6.5 - - - +
108A TYR* 3.1 42.6 + - + +
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Residues in contact with VAL 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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41A TYR* 3.6 25.1 - - + +
42A GLY* 4.4 0.7 - - - -
59A LYS* 4.0 24.2 - - + -
60A LYS* 1.3 79.2 - - - +
62A ASN* 1.3 72.3 + - - +
64A MET* 4.5 10.1 - - + +
74A ILE* 3.1 42.0 - - + -
77A GLU* 5.6 0.2 - - - +
105A ASP 4.1 0.5 - - - +
106A GLU* 3.4 7.1 - - - +
107A LEU* 3.0 31.8 + - + +
109A ILE* 4.3 12.1 - - + -
430A ANP 5.3 0.4 - - - +
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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