Contacts of the strand formed by residues 49 - 57 (chain R) in PDB entry 1NVU
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 GLU 49 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2R THR* 4.8 9.2 + - - -
4R TYR* 4.2 5.9 + - - -
45R VAL* 3.6 1.0 - - - -
46R ILE 2.9 31.1 + - - +
47R ASP 3.1 3.9 + - - +
48R GLY* 1.3 78.6 - - - +
50R THR* 1.3 67.6 + - - +
51R CYS* 3.7 0.9 + - - -
164R ARG* 3.2 47.7 + - - +
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Residues in contact with THR 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1R MET* 3.9 32.5 - - + +
2R THR* 4.8 3.1 + - - -
43R GLN* 3.9 21.8 - - + +
44R VAL 3.4 11.2 - - - +
45R VAL* 3.4 20.1 - - + +
48R GLY 3.9 3.2 + - - -
49R GLU* 1.3 79.4 - - - +
51R CYS* 1.3 65.1 + - - +
164R ARG* 4.9 0.2 + - - -
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Residues in contact with CYS 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1R MET* 3.7 9.6 - - - -
2R THR* 3.5 16.8 - - - +
4R TYR* 3.6 25.6 - - + -
43R GLN* 3.4 5.4 - - - +
44R VAL* 2.8 46.5 + - - +
46R ILE* 4.0 7.6 - - - -
49R GLU 4.4 0.9 - - - -
50R THR* 1.3 77.0 - - - +
52R LEU* 1.3 59.7 + - - +
53R LEU* 3.6 24.7 - - - -
164R ARG* 3.9 14.4 - - - +
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Residues in contact with LEU 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1R MET* 3.9 14.1 - - + +
2R THR 2.9 12.9 + - - +
3R GLU* 3.2 31.3 - - + +
4R TYR* 2.7 28.4 + - - +
41R ARG* 4.3 21.8 - - + +
42R LYS* 3.6 31.0 - - - +
43R GLN* 3.9 11.2 - - + +
51R CYS* 1.3 73.3 - - - +
53R LEU* 1.3 66.0 + - - +
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Residues in contact with LEU 53 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4R TYR* 3.7 8.5 - - + -
6R LEU* 4.0 19.7 - - + -
23R LEU* 4.4 20.0 - - + -
40R TYR 3.7 1.2 - - - +
41R ARG* 3.2 7.8 - - - +
42R LYS* 2.9 37.2 + - + +
44R VAL* 3.8 25.6 - - + -
51R CYS* 3.6 29.4 - - - -
52R LEU* 1.3 76.7 - - - +
54R ASP* 1.3 59.2 + - - +
55R ILE* 3.9 12.8 - - + +
156R PHE* 4.9 3.8 - - + -
157R TYR* 4.6 10.8 - - + -
160R VAL* 4.0 18.8 - - + -
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Residues in contact with ASP 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3R GLU* 3.8 24.0 - - + +
4R TYR 2.8 14.8 + - - +
5R LYS* 3.4 18.1 - - + -
6R LEU* 2.8 27.0 + - - +
40R TYR* 3.7 4.4 - - - -
41R ARG* 3.0 37.6 + - - +
52R LEU 3.8 0.6 + - - -
53R LEU* 1.3 73.0 - - - +
55R ILE* 1.3 61.4 + - - +
56R LEU* 4.0 1.0 + - - +
911S HIS* 2.9 29.9 + - - -
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Residues in contact with ILE 55 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6R LEU* 3.4 15.5 - - + +
8R VAL* 3.9 18.2 - - + -
20R THR* 3.8 31.9 - - + +
23R LEU* 3.1 36.8 - - + -
24R ILE* 3.4 22.9 - - + -
40R TYR* 3.0 21.6 + - - +
53R LEU* 4.6 6.3 - - + -
54R ASP* 1.3 80.3 + - - +
56R LEU* 1.3 64.2 + - - +
57R ASP 3.8 2.1 + - - -
156R PHE* 4.0 13.2 - - + -
911S HIS* 3.2 17.8 - - - -
939S LYS* 5.8 0.9 + - - -
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Residues in contact with LEU 56 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6R LEU 2.8 13.7 + - - +
7R VAL* 3.5 15.8 - - + +
8R VAL* 3.0 28.2 + - - +
54R ASP* 4.0 1.3 + - - +
55R ILE* 1.3 71.9 - - - +
57R ASP* 1.3 64.1 + - - +
58R THR* 4.2 17.2 + - + +
71R TYR* 3.6 52.9 - - + +
74R THR* 3.8 11.4 - - + +
911S HIS* 3.9 25.8 - - + +
912S TYR* 6.4 0.9 - - + -
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Residues in contact with ASP 57 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8R VAL* 4.6 7.0 - - + +
16R LYS* 3.7 17.5 - - - +
17R SER* 3.2 21.9 + - - -
20R THR* 3.4 33.0 - - + +
55R ILE 3.8 3.0 + - - -
56R LEU* 1.3 78.3 - - - +
58R THR* 1.3 62.4 + - - +
59R GLY* 3.0 20.4 + - - -
61R GLN* 5.2 0.2 + - - -
911S HIS* 5.3 0.2 - - - -
935S THR* 3.9 8.0 - - - +
939S LYS* 2.8 40.7 + - - +
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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