Contacts of the strand formed by residues 39 - 49 (chain A) in PDB entry 5NXR
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 ARG 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LYS* 5.1 6.3 - - - +
17A VAL* 4.8 0.3 - - - +
18A ASP* 2.8 66.0 + - + +
19A VAL* 5.6 0.2 - - - +
20A ARG* 3.4 31.4 - - - +
22A TYR* 4.1 0.2 + - - -
37A ASP* 2.9 44.9 + - - -
38A SER* 1.3 75.2 - - - +
40A VAL* 1.3 67.5 + - - +
63A GLU* 4.1 30.8 + - + +
64A THR 3.2 16.4 - - - +
65A LYS* 3.5 21.3 - - - +
66A THR* 3.8 2.9 - - - -
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Residues in contact with VAL 40 (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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16A LYS 3.4 11.9 - - - +
17A VAL* 4.3 13.5 - - + -
39A ARG* 1.3 80.8 - - - +
41A ARG* 1.3 70.1 + - - +
42A LEU* 4.4 7.4 - - + -
62A TRP* 4.9 1.2 - - + -
63A GLU* 3.1 6.7 - - - +
64A THR* 2.9 40.2 + - + +
66A THR* 3.8 6.5 - - + -
60B PHE* 3.6 51.6 - - + -
80B ALA* 3.8 20.2 - - + -
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Residues in contact with ARG 41 (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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14A TYR* 4.7 8.5 - - + -
15A GLY* 2.9 4.4 - - - -
16A LYS* 2.8 75.4 + - + +
40A VAL* 1.3 75.6 - - - +
42A LEU* 1.3 75.8 + - - +
61A GLU* 4.0 26.8 + - + -
62A TRP* 3.2 13.5 - - - +
63A GLU* 2.8 28.0 + - + +
78A ARG* 3.1 37.2 - - - +
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Residues in contact with LEU 42 (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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14A TYR* 3.6 6.5 - - - +
15A GLY* 4.3 0.9 - - - -
16A LYS 5.1 0.2 - - - +
40A VAL* 4.4 11.0 - - + -
41A ARG* 1.3 87.1 - - - +
43A GLY* 1.3 59.7 + - - +
60A PHE* 5.6 0.4 - - - -
61A GLU* 3.6 2.9 - - - +
62A TRP* 2.8 65.2 + - + +
352A PHE* 4.1 24.9 - - + -
44B VAL* 4.6 11.0 - - + -
60B PHE* 4.1 14.6 - - + -
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Residues in contact with GLY 43 (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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13A VAL* 3.5 8.0 - - - +
14A TYR* 2.8 59.4 + - - +
42A LEU* 1.3 75.7 - - - +
44A VAL* 1.3 61.1 + - - +
60A PHE* 3.2 12.8 - - - -
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Residues in contact with VAL 44 (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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11A LEU* 4.2 26.9 - - + -
12A ASP 3.4 9.4 - - - +
13A VAL* 4.4 9.2 - - + -
14A TYR* 4.4 1.3 - - - -
43A GLY* 1.3 74.6 - - - +
45A LYS* 1.3 66.7 - - - +
46A GLY 4.9 0.4 - - - +
58A GLY 4.6 0.2 - - - -
59A ARG* 3.3 3.1 - - - +
60A PHE* 2.8 59.6 + - + +
17C VAL* 6.0 3.1 - - + -
42C LEU* 4.5 21.5 - - + -
352C PHE* 4.3 18.8 - - + -
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Residues in contact with LYS 45 (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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10A LYS 4.0 0.3 - - - +
11A LEU* 3.7 0.5 - - - -
12A ASP* 2.8 67.1 + - + +
14A TYR* 4.2 14.5 - - + -
44A VAL* 1.3 78.1 - - - +
46A GLY* 1.3 60.4 + - - +
47A ASP* 5.0 5.2 - - - +
58A GLY 3.3 10.1 - - - +
59A ARG* 4.0 41.6 - - + +
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Residues in contact with GLY 46 (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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10A LYS 3.3 6.7 - - - -
11A LEU* 3.9 6.7 - - - +
44A VAL* 4.3 1.4 - - - +
45A LYS* 1.3 74.3 - - - +
47A ASP* 1.3 63.1 + - - +
57A PHE* 3.1 7.6 - - - +
58A GLY 2.8 35.6 + - - +
350C TYR* 3.2 26.7 - - - -
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Residues in contact with ASP 47 (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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9A ASN* 3.2 7.1 - - - +
10A LYS* 2.8 67.0 + - + +
45A LYS* 5.0 5.7 - - - +
46A GLY* 1.3 79.4 + - - +
48A THR* 1.3 62.4 + - - +
55A THR* 5.1 12.0 + - + +
56A GLY 3.3 5.0 - - - +
57A PHE* 4.4 13.0 - - - +
350C TYR* 3.6 1.6 - - - -
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Residues in contact with THR 48 (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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8A GLY 2.9 17.7 + - - -
9A ASN* 4.3 0.4 - - - -
47A ASP* 1.3 76.5 - - - +
49A GLN* 1.3 59.0 + - - +
50A ILE* 3.4 2.5 + - + -
55A THR* 3.1 9.7 - - - -
56A GLY* 2.7 55.9 + - - +
313C ASN* 3.2 20.1 + - - +
315C ASN* 3.4 30.4 + - + +
316C MET* 4.0 15.0 - - + -
350C TYR* 3.7 15.0 - - + -
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Residues in contact with GLN 49 (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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8A GLY* 3.1 31.7 + - - +
48A THR* 1.3 70.5 - - - +
50A ILE* 1.3 63.0 + - - +
51A THR 3.0 27.3 + - - +
52A ASP* 4.0 18.2 + - - +
55A THR* 2.9 26.4 - - + +
313C ASN* 3.6 9.2 + - - -
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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