Contacts of the strand formed by residues 45 - 53 (chain A) in PDB entry 2NQY
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 ASN 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A TRP* 3.8 15.3 - - + -
20A LYS* 3.2 20.0 - - - +
21A ASP* 2.9 42.8 + - - +
43A VAL* 4.5 3.4 - - - +
44A SER* 1.3 80.7 + - - +
46A ILE* 1.3 61.7 + - - +
47A LEU* 5.2 1.3 - - + -
184A GLU* 4.4 7.1 + - - -
185A GLY 3.6 2.7 + - - -
186A TYR* 3.1 25.2 - - - -
3001A XYP 2.8 33.0 + - - -
1C XYP 4.7 6.6 + - - -
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Residues in contact with ILE 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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18A PHE* 4.0 6.5 - - + -
19A TRP 3.2 12.1 - - - +
20A LYS* 3.7 21.8 - - + -
26A GLY* 3.7 22.2 - - - -
40A TRP* 3.9 7.2 - - + -
43A VAL* 3.7 29.6 - - + -
45A ASN* 1.3 76.3 - - - +
47A LEU* 1.3 70.6 + - - +
48A PHE* 3.4 38.8 - - + -
184A GLU* 3.3 8.7 - - - +
185A GLY* 2.9 44.2 + - - +
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Residues in contact with LEU 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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17A GLU 3.8 1.0 - - - +
18A PHE* 3.7 4.2 - - - -
19A TRP* 2.7 46.3 + - + +
45A ASN* 5.2 0.7 - - + -
46A ILE* 1.3 85.2 - - - +
48A PHE* 1.3 67.6 + - - +
49A ARG* 4.1 15.5 - - - +
85A TYR* 3.5 39.3 - - + -
182A THR* 4.1 11.4 - - + -
183A VAL 3.5 3.8 - - - +
184A GLU* 3.9 21.1 - - + +
1C XYP 3.7 17.3 - - - +
2C XYP 3.3 26.0 - - - +
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Residues in contact with PHE 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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17A GLU 3.7 4.0 - - - -
18A PHE* 3.9 15.7 - + - -
27A THR 3.7 24.2 - - - -
28A MET* 3.6 24.2 - - + -
36A PHE* 3.6 22.3 - - + -
38A ALA* 3.5 15.0 - - + -
39A SER 3.4 20.0 - - - -
40A TRP* 3.8 16.6 - + + -
46A ILE* 3.4 41.7 - - + -
47A LEU* 1.3 76.4 - - - +
49A ARG* 1.3 60.1 + - - +
182A THR* 3.1 5.5 - - - +
183A VAL* 2.8 50.8 + - + +
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Residues in contact with ARG 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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15A ASP 4.3 0.2 - - - -
16A TYR* 3.1 5.0 - - - +
17A GLU* 2.9 72.3 + - - +
19A TRP* 4.4 2.6 - - - +
28A MET* 3.4 12.1 - - - +
36A PHE* 4.1 2.5 - - - -
47A LEU* 4.1 11.9 - - - +
48A PHE* 1.3 74.1 - - - +
50A LYS* 1.3 62.1 + - - +
53A LYS* 4.9 0.2 - - - +
85A TYR* 3.6 19.3 - - + -
87A TRP* 4.6 4.6 - - - +
135A ILE* 5.2 0.2 - - - +
177A TYR* 5.0 2.6 - - - -
178A GLU* 2.7 43.6 + - - -
180A ALA* 3.6 8.1 - - + -
181A LEU 3.3 7.4 - - - +
182A THR* 3.1 33.4 - - + +
2C XYP 2.8 37.0 + - - -
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Residues in contact with LYS 50 (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 HIS* 2.9 36.2 + - - -
14A TYR* 3.9 12.1 - - + -
15A ASP 3.2 3.6 - - - -
16A TYR* 3.7 11.9 - - + -
28A MET* 4.7 1.1 - - + -
30A LEU* 4.1 12.6 - - - -
31A ASN 2.8 24.7 + - - +
33A GLY 2.7 23.4 + - - +
34A GLY* 3.5 29.8 - - - +
35A THR 3.0 10.5 + - - +
36A PHE* 4.0 10.9 - - + -
49A ARG* 1.3 79.2 - - - +
51A GLY* 1.3 57.9 - - - +
180A ALA* 3.7 3.1 - - - -
181A LEU 3.3 15.5 + - - -
197A ASN* 3.1 19.7 + - - +
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Residues in contact with GLY 51 (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 12.0 - - - -
15A ASP 2.9 30.8 + - - -
50A LYS* 1.3 74.3 - - - +
52A LYS* 1.3 59.5 + - - -
68A ILE* 6.4 0.4 - - - -
179A VAL 3.3 12.3 - - - -
180A ALA* 3.7 6.2 - - - +
199A LEU* 4.2 5.6 - - - -
206A LEU* 3.3 16.6 - - - +
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Residues in contact with LYS 52 (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 ASN* 6.0 2.0 - - - +
15A ASP* 3.6 10.2 + - - +
51A GLY* 1.3 74.5 - - - +
53A LYS* 1.3 76.0 + - - +
54A PHE* 3.5 35.0 - - + -
178A GLU* 3.3 4.5 + - - +
179A VAL* 2.8 35.3 + - + +
180A ALA* 4.7 0.6 - - - +
199A LEU* 3.5 20.8 - - + +
201A ILE* 4.4 4.3 - - + -
206A LEU* 4.1 24.2 - - + +
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Residues in contact with LYS 53 (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 THR* 4.5 19.0 + - + +
15A ASP* 2.8 30.4 + - + +
16A TYR 4.5 6.3 + - - -
17A GLU* 2.9 38.9 + - - +
52A LYS* 1.3 90.6 + - - +
54A PHE* 1.3 63.6 + - - +
177A TYR* 3.4 34.5 - - + +
178A GLU* 3.1 32.2 + - + +
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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